/* Generated by Cython 0.29.35 */

/* BEGIN: Cython Metadata
{
    "distutils": {
        "depends": [],
        "extra_compile_args": [
            "-std=c++11",
            "-Werror=return-type",
            "-Werror=narrowing"
        ],
        "include_dirs": [
            "src/"
        ],
        "language": "c++",
        "name": "whatshap.core",
        "sources": [
            "whatshap/core.pyx",
            "src/pedigree.cpp",
            "src/pedigreedptable.cpp",
            "src/pedigreecolumncostcomputer.cpp",
            "src/columnindexingiterator.cpp",
            "src/columnindexingscheme.cpp",
            "src/entry.cpp",
            "src/graycodes.cpp",
            "src/read.cpp",
            "src/readset.cpp",
            "src/columniterator.cpp",
            "src/indexset.cpp",
            "src/genotype.cpp",
            "src/binomial.cpp",
            "src/multinomial.cpp",
            "src/pedigreepartitions.cpp",
            "src/phredgenotypelikelihoods.cpp",
            "src/genotyper.cpp",
            "src/genotypedistribution.cpp",
            "src/genotypedptable.cpp",
            "src/genotypecolumncostcomputer.cpp",
            "src/backwardcolumniterator.cpp",
            "src/transitionprobabilitycomputer.cpp",
            "src/hapchat/basictypes.cpp",
            "src/hapchat/balancedcombinations.cpp",
            "src/hapchat/binomialcoefficient.cpp",
            "src/hapchat/hapchatcore.cpp",
            "src/hapchat/hapchatcolumniterator.cpp"
        ],
        "undef_macros": [
            "NDEBUG"
        ]
    },
    "module_name": "whatshap.core"
}
END: Cython Metadata */

#ifndef PY_SSIZE_T_CLEAN
#define PY_SSIZE_T_CLEAN
#endif /* PY_SSIZE_T_CLEAN */
#include "Python.h"
#ifndef Py_PYTHON_H
    #error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
    #error Cython requires Python 2.6+ or Python 3.3+.
#else
#define CYTHON_ABI "0_29_35"
#define CYTHON_HEX_VERSION 0x001D23F0
#define CYTHON_FUTURE_DIVISION 1
#include <stddef.h>
#ifndef offsetof
  #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
#if !defined(WIN32) && !defined(MS_WINDOWS)
  #ifndef __stdcall
    #define __stdcall
  #endif
  #ifndef __cdecl
    #define __cdecl
  #endif
  #ifndef __fastcall
    #define __fastcall
  #endif
#endif
#ifndef DL_IMPORT
  #define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
  #define DL_EXPORT(t) t
#endif
#define __PYX_COMMA ,
#ifndef HAVE_LONG_LONG
  #if PY_VERSION_HEX >= 0x02070000
    #define HAVE_LONG_LONG
  #endif
#endif
#ifndef PY_LONG_LONG
  #define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
  #define Py_HUGE_VAL HUGE_VAL
#endif
#ifdef PYPY_VERSION
  #define CYTHON_COMPILING_IN_PYPY 1
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #define CYTHON_COMPILING_IN_NOGIL 0
  #undef CYTHON_USE_TYPE_SLOTS
  #define CYTHON_USE_TYPE_SLOTS 0
  #undef CYTHON_USE_PYTYPE_LOOKUP
  #define CYTHON_USE_PYTYPE_LOOKUP 0
  #if PY_VERSION_HEX < 0x03050000
    #undef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 0
  #elif !defined(CYTHON_USE_ASYNC_SLOTS)
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #undef CYTHON_USE_UNICODE_INTERNALS
  #define CYTHON_USE_UNICODE_INTERNALS 0
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #undef CYTHON_AVOID_BORROWED_REFS
  #define CYTHON_AVOID_BORROWED_REFS 1
  #undef CYTHON_ASSUME_SAFE_MACROS
  #define CYTHON_ASSUME_SAFE_MACROS 0
  #undef CYTHON_UNPACK_METHODS
  #define CYTHON_UNPACK_METHODS 0
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
  #if PY_VERSION_HEX < 0x03090000
    #undef CYTHON_PEP489_MULTI_PHASE_INIT
    #define CYTHON_PEP489_MULTI_PHASE_INIT 0
  #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
    #define CYTHON_PEP489_MULTI_PHASE_INIT 1
  #endif
  #undef CYTHON_USE_TP_FINALIZE
  #define CYTHON_USE_TP_FINALIZE 0
  #undef CYTHON_USE_DICT_VERSIONS
  #define CYTHON_USE_DICT_VERSIONS 0
  #undef CYTHON_USE_EXC_INFO_STACK
  #define CYTHON_USE_EXC_INFO_STACK 0
  #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
    #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
  #endif
#elif defined(PYSTON_VERSION)
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 1
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #define CYTHON_COMPILING_IN_NOGIL 0
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #undef CYTHON_USE_PYTYPE_LOOKUP
  #define CYTHON_USE_PYTYPE_LOOKUP 0
  #undef CYTHON_USE_ASYNC_SLOTS
  #define CYTHON_USE_ASYNC_SLOTS 0
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
  #undef CYTHON_PEP489_MULTI_PHASE_INIT
  #define CYTHON_PEP489_MULTI_PHASE_INIT 0
  #undef CYTHON_USE_TP_FINALIZE
  #define CYTHON_USE_TP_FINALIZE 0
  #undef CYTHON_USE_DICT_VERSIONS
  #define CYTHON_USE_DICT_VERSIONS 0
  #undef CYTHON_USE_EXC_INFO_STACK
  #define CYTHON_USE_EXC_INFO_STACK 0
  #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
    #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
  #endif
#elif defined(PY_NOGIL)
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #define CYTHON_COMPILING_IN_NOGIL 1
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #undef CYTHON_USE_PYTYPE_LOOKUP
  #define CYTHON_USE_PYTYPE_LOOKUP 0
  #ifndef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
  #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
    #define CYTHON_PEP489_MULTI_PHASE_INIT 1
  #endif
  #ifndef CYTHON_USE_TP_FINALIZE
    #define CYTHON_USE_TP_FINALIZE 1
  #endif
  #undef CYTHON_USE_DICT_VERSIONS
  #define CYTHON_USE_DICT_VERSIONS 0
  #undef CYTHON_USE_EXC_INFO_STACK
  #define CYTHON_USE_EXC_INFO_STACK 0
#else
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 1
  #define CYTHON_COMPILING_IN_NOGIL 0
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #if PY_VERSION_HEX < 0x02070000
    #undef CYTHON_USE_PYTYPE_LOOKUP
    #define CYTHON_USE_PYTYPE_LOOKUP 0
  #elif !defined(CYTHON_USE_PYTYPE_LOOKUP)
    #define CYTHON_USE_PYTYPE_LOOKUP 1
  #endif
  #if PY_MAJOR_VERSION < 3
    #undef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 0
  #elif !defined(CYTHON_USE_ASYNC_SLOTS)
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #if PY_VERSION_HEX < 0x02070000
    #undef CYTHON_USE_PYLONG_INTERNALS
    #define CYTHON_USE_PYLONG_INTERNALS 0
  #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
    #define CYTHON_USE_PYLONG_INTERNALS (PY_VERSION_HEX < 0x030C00A5)
  #endif
  #ifndef CYTHON_USE_PYLIST_INTERNALS
    #define CYTHON_USE_PYLIST_INTERNALS 1
  #endif
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
    #undef CYTHON_USE_UNICODE_WRITER
    #define CYTHON_USE_UNICODE_WRITER 0
  #elif !defined(CYTHON_USE_UNICODE_WRITER)
    #define CYTHON_USE_UNICODE_WRITER 1
  #endif
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #if PY_VERSION_HEX >= 0x030B00A4
    #undef CYTHON_FAST_THREAD_STATE
    #define CYTHON_FAST_THREAD_STATE 0
  #elif !defined(CYTHON_FAST_THREAD_STATE)
    #define CYTHON_FAST_THREAD_STATE 1
  #endif
  #ifndef CYTHON_FAST_PYCALL
    #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000)
  #endif
  #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
    #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000)
  #endif
  #ifndef CYTHON_USE_TP_FINALIZE
    #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1)
  #endif
  #ifndef CYTHON_USE_DICT_VERSIONS
    #define CYTHON_USE_DICT_VERSIONS ((PY_VERSION_HEX >= 0x030600B1) && (PY_VERSION_HEX < 0x030C00A5))
  #endif
  #if PY_VERSION_HEX >= 0x030B00A4
    #undef CYTHON_USE_EXC_INFO_STACK
    #define CYTHON_USE_EXC_INFO_STACK 0
  #elif !defined(CYTHON_USE_EXC_INFO_STACK)
    #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
  #endif
  #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
    #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
  #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
  #if PY_MAJOR_VERSION < 3
    #include "longintrepr.h"
  #endif
  #undef SHIFT
  #undef BASE
  #undef MASK
  #ifdef SIZEOF_VOID_P
    enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) };
  #endif
#endif
#ifndef __has_attribute
  #define __has_attribute(x) 0
#endif
#ifndef __has_cpp_attribute
  #define __has_cpp_attribute(x) 0
#endif
#ifndef CYTHON_RESTRICT
  #if defined(__GNUC__)
    #define CYTHON_RESTRICT __restrict__
  #elif defined(_MSC_VER) && _MSC_VER >= 1400
    #define CYTHON_RESTRICT __restrict
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_RESTRICT restrict
  #else
    #define CYTHON_RESTRICT
  #endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
#   if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
#     define CYTHON_UNUSED __attribute__ ((__unused__))
#   else
#     define CYTHON_UNUSED
#   endif
# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
#   define CYTHON_UNUSED __attribute__ ((__unused__))
# else
#   define CYTHON_UNUSED
# endif
#endif
#ifndef CYTHON_MAYBE_UNUSED_VAR
#  if defined(__cplusplus)
     template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
#  else
#    define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
#  endif
#endif
#ifndef CYTHON_NCP_UNUSED
# if CYTHON_COMPILING_IN_CPYTHON
#  define CYTHON_NCP_UNUSED
# else
#  define CYTHON_NCP_UNUSED CYTHON_UNUSED
# endif
#endif
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
#ifdef _MSC_VER
    #ifndef _MSC_STDINT_H_
        #if _MSC_VER < 1300
           typedef unsigned char     uint8_t;
           typedef unsigned int      uint32_t;
        #else
           typedef unsigned __int8   uint8_t;
           typedef unsigned __int32  uint32_t;
        #endif
    #endif
#else
   #include <stdint.h>
#endif
#ifndef CYTHON_FALLTHROUGH
  #if defined(__cplusplus) && __cplusplus >= 201103L
    #if __has_cpp_attribute(fallthrough)
      #define CYTHON_FALLTHROUGH [[fallthrough]]
    #elif __has_cpp_attribute(clang::fallthrough)
      #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
    #elif __has_cpp_attribute(gnu::fallthrough)
      #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
    #endif
  #endif
  #ifndef CYTHON_FALLTHROUGH
    #if __has_attribute(fallthrough)
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
    #else
      #define CYTHON_FALLTHROUGH
    #endif
  #endif
  #if defined(__clang__ ) && defined(__apple_build_version__)
    #if __apple_build_version__ < 7000000
      #undef  CYTHON_FALLTHROUGH
      #define CYTHON_FALLTHROUGH
    #endif
  #endif
#endif

#ifndef __cplusplus
  #error "Cython files generated with the C++ option must be compiled with a C++ compiler."
#endif
#ifndef CYTHON_INLINE
  #if defined(__clang__)
    #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
  #else
    #define CYTHON_INLINE inline
  #endif
#endif
template<typename T>
void __Pyx_call_destructor(T& x) {
    x.~T();
}
template<typename T>
class __Pyx_FakeReference {
  public:
    __Pyx_FakeReference() : ptr(NULL) { }
    __Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { }
    T *operator->() { return ptr; }
    T *operator&() { return ptr; }
    operator T&() { return *ptr; }
    template<typename U> bool operator ==(U other) { return *ptr == other; }
    template<typename U> bool operator !=(U other) { return *ptr != other; }
  private:
    T *ptr;
};

#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
  #define Py_OptimizeFlag 0
#endif
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyClass_Type
#else
  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
  #define __Pyx_DefaultClassType PyType_Type
#if PY_VERSION_HEX >= 0x030B00A1
    static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f,
                                                    PyObject *code, PyObject *c, PyObject* n, PyObject *v,
                                                    PyObject *fv, PyObject *cell, PyObject* fn,
                                                    PyObject *name, int fline, PyObject *lnos) {
        PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL;
        PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL;
        const char *fn_cstr=NULL;
        const char *name_cstr=NULL;
        PyCodeObject* co=NULL;
        PyObject *type, *value, *traceback;
        PyErr_Fetch(&type, &value, &traceback);
        if (!(kwds=PyDict_New())) goto end;
        if (!(argcount=PyLong_FromLong(a))) goto end;
        if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end;
        if (!(posonlyargcount=PyLong_FromLong(0))) goto end;
        if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end;
        if (!(kwonlyargcount=PyLong_FromLong(k))) goto end;
        if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end;
        if (!(nlocals=PyLong_FromLong(l))) goto end;
        if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end;
        if (!(stacksize=PyLong_FromLong(s))) goto end;
        if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end;
        if (!(flags=PyLong_FromLong(f))) goto end;
        if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end;
        if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end;
        if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end;
        if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end;
        if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end;
        if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too;
        if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here
        if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too;
        Py_XDECREF((PyObject*)co);
        co = (PyCodeObject*)call_result;
        call_result = NULL;
        if (0) {
            cleanup_code_too:
            Py_XDECREF((PyObject*)co);
            co = NULL;
        }
        end:
        Py_XDECREF(kwds);
        Py_XDECREF(argcount);
        Py_XDECREF(posonlyargcount);
        Py_XDECREF(kwonlyargcount);
        Py_XDECREF(nlocals);
        Py_XDECREF(stacksize);
        Py_XDECREF(replace);
        Py_XDECREF(call_result);
        Py_XDECREF(empty);
        if (type) {
            PyErr_Restore(type, value, traceback);
        }
        return co;
    }
#else
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
  #define __Pyx_DefaultClassType PyType_Type
#endif
#ifndef Py_TPFLAGS_CHECKTYPES
  #define Py_TPFLAGS_CHECKTYPES 0
#endif
#ifndef Py_TPFLAGS_HAVE_INDEX
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#ifndef Py_TPFLAGS_HAVE_NEWBUFFER
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#ifndef Py_TPFLAGS_HAVE_FINALIZE
  #define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
#ifndef METH_STACKLESS
  #define METH_STACKLESS 0
#endif
#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL)
  #ifndef METH_FASTCALL
     #define METH_FASTCALL 0x80
  #endif
  typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs);
  typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
                                                          Py_ssize_t nargs, PyObject *kwnames);
#else
  #define __Pyx_PyCFunctionFast _PyCFunctionFast
  #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
#endif
#if CYTHON_FAST_PYCCALL
#define __Pyx_PyFastCFunction_Check(func)\
    ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS)))))
#else
#define __Pyx_PyFastCFunction_Check(func) 0
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
  #define PyObject_Malloc(s)   PyMem_Malloc(s)
  #define PyObject_Free(p)     PyMem_Free(p)
  #define PyObject_Realloc(p)  PyMem_Realloc(p)
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1
  #define PyMem_RawMalloc(n)           PyMem_Malloc(n)
  #define PyMem_RawRealloc(p, n)       PyMem_Realloc(p, n)
  #define PyMem_RawFree(p)             PyMem_Free(p)
#endif
#if CYTHON_COMPILING_IN_PYSTON
  #define __Pyx_PyCode_HasFreeVars(co)  PyCode_HasFreeVars(co)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
#else
  #define __Pyx_PyCode_HasFreeVars(co)  (PyCode_GetNumFree(co) > 0)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
#endif
#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000
  #define __Pyx_PyThreadState_Current PyThreadState_GET()
#elif PY_VERSION_HEX >= 0x03060000
  #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet()
#elif PY_VERSION_HEX >= 0x03000000
  #define __Pyx_PyThreadState_Current PyThreadState_GET()
#else
  #define __Pyx_PyThreadState_Current _PyThreadState_Current
#endif
#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT)
#include "pythread.h"
#define Py_tss_NEEDS_INIT 0
typedef int Py_tss_t;
static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) {
  *key = PyThread_create_key();
  return 0;
}
static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) {
  Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t));
  *key = Py_tss_NEEDS_INIT;
  return key;
}
static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) {
  PyObject_Free(key);
}
static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) {
  return *key != Py_tss_NEEDS_INIT;
}
static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) {
  PyThread_delete_key(*key);
  *key = Py_tss_NEEDS_INIT;
}
static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) {
  return PyThread_set_key_value(*key, value);
}
static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
  return PyThread_get_key_value(*key);
}
#endif
#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized)
#define __Pyx_PyDict_NewPresized(n)  ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n))
#else
#define __Pyx_PyDict_NewPresized(n)  PyDict_New()
#endif
#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
#else
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_Divide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(x,y)
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS
#define __Pyx_PyDict_GetItemStr(dict, name)  _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash)
#else
#define __Pyx_PyDict_GetItemStr(dict, name)  PyDict_GetItem(dict, name)
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
  #define CYTHON_PEP393_ENABLED 1
  #if PY_VERSION_HEX >= 0x030C0000
    #define __Pyx_PyUnicode_READY(op)       (0)
  #else
    #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ?\
                                                0 : _PyUnicode_Ready((PyObject *)(op)))
  #endif
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   PyUnicode_MAX_CHAR_VALUE(u)
  #define __Pyx_PyUnicode_KIND(u)         PyUnicode_KIND(u)
  #define __Pyx_PyUnicode_DATA(u)         PyUnicode_DATA(u)
  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  PyUnicode_WRITE(k, d, i, ch)
  #if PY_VERSION_HEX >= 0x030C0000
    #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != PyUnicode_GET_LENGTH(u))
  #else
    #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000
    #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length))
    #else
    #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
    #endif
  #endif
#else
  #define CYTHON_PEP393_ENABLED 0
  #define PyUnicode_1BYTE_KIND  1
  #define PyUnicode_2BYTE_KIND  2
  #define PyUnicode_4BYTE_KIND  4
  #define __Pyx_PyUnicode_READY(op)       (0)
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
  #define __Pyx_PyUnicode_KIND(u)         (sizeof(Py_UNICODE))
  #define __Pyx_PyUnicode_DATA(u)         ((void*)PyUnicode_AS_UNICODE(u))
  #define __Pyx_PyUnicode_READ(k, d, i)   ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
  #define __Pyx_PyUnicode_Concat(a, b)      PyNumber_Add(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  PyNumber_Add(a, b)
#else
  #define __Pyx_PyUnicode_Concat(a, b)      PyUnicode_Concat(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
      PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
  #define PyUnicode_Contains(u, s)  PySequence_Contains(u, s)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
  #define PyByteArray_Check(obj)  PyObject_TypeCheck(obj, &PyByteArray_Type)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
  #define PyObject_Format(obj, fmt)  PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
#define __Pyx_PyString_FormatSafe(a, b)   ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b)  ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyString_Format(a, b)  PyUnicode_Format(a, b)
#else
  #define __Pyx_PyString_Format(a, b)  PyString_Format(a, b)
#endif
#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
  #define PyObject_ASCII(o)            PyObject_Repr(o)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBaseString_Type            PyUnicode_Type
  #define PyStringObject               PyUnicodeObject
  #define PyString_Type                PyUnicode_Type
  #define PyString_Check               PyUnicode_Check
  #define PyString_CheckExact          PyUnicode_CheckExact
#ifndef PyObject_Unicode
  #define PyObject_Unicode             PyObject_Str
#endif
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
  #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
#else
  #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
  #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
#endif
#ifndef PySet_CheckExact
  #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
#endif
#if PY_VERSION_HEX >= 0x030900A4
  #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt)
  #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size)
#else
  #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt)
  #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size)
#endif
#if CYTHON_ASSUME_SAFE_MACROS
  #define __Pyx_PySequence_SIZE(seq)  Py_SIZE(seq)
#else
  #define __Pyx_PySequence_SIZE(seq)  PySequence_Size(seq)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyIntObject                  PyLongObject
  #define PyInt_Type                   PyLong_Type
  #define PyInt_Check(op)              PyLong_Check(op)
  #define PyInt_CheckExact(op)         PyLong_CheckExact(op)
  #define PyInt_FromString             PyLong_FromString
  #define PyInt_FromUnicode            PyLong_FromUnicode
  #define PyInt_FromLong               PyLong_FromLong
  #define PyInt_FromSize_t             PyLong_FromSize_t
  #define PyInt_FromSsize_t            PyLong_FromSsize_t
  #define PyInt_AsLong                 PyLong_AsLong
  #define PyInt_AS_LONG                PyLong_AS_LONG
  #define PyInt_AsSsize_t              PyLong_AsSsize_t
  #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
  #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
  #define PyNumber_Int                 PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBoolObject                 PyLongObject
#endif
#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
  #ifndef PyUnicode_InternFromString
    #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
  #endif
#endif
#if PY_VERSION_HEX < 0x030200A4
  typedef long Py_hash_t;
  #define __Pyx_PyInt_FromHash_t PyInt_FromLong
  #define __Pyx_PyInt_AsHash_t   __Pyx_PyIndex_AsHash_t
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   __Pyx_PyIndex_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func))
#else
  #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
#if CYTHON_USE_ASYNC_SLOTS
  #if PY_VERSION_HEX >= 0x030500B1
    #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
    #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
  #else
    #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
  #endif
#else
  #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef __Pyx_PyAsyncMethodsStruct
    typedef struct {
        unaryfunc am_await;
        unaryfunc am_aiter;
        unaryfunc am_anext;
    } __Pyx_PyAsyncMethodsStruct;
#endif

#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
  #if !defined(_USE_MATH_DEFINES)
    #define _USE_MATH_DEFINES
  #endif
#endif
#include <math.h>
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
  float value;
  memset(&value, 0xFF, sizeof(value));
  return value;
}
#endif
#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
#define __Pyx_truncl trunc
#else
#define __Pyx_truncl truncl
#endif

#define __PYX_MARK_ERR_POS(f_index, lineno) \
    { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
#define __PYX_ERR(f_index, lineno, Ln_error) \
    { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }

#ifndef __PYX_EXTERN_C
  #ifdef __cplusplus
    #define __PYX_EXTERN_C extern "C"
  #else
    #define __PYX_EXTERN_C extern
  #endif
#endif

#define __PYX_HAVE__whatshap__core
#define __PYX_HAVE_API__whatshap__core
/* Early includes */
#include <stdint.h>
#include <string.h>
#include <string>
#include "ios"
#include "new"
#include "stdexcept"
#include "typeinfo"
#include <vector>
#include <utility>

    #if __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600)
    // move should be defined for these versions of MSVC, but __cplusplus isn't set usefully
    #include <type_traits>

    namespace cython_std {
    template <typename T> typename std::remove_reference<T>::type&& move(T& t) noexcept { return std::move(t); }
    template <typename T> typename std::remove_reference<T>::type&& move(T&& t) noexcept { return std::move(t); }
    }

    #endif
    
#include <unordered_map>
#include "read.h"
#include "indexset.h"
#include "readset.h"
#include "pedigree.h"
#include "pedigreedptable.h"
#include "binomial.h"
#include "genotype.h"
#include "genotypedptable.h"
#include "phredgenotypelikelihoods.h"
#include "genotypedistribution.h"
#include "genotyper.h"
#include "hapchat/hapchatcore.cpp"
#include "polyphase/clustereditingsolver.h"
#include "polyphase/clustereditingsolution.h"
#include "polyphase/allelematrix.h"
#include "polyphase/trianglesparsematrix.h"
#include "polyphase/readscoring.h"
#include "polyphase/haplothreader.h"
#include "polyphase/switchflipcalculator.h"
#include "polyphase/progenygenotypelikelihoods.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */

#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
#define CYTHON_WITHOUT_ASSERTIONS
#endif

typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;

#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8)
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#define __Pyx_uchar_cast(c) ((unsigned char)c)
#define __Pyx_long_cast(x) ((long)x)
#define __Pyx_fits_Py_ssize_t(v, type, is_signed)  (\
    (sizeof(type) < sizeof(Py_ssize_t))  ||\
    (sizeof(type) > sizeof(Py_ssize_t) &&\
          likely(v < (type)PY_SSIZE_T_MAX ||\
                 v == (type)PY_SSIZE_T_MAX)  &&\
          (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
                                v == (type)PY_SSIZE_T_MIN)))  ||\
    (sizeof(type) == sizeof(Py_ssize_t) &&\
          (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
                               v == (type)PY_SSIZE_T_MAX)))  )
static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
    return (size_t) i < (size_t) limit;
}
#if defined (__cplusplus) && __cplusplus >= 201103L
    #include <cstdlib>
    #define __Pyx_sst_abs(value) std::abs(value)
#elif SIZEOF_INT >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) abs(value)
#elif SIZEOF_LONG >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) labs(value)
#elif defined (_MSC_VER)
    #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define __Pyx_sst_abs(value) llabs(value)
#elif defined (__GNUC__)
    #define __Pyx_sst_abs(value) __builtin_llabs(value)
#else
    #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
#endif
static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
#define __Pyx_PyBytes_FromString        PyBytes_FromString
#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
#if PY_MAJOR_VERSION < 3
    #define __Pyx_PyStr_FromString        __Pyx_PyBytes_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#else
    #define __Pyx_PyStr_FromString        __Pyx_PyUnicode_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
#endif
#define __Pyx_PyBytes_AsWritableString(s)     ((char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsWritableSString(s)    ((signed char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsWritableUString(s)    ((unsigned char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsString(s)     ((const char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsSString(s)    ((const signed char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsUString(s)    ((const unsigned char*) PyBytes_AS_STRING(s))
#define __Pyx_PyObject_AsWritableString(s)    ((char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsWritableSString(s)    ((signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsWritableUString(s)    ((unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsSString(s)    ((const signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsUString(s)    ((const unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_FromCString(s)  __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromCString(s)   __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
    const Py_UNICODE *u_end = u;
    while (*u_end++) ;
    return (size_t)(u_end - u - 1);
}
#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
#define __Pyx_PySequence_Tuple(obj)\
    (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
#else
#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
#endif
#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    const char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    if (strcmp(default_encoding_c, "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        char ascii_chars[128];
        int c;
        for (c = 0; c < 128; c++) {
            ascii_chars[c] = c;
        }
        __Pyx_sys_getdefaultencoding_not_ascii = 1;
        ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
        if (!ascii_chars_u) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
            PyErr_Format(
                PyExc_ValueError,
                "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
        Py_DECREF(ascii_chars_u);
        Py_DECREF(ascii_chars_b);
    }
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return -1;
}
#endif
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
#else
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
    if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
    strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    return -1;
}
#endif
#endif


/* Test for GCC > 2.95 */
#if defined(__GNUC__)     && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
  #define likely(x)   __builtin_expect(!!(x), 1)
  #define unlikely(x) __builtin_expect(!!(x), 0)
#else /* !__GNUC__ or GCC < 2.95 */
  #define likely(x)   (x)
  #define unlikely(x) (x)
#endif /* __GNUC__ */
static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }

static PyObject *__pyx_m = NULL;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_cython_runtime = NULL;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
static PyObject *__pyx_empty_unicode;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;


static const char *__pyx_f[] = {
  "stringsource",
  "whatshap/core.pyx",
};

/*--- Type declarations ---*/
struct __pyx_obj_8whatshap_4core_NumericSampleIds;
struct __pyx_obj_8whatshap_4core_Read;
struct __pyx_obj_8whatshap_4core_ReadSet;
struct __pyx_obj_8whatshap_4core_Pedigree;
struct __pyx_obj_8whatshap_4core_PedigreeDPTable;
struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods;
struct __pyx_obj_8whatshap_4core_Genotype;
struct __pyx_obj_8whatshap_4core_GenotypeDPTable;
struct __pyx_obj_8whatshap_4core_HapChatCore;
struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__;
struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__;
struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__;

/* "whatshap/core.pxd":8
 * 
 * 
 * cdef class NumericSampleIds:             # <<<<<<<<<<<<<<
 * 	cdef dict mapping
 * 	cdef bool frozen
 */
struct __pyx_obj_8whatshap_4core_NumericSampleIds {
  PyObject_HEAD
  PyObject *mapping;
  bool frozen;
};


/* "whatshap/core.pxd":13
 * 
 * 
 * cdef class Read:             # <<<<<<<<<<<<<<
 * 	cdef cpp.Read *thisptr
 * 	cdef bool ownsptr
 */
struct __pyx_obj_8whatshap_4core_Read {
  PyObject_HEAD
  Read *thisptr;
  bool ownsptr;
};


/* "whatshap/core.pxd":18
 * 
 * 
 * cdef class ReadSet:             # <<<<<<<<<<<<<<
 * 	cdef cpp.ReadSet *thisptr
 * 
 */
struct __pyx_obj_8whatshap_4core_ReadSet {
  PyObject_HEAD
  ReadSet *thisptr;
};


/* "whatshap/core.pxd":22
 * 
 * 
 * cdef class Pedigree:             # <<<<<<<<<<<<<<
 * 	cdef cpp.Pedigree *thisptr
 * 	cdef NumericSampleIds numeric_sample_ids
 */
struct __pyx_obj_8whatshap_4core_Pedigree {
  PyObject_HEAD
  Pedigree *thisptr;
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *numeric_sample_ids;
};


/* "whatshap/core.pxd":27
 * 
 * 
 * cdef class PedigreeDPTable:             # <<<<<<<<<<<<<<
 * 	cdef cpp.PedigreeDPTable *thisptr
 * 	cdef Pedigree pedigree
 */
struct __pyx_obj_8whatshap_4core_PedigreeDPTable {
  PyObject_HEAD
  PedigreeDPTable *thisptr;
  struct __pyx_obj_8whatshap_4core_Pedigree *pedigree;
};


/* "whatshap/core.pxd":32
 * 
 * 
 * cdef class PhredGenotypeLikelihoods:             # <<<<<<<<<<<<<<
 * 	cdef cpp.PhredGenotypeLikelihoods *thisptr
 * 
 */
struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods {
  PyObject_HEAD
  PhredGenotypeLikelihoods *thisptr;
};


/* "whatshap/core.pxd":36
 * 
 * 
 * cdef class Genotype:             # <<<<<<<<<<<<<<
 * 	cdef cpp.Genotype *thisptr
 * 
 */
struct __pyx_obj_8whatshap_4core_Genotype {
  PyObject_HEAD
  Genotype *thisptr;
};


/* "whatshap/core.pxd":40
 * 
 * 
 * cdef class GenotypeDPTable:             # <<<<<<<<<<<<<<
 * 	cdef cpp.GenotypeDPTable *thisptr
 * 	cdef Pedigree pedigree
 */
struct __pyx_obj_8whatshap_4core_GenotypeDPTable {
  PyObject_HEAD
  GenotypeDPTable *thisptr;
  struct __pyx_obj_8whatshap_4core_Pedigree *pedigree;
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *numeric_sample_ids;
};


/* "whatshap/core.pxd":46
 * 
 * 
 * cdef class HapChatCore:             # <<<<<<<<<<<<<<
 * 	cdef cpp.HapChatCore *thisptr
 */
struct __pyx_obj_8whatshap_4core_HapChatCore {
  PyObject_HEAD
  HapChatCore *thisptr;
};


/* "whatshap/core.pyx":115
 * 			return self.thisptr.getBXTag().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		"""Iterate over all variants in this read"""
 * 		assert self.thisptr != NULL
 */
struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ {
  PyObject_HEAD
  Py_ssize_t __pyx_v_i;
  struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self;
  Py_ssize_t __pyx_t_0;
  Py_ssize_t __pyx_t_1;
  Py_ssize_t __pyx_t_2;
};


/* "whatshap/core.pyx":232
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for i in range(self.thisptr.size()):
 * 			yield self[i]
 */
struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ {
  PyObject_HEAD
  int __pyx_v_i;
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self;
  int __pyx_t_0;
  int __pyx_t_1;
  int __pyx_t_2;
};


/* "whatshap/core.pyx":427
 * 		return self.thisptr.size()
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for genotype in self.genotypes():
 * 			yield self[genotype]
 */
struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ {
  PyObject_HEAD
  PyObject *__pyx_v_genotype;
  struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self;
  PyObject *__pyx_t_0;
  Py_ssize_t __pyx_t_1;
  PyObject *(*__pyx_t_2)(PyObject *);
};


/* --- Runtime support code (head) --- */
/* Refnanny.proto */
#ifndef CYTHON_REFNANNY
  #define CYTHON_REFNANNY 0
#endif
#if CYTHON_REFNANNY
  typedef struct {
    void (*INCREF)(void*, PyObject*, int);
    void (*DECREF)(void*, PyObject*, int);
    void (*GOTREF)(void*, PyObject*, int);
    void (*GIVEREF)(void*, PyObject*, int);
    void* (*SetupContext)(const char*, int, const char*);
    void (*FinishContext)(void**);
  } __Pyx_RefNannyAPIStruct;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
  #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
  #define __Pyx_RefNannySetupContext(name, acquire_gil)\
          if (acquire_gil) {\
              PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
              PyGILState_Release(__pyx_gilstate_save);\
          } else {\
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
          }
#else
  #define __Pyx_RefNannySetupContext(name, acquire_gil)\
          __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
#endif
  #define __Pyx_RefNannyFinishContext()\
          __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
  #define __Pyx_INCREF(r)  __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_DECREF(r)  __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GOTREF(r)  __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_XINCREF(r)  do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
  #define __Pyx_XDECREF(r)  do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
  #define __Pyx_XGOTREF(r)  do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
  #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
  #define __Pyx_RefNannyDeclarations
  #define __Pyx_RefNannySetupContext(name, acquire_gil)
  #define __Pyx_RefNannyFinishContext()
  #define __Pyx_INCREF(r) Py_INCREF(r)
  #define __Pyx_DECREF(r) Py_DECREF(r)
  #define __Pyx_GOTREF(r)
  #define __Pyx_GIVEREF(r)
  #define __Pyx_XINCREF(r) Py_XINCREF(r)
  #define __Pyx_XDECREF(r) Py_XDECREF(r)
  #define __Pyx_XGOTREF(r)
  #define __Pyx_XGIVEREF(r)
#endif
#define __Pyx_XDECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_XDECREF(tmp);\
    } while (0)
#define __Pyx_DECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_DECREF(tmp);\
    } while (0)
#define __Pyx_CLEAR(r)    do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r)   do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)

/* PyObjectGetAttrStr.proto */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name);
#else
#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
#endif

/* GetBuiltinName.proto */
static PyObject *__Pyx_GetBuiltinName(PyObject *name);

/* RaiseArgTupleInvalid.proto */
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
    Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);

/* KeywordStringCheck.proto */
static int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed);

/* PyDictContains.proto */
static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) {
    int result = PyDict_Contains(dict, item);
    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}

/* DictGetItem.proto */
#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key);
#define __Pyx_PyObject_Dict_GetItem(obj, name)\
    (likely(PyDict_CheckExact(obj)) ?\
     __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name))
#else
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#define __Pyx_PyObject_Dict_GetItem(obj, name)  PyObject_GetItem(obj, name)
#endif

/* PyCFunctionFastCall.proto */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
#else
#define __Pyx_PyCFunction_FastCall(func, args, nargs)  (assert(0), NULL)
#endif

/* PyFunctionFastCall.proto */
#if CYTHON_FAST_PYCALL
#define __Pyx_PyFunction_FastCall(func, args, nargs)\
    __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs);
#else
#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
#endif
#define __Pyx_BUILD_ASSERT_EXPR(cond)\
    (sizeof(char [1 - 2*!(cond)]) - 1)
#ifndef Py_MEMBER_SIZE
#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
#endif
#if CYTHON_FAST_PYCALL
  static size_t __pyx_pyframe_localsplus_offset = 0;
  #include "frameobject.h"
#if PY_VERSION_HEX >= 0x030b00a6
  #ifndef Py_BUILD_CORE
    #define Py_BUILD_CORE 1
  #endif
  #include "internal/pycore_frame.h"
#endif
  #define __Pxy_PyFrame_Initialize_Offsets()\
    ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
     (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
  #define __Pyx_PyFrame_GetLocalsplus(frame)\
    (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
#endif // CYTHON_FAST_PYCALL
#endif

/* PyObjectCall.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
#else
#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
#endif

/* PyObjectCallMethO.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
#endif

/* PyObjectCallOneArg.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);

/* IterFinish.proto */
static CYTHON_INLINE int __Pyx_IterFinish(void);

/* PyObjectCallNoArg.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#else
#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
#endif

/* PyObjectGetMethod.proto */
static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method);

/* PyObjectCallMethod0.proto */
static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name);

/* RaiseNeedMoreValuesToUnpack.proto */
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);

/* RaiseTooManyValuesToUnpack.proto */
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);

/* UnpackItemEndCheck.proto */
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);

/* RaiseNoneIterError.proto */
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);

/* UnpackTupleError.proto */
static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index);

/* UnpackTuple2.proto */
#define __Pyx_unpack_tuple2(tuple, value1, value2, is_tuple, has_known_size, decref_tuple)\
    (likely(is_tuple || PyTuple_Check(tuple)) ?\
        (likely(has_known_size || PyTuple_GET_SIZE(tuple) == 2) ?\
            __Pyx_unpack_tuple2_exact(tuple, value1, value2, decref_tuple) :\
            (__Pyx_UnpackTupleError(tuple, 2), -1)) :\
        __Pyx_unpack_tuple2_generic(tuple, value1, value2, has_known_size, decref_tuple))
static CYTHON_INLINE int __Pyx_unpack_tuple2_exact(
    PyObject* tuple, PyObject** value1, PyObject** value2, int decref_tuple);
static int __Pyx_unpack_tuple2_generic(
    PyObject* tuple, PyObject** value1, PyObject** value2, int has_known_size, int decref_tuple);

/* dict_iter.proto */
static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
                                                   Py_ssize_t* p_orig_length, int* p_is_dict);
static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
                                              PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);

/* PyThreadStateGet.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyThreadState_declare  PyThreadState *__pyx_tstate;
#define __Pyx_PyThreadState_assign  __pyx_tstate = __Pyx_PyThreadState_Current;
#define __Pyx_PyErr_Occurred()  __pyx_tstate->curexc_type
#else
#define __Pyx_PyThreadState_declare
#define __Pyx_PyThreadState_assign
#define __Pyx_PyErr_Occurred()  PyErr_Occurred()
#endif

/* PyErrFetchRestore.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL)
#define __Pyx_ErrRestoreWithState(type, value, tb)  __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrFetchWithState(type, value, tb)    __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrRestore(type, value, tb)  __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
#define __Pyx_ErrFetch(type, value, tb)    __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
#if CYTHON_COMPILING_IN_CPYTHON
#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL))
#else
#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
#endif
#else
#define __Pyx_PyErr_Clear() PyErr_Clear()
#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
#define __Pyx_ErrRestoreWithState(type, value, tb)  PyErr_Restore(type, value, tb)
#define __Pyx_ErrFetchWithState(type, value, tb)  PyErr_Fetch(type, value, tb)
#define __Pyx_ErrRestoreInState(tstate, type, value, tb)  PyErr_Restore(type, value, tb)
#define __Pyx_ErrFetchInState(tstate, type, value, tb)  PyErr_Fetch(type, value, tb)
#define __Pyx_ErrRestore(type, value, tb)  PyErr_Restore(type, value, tb)
#define __Pyx_ErrFetch(type, value, tb)  PyErr_Fetch(type, value, tb)
#endif

/* RaiseException.proto */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);

/* RaiseDoubleKeywords.proto */
static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);

/* ParseKeywords.proto */
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
    PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
    const char* function_name);

/* ArgTypeTest.proto */
#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\
    ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\
        __Pyx__ArgTypeTest(obj, type, name, exact))
static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact);

/* WriteUnraisableException.proto */
static void __Pyx_WriteUnraisable(const char *name, int clineno,
                                  int lineno, const char *filename,
                                  int full_traceback, int nogil);

/* IncludeCppStringH.proto */
#include <string>

/* decode_c_string_utf16.proto */
static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) {
    int byteorder = 0;
    return PyUnicode_DecodeUTF16(s, size, errors, &byteorder);
}
static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) {
    int byteorder = -1;
    return PyUnicode_DecodeUTF16(s, size, errors, &byteorder);
}
static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) {
    int byteorder = 1;
    return PyUnicode_DecodeUTF16(s, size, errors, &byteorder);
}

/* decode_c_bytes.proto */
static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes(
         const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop,
         const char* encoding, const char* errors,
         PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));

/* decode_cpp_string.proto */
static CYTHON_INLINE PyObject* __Pyx_decode_cpp_string(
         std::string cppstring, Py_ssize_t start, Py_ssize_t stop,
         const char* encoding, const char* errors,
         PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
    return __Pyx_decode_c_bytes(
        cppstring.data(), cppstring.size(), start, stop, encoding, errors, decode_func);
}

/* GetItemInt.proto */
#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
    (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
               __Pyx_GetItemInt_Generic(o, to_py_func(i))))
#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
    (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
    (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                     int is_list, int wraparound, int boundscheck);

/* PyObjectCall2Args.proto */
static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2);

/* PyDictVersioning.proto */
#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
#define __PYX_DICT_VERSION_INIT  ((PY_UINT64_T) -1)
#define __PYX_GET_DICT_VERSION(dict)  (((PyDictObject*)(dict))->ma_version_tag)
#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\
    (version_var) = __PYX_GET_DICT_VERSION(dict);\
    (cache_var) = (value);
#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\
    static PY_UINT64_T __pyx_dict_version = 0;\
    static PyObject *__pyx_dict_cached_value = NULL;\
    if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\
        (VAR) = __pyx_dict_cached_value;\
    } else {\
        (VAR) = __pyx_dict_cached_value = (LOOKUP);\
        __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\
    }\
}
static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj);
static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj);
static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version);
#else
#define __PYX_GET_DICT_VERSION(dict)  (0)
#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)
#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP)  (VAR) = (LOOKUP);
#endif

/* GetModuleGlobalName.proto */
#if CYTHON_USE_DICT_VERSIONS
#define __Pyx_GetModuleGlobalName(var, name)  do {\
    static PY_UINT64_T __pyx_dict_version = 0;\
    static PyObject *__pyx_dict_cached_value = NULL;\
    (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\
        (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\
        __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
} while(0)
#define __Pyx_GetModuleGlobalNameUncached(var, name)  do {\
    PY_UINT64_T __pyx_dict_version;\
    PyObject *__pyx_dict_cached_value;\
    (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
} while(0)
static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value);
#else
#define __Pyx_GetModuleGlobalName(var, name)  (var) = __Pyx__GetModuleGlobalName(name)
#define __Pyx_GetModuleGlobalNameUncached(var, name)  (var) = __Pyx__GetModuleGlobalName(name)
static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name);
#endif

/* ListCompAppend.proto */
#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
    PyListObject* L = (PyListObject*) list;
    Py_ssize_t len = Py_SIZE(list);
    if (likely(L->allocated > len)) {
        Py_INCREF(x);
        PyList_SET_ITEM(list, len, x);
        __Pyx_SET_SIZE(list, len + 1);
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
#endif

/* SliceObject.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
        PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
        PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
        int has_cstart, int has_cstop, int wraparound);

/* ListAppend.proto */
#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
    PyListObject* L = (PyListObject*) list;
    Py_ssize_t len = Py_SIZE(list);
    if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
        Py_INCREF(x);
        PyList_SET_ITEM(list, len, x);
        __Pyx_SET_SIZE(list, len + 1);
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif

/* ExtTypeTest.proto */
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);

/* ObjectGetItem.proto */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key);
#else
#define __Pyx_PyObject_GetItem(obj, key)  PyObject_GetItem(obj, key)
#endif

/* IncludeStringH.proto */
#include <string.h>

/* PyObject_GenericGetAttrNoDict.proto */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name);
#else
#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr
#endif

/* PyObject_GenericGetAttr.proto */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name);
#else
#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr
#endif

/* PyErrExceptionMatches.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
#else
#define __Pyx_PyErr_ExceptionMatches(err)  PyErr_ExceptionMatches(err)
#endif

/* PyObjectGetAttrStrNoError.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name);

/* SetupReduce.proto */
static int __Pyx_setup_reduce(PyObject* type_obj);

/* Import.proto */
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);

/* ImportFrom.proto */
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);

/* CLineInTraceback.proto */
#ifdef CYTHON_CLINE_IN_TRACEBACK
#define __Pyx_CLineForTraceback(tstate, c_line)  (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
#else
static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
#endif

/* CodeObjectCache.proto */
typedef struct {
    PyCodeObject* code_object;
    int code_line;
} __Pyx_CodeObjectCacheEntry;
struct __Pyx_CodeObjectCache {
    int count;
    int max_count;
    __Pyx_CodeObjectCacheEntry* entries;
};
static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
static PyCodeObject *__pyx_find_code_object(int code_line);
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);

/* AddTraceback.proto */
static void __Pyx_AddTraceback(const char *funcname, int c_line,
                               int py_line, const char *filename);

/* GCCDiagnostics.proto */
#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
#define __Pyx_HAS_GCC_DIAGNOSTIC
#endif

/* CppExceptionConversion.proto */
#ifndef __Pyx_CppExn2PyErr
#include <new>
#include <typeinfo>
#include <stdexcept>
#include <ios>
static void __Pyx_CppExn2PyErr() {
  try {
    if (PyErr_Occurred())
      ; // let the latest Python exn pass through and ignore the current one
    else
      throw;
  } catch (const std::bad_alloc& exn) {
    PyErr_SetString(PyExc_MemoryError, exn.what());
  } catch (const std::bad_cast& exn) {
    PyErr_SetString(PyExc_TypeError, exn.what());
  } catch (const std::bad_typeid& exn) {
    PyErr_SetString(PyExc_TypeError, exn.what());
  } catch (const std::domain_error& exn) {
    PyErr_SetString(PyExc_ValueError, exn.what());
  } catch (const std::invalid_argument& exn) {
    PyErr_SetString(PyExc_ValueError, exn.what());
  } catch (const std::ios_base::failure& exn) {
    PyErr_SetString(PyExc_IOError, exn.what());
  } catch (const std::out_of_range& exn) {
    PyErr_SetString(PyExc_IndexError, exn.what());
  } catch (const std::overflow_error& exn) {
    PyErr_SetString(PyExc_OverflowError, exn.what());
  } catch (const std::range_error& exn) {
    PyErr_SetString(PyExc_ArithmeticError, exn.what());
  } catch (const std::underflow_error& exn) {
    PyErr_SetString(PyExc_ArithmeticError, exn.what());
  } catch (const std::exception& exn) {
    PyErr_SetString(PyExc_RuntimeError, exn.what());
  }
  catch (...)
  {
    PyErr_SetString(PyExc_RuntimeError, "Unknown exception");
  }
}
#endif

/* CIntFromPy.proto */
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);

/* CIntFromPy.proto */
static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *);

/* CIntFromPy.proto */
static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value);

/* CIntFromPy.proto */
static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value);

/* CIntFromPy.proto */
static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *);

/* CIntFromPy.proto */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);

/* FastTypeChecks.proto */
#if CYTHON_COMPILING_IN_CPYTHON
#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
#else
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
#endif
#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)

/* FetchCommonType.proto */
static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);

/* GetTopmostException.proto */
#if CYTHON_USE_EXC_INFO_STACK
static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate);
#endif

/* SaveResetException.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_ExceptionSave(type, value, tb)  __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
#define __Pyx_ExceptionReset(type, value, tb)  __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
#else
#define __Pyx_ExceptionSave(type, value, tb)   PyErr_GetExcInfo(type, value, tb)
#define __Pyx_ExceptionReset(type, value, tb)  PyErr_SetExcInfo(type, value, tb)
#endif

/* SwapException.proto */
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_ExceptionSwap(type, value, tb)  __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb)
static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
#else
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb);
#endif

/* PyObjectCallMethod1.proto */
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);

/* CoroutineBase.proto */
typedef PyObject *(*__pyx_coroutine_body_t)(PyObject *, PyThreadState *, PyObject *);
#if CYTHON_USE_EXC_INFO_STACK
#define __Pyx_ExcInfoStruct  _PyErr_StackItem
#else
typedef struct {
    PyObject *exc_type;
    PyObject *exc_value;
    PyObject *exc_traceback;
} __Pyx_ExcInfoStruct;
#endif
typedef struct {
    PyObject_HEAD
    __pyx_coroutine_body_t body;
    PyObject *closure;
    __Pyx_ExcInfoStruct gi_exc_state;
    PyObject *gi_weakreflist;
    PyObject *classobj;
    PyObject *yieldfrom;
    PyObject *gi_name;
    PyObject *gi_qualname;
    PyObject *gi_modulename;
    PyObject *gi_code;
    PyObject *gi_frame;
    int resume_label;
    char is_running;
} __pyx_CoroutineObject;
static __pyx_CoroutineObject *__Pyx__Coroutine_New(
    PyTypeObject *type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
    PyObject *name, PyObject *qualname, PyObject *module_name);
static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit(
            __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
            PyObject *name, PyObject *qualname, PyObject *module_name);
static CYTHON_INLINE void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *self);
static int __Pyx_Coroutine_clear(PyObject *self);
static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value);
static PyObject *__Pyx_Coroutine_Close(PyObject *self);
static PyObject *__Pyx_Coroutine_Throw(PyObject *gen, PyObject *args);
#if CYTHON_USE_EXC_INFO_STACK
#define __Pyx_Coroutine_SwapException(self)
#define __Pyx_Coroutine_ResetAndClearException(self)  __Pyx_Coroutine_ExceptionClear(&(self)->gi_exc_state)
#else
#define __Pyx_Coroutine_SwapException(self) {\
    __Pyx_ExceptionSwap(&(self)->gi_exc_state.exc_type, &(self)->gi_exc_state.exc_value, &(self)->gi_exc_state.exc_traceback);\
    __Pyx_Coroutine_ResetFrameBackpointer(&(self)->gi_exc_state);\
    }
#define __Pyx_Coroutine_ResetAndClearException(self) {\
    __Pyx_ExceptionReset((self)->gi_exc_state.exc_type, (self)->gi_exc_state.exc_value, (self)->gi_exc_state.exc_traceback);\
    (self)->gi_exc_state.exc_type = (self)->gi_exc_state.exc_value = (self)->gi_exc_state.exc_traceback = NULL;\
    }
#endif
#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyGen_FetchStopIterationValue(pvalue)\
    __Pyx_PyGen__FetchStopIterationValue(__pyx_tstate, pvalue)
#else
#define __Pyx_PyGen_FetchStopIterationValue(pvalue)\
    __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, pvalue)
#endif
static int __Pyx_PyGen__FetchStopIterationValue(PyThreadState *tstate, PyObject **pvalue);
static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state);

/* PatchModuleWithCoroutine.proto */
static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code);

/* PatchGeneratorABC.proto */
static int __Pyx_patch_abc(void);

/* Generator.proto */
#define __Pyx_Generator_USED
static PyTypeObject *__pyx_GeneratorType = 0;
#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
#define __Pyx_Generator_New(body, code, closure, name, qualname, module_name)\
    __Pyx__Coroutine_New(__pyx_GeneratorType, body, code, closure, name, qualname, module_name)
static PyObject *__Pyx_Generator_Next(PyObject *self);
static int __pyx_Generator_init(void);

/* CheckBinaryVersion.proto */
static int __Pyx_check_binary_version(void);

/* InitStrings.proto */
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);


/* Module declarations from 'libcpp' */

/* Module declarations from 'libc.stdint' */

/* Module declarations from 'whatshap' */

/* Module declarations from 'libc.string' */

/* Module declarations from 'libcpp.string' */

/* Module declarations from 'libcpp.vector' */

/* Module declarations from 'libcpp.utility' */

/* Module declarations from 'libcpp.pair' */

/* Module declarations from 'libcpp.unordered_map' */

/* Module declarations from 'whatshap.cpp' */

/* Module declarations from 'whatshap.core' */
static PyTypeObject *__pyx_ptype_8whatshap_4core_NumericSampleIds = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_Read = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_ReadSet = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_Pedigree = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_PedigreeDPTable = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_Genotype = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_GenotypeDPTable = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core_HapChatCore = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core___pyx_scope_struct____iter__ = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core___pyx_scope_struct_1___iter__ = 0;
static PyTypeObject *__pyx_ptype_8whatshap_4core___pyx_scope_struct_2___iter__ = 0;
static std::vector<double>  __pyx_convert_vector_from_py_double(PyObject *); /*proto*/
static std::vector<uint32_t>  __pyx_convert_vector_from_py_uint32_t(PyObject *); /*proto*/
static std::string __pyx_convert_string_from_py_std__in_string(PyObject *); /*proto*/
static PyObject *__pyx_convert_vector_to_py_int(const std::vector<int>  &); /*proto*/
static CYTHON_INLINE PyObject *__pyx_convert_PyObject_string_to_py_std__in_string(std::string const &); /*proto*/
static CYTHON_INLINE PyObject *__pyx_convert_PyUnicode_string_to_py_std__in_string(std::string const &); /*proto*/
static CYTHON_INLINE PyObject *__pyx_convert_PyStr_string_to_py_std__in_string(std::string const &); /*proto*/
static CYTHON_INLINE PyObject *__pyx_convert_PyBytes_string_to_py_std__in_string(std::string const &); /*proto*/
static CYTHON_INLINE PyObject *__pyx_convert_PyByteArray_string_to_py_std__in_string(std::string const &); /*proto*/
static PyObject *__pyx_convert_vector_to_py_unsigned_int(const std::vector<unsigned int>  &); /*proto*/
static std::vector<unsigned int>  __pyx_convert_vector_from_py_unsigned_int(PyObject *); /*proto*/
static PyObject *__pyx_convert_vector_to_py_uint32_t(const std::vector<uint32_t>  &); /*proto*/
static PyObject *__pyx_convert_vector_to_py_double(const std::vector<double>  &); /*proto*/
static PyObject *__pyx_convert_vector_to_py_long__double(const std::vector<long double>  &); /*proto*/
#define __Pyx_MODULE_NAME "whatshap.core"
extern int __pyx_module_is_main_whatshap__core;
int __pyx_module_is_main_whatshap__core = 0;

/* Implementation of 'whatshap.core' */
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_IndexError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_KeyError;
static const char __pyx_k_i[] = "i";
static const char __pyx_k_k[] = "k";
static const char __pyx_k_n[] = "n";
static const char __pyx_k__3[] = "";
static const char __pyx_k_gl[] = "gl";
static const char __pyx_k_id[] = "id";
static const char __pyx_k__22[] = "*";
static const char __pyx_k_add[] = "add";
static const char __pyx_k_gls[] = "gls";
static const char __pyx_k_pos[] = "pos";
static const char __pyx_k_Read[] = "Read";
static const char __pyx_k_args[] = "args";
static const char __pyx_k_iter[] = "__iter__";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_mapq[] = "mapq";
static const char __pyx_k_name[] = "name";
static const char __pyx_k_send[] = "send";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_UTF_8[] = "UTF-8";
static const char __pyx_k_close[] = "close";
static const char __pyx_k_items[] = "items";
static const char __pyx_k_mapqs[] = "mapqs";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_throw[] = "throw";
static const char __pyx_k_BX_tag[] = "BX_tag";
static const char __pyx_k_allele[] = "allele";
static const char __pyx_k_encode[] = "encode";
static const char __pyx_k_format[] = "format";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_name_2[] = "__name__";
static const char __pyx_k_ploidy[] = "ploidy";
static const char __pyx_k_reduce[] = "__reduce__";
static const char __pyx_k_ReadSet[] = "ReadSet";
static const char __pyx_k_Variant[] = "Variant";
static const char __pyx_k_alleles[] = "alleles";
static const char __pyx_k_quality[] = "quality";
static const char __pyx_k_readset[] = "readset";
static const char __pyx_k_variant[] = "variant";
static const char __pyx_k_Genotype[] = "Genotype";
static const char __pyx_k_KeyError[] = "KeyError";
static const char __pyx_k_Pedigree[] = "Pedigree";
static const char __pyx_k_add_mapq[] = "add_mapq";
static const char __pyx_k_child_id[] = "child_id";
static const char __pyx_k_genotype[] = "genotype";
static const char __pyx_k_getstate[] = "__getstate__";
static const char __pyx_k_pedigree[] = "pedigree";
static const char __pyx_k_position[] = "position";
static const char __pyx_k_setstate[] = "__setstate__";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_as_vector[] = "as_vector";
static const char __pyx_k_father_id[] = "father_id";
static const char __pyx_k_genotypes[] = "genotypes";
static const char __pyx_k_gl_vector[] = "gl_vector";
static const char __pyx_k_mother_id[] = "mother_id";
static const char __pyx_k_positions[] = "positions";
static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
static const char __pyx_k_sample_id[] = "sample_id";
static const char __pyx_k_source_id[] = "source_id";
static const char __pyx_k_IndexError[] = "IndexError";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_namedtuple[] = "namedtuple";
static const char __pyx_k_nr_alleles[] = "nr_alleles";
static const char __pyx_k_recombcost[] = "recombcost";
static const char __pyx_k_HapChatCore[] = "HapChatCore";
static const char __pyx_k_Invalid_key[] = "Invalid key: {}";
static const char __pyx_k_Read___iter[] = "Read.__iter__";
static const char __pyx_k_add_variant[] = "add_variant";
static const char __pyx_k_c_positions[] = "c_positions";
static const char __pyx_k_collections[] = "collections";
static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
static const char __pyx_k_variant_index[] = "variant_index";
static const char __pyx_k_whatshap_core[] = "whatshap.core";
static const char __pyx_k_ReadSet___iter[] = "ReadSet.__iter__";
static const char __pyx_k_GenotypeDPTable[] = "GenotypeDPTable";
static const char __pyx_k_PedigreeDPTable[] = "PedigreeDPTable";
static const char __pyx_k_reference_start[] = "reference_start";
static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
static const char __pyx_k_NumericSampleIds[] = "NumericSampleIds";
static const char __pyx_k_genotypes_vector[] = "genotypes_vector";
static const char __pyx_k_compute_genotypes[] = "compute_genotypes";
static const char __pyx_k_whatshap_core_pyx[] = "whatshap/core.pyx";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_distrust_genotypes[] = "distrust_genotypes";
static const char __pyx_k_numeric_sample_ids[] = "numeric_sample_ids";
static const char __pyx_k_Index_out_of_bounds[] = "Index out of bounds: {}";
static const char __pyx_k_NotImplementedError[] = "NotImplementedError";
static const char __pyx_k_binomial_coefficient[] = "binomial_coefficient";
static const char __pyx_k_genotype_likelihoods[] = "genotype_likelihoods";
static const char __pyx_k_get_max_genotype_ploidy[] = "get_max_genotype_ploidy";
static const char __pyx_k_PhredGenotypeLikelihoods[] = "PhredGenotypeLikelihoods";
static const char __pyx_k_get_max_genotype_alleles[] = "get_max_genotype_alleles";
static const char __pyx_k_is_diploid_and_biallelic[] = "is_diploid_and_biallelic";
static const char __pyx_k_Wrappers_for_core_C_classes[] = "\nWrappers for core C++ classes.\n";
static const char __pyx_k_Read_does_not_support_slices[] = "Read does not support slices";
static const char __pyx_k_PhredGenotypeLikelihoods___iter[] = "PhredGenotypeLikelihoods.__iter__";
static const char __pyx_k_Querying_a_ReadSet_by_read_name[] = "Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead";
static const char __pyx_k_ReadSet_does_not_support_slices[] = "ReadSet does not support slices";
static const char __pyx_k_Expected_instance_of_Variant_but[] = "Expected instance of Variant, but found {}";
static const char __pyx_k_Read_name_r_mapq_source_id_sampl[] = "Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})";
static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__";
static PyObject *__pyx_n_s_BX_tag;
static PyObject *__pyx_kp_u_Expected_instance_of_Variant_but;
static PyObject *__pyx_n_s_Genotype;
static PyObject *__pyx_n_s_GenotypeDPTable;
static PyObject *__pyx_n_s_HapChatCore;
static PyObject *__pyx_n_s_IndexError;
static PyObject *__pyx_kp_u_Index_out_of_bounds;
static PyObject *__pyx_kp_u_Invalid_key;
static PyObject *__pyx_n_s_KeyError;
static PyObject *__pyx_n_s_NotImplementedError;
static PyObject *__pyx_n_s_NumericSampleIds;
static PyObject *__pyx_n_s_Pedigree;
static PyObject *__pyx_n_s_PedigreeDPTable;
static PyObject *__pyx_n_s_PhredGenotypeLikelihoods;
static PyObject *__pyx_n_s_PhredGenotypeLikelihoods___iter;
static PyObject *__pyx_kp_u_Querying_a_ReadSet_by_read_name;
static PyObject *__pyx_n_s_Read;
static PyObject *__pyx_n_s_ReadSet;
static PyObject *__pyx_n_s_ReadSet___iter;
static PyObject *__pyx_kp_u_ReadSet_does_not_support_slices;
static PyObject *__pyx_n_s_Read___iter;
static PyObject *__pyx_kp_u_Read_does_not_support_slices;
static PyObject *__pyx_kp_u_Read_name_r_mapq_source_id_sampl;
static PyObject *__pyx_n_s_TypeError;
static PyObject *__pyx_kp_u_UTF_8;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_n_s_Variant;
static PyObject *__pyx_kp_u__22;
static PyObject *__pyx_kp_b__3;
static PyObject *__pyx_kp_u__3;
static PyObject *__pyx_n_s_add;
static PyObject *__pyx_n_s_add_mapq;
static PyObject *__pyx_n_s_add_variant;
static PyObject *__pyx_n_s_allele;
static PyObject *__pyx_n_s_alleles;
static PyObject *__pyx_n_s_args;
static PyObject *__pyx_n_s_as_vector;
static PyObject *__pyx_n_s_binomial_coefficient;
static PyObject *__pyx_n_s_c_positions;
static PyObject *__pyx_n_s_child_id;
static PyObject *__pyx_n_s_cline_in_traceback;
static PyObject *__pyx_n_s_close;
static PyObject *__pyx_n_s_collections;
static PyObject *__pyx_n_s_compute_genotypes;
static PyObject *__pyx_n_s_distrust_genotypes;
static PyObject *__pyx_n_s_encode;
static PyObject *__pyx_n_s_father_id;
static PyObject *__pyx_n_s_format;
static PyObject *__pyx_n_s_genotype;
static PyObject *__pyx_n_s_genotype_likelihoods;
static PyObject *__pyx_n_s_genotypes;
static PyObject *__pyx_n_s_genotypes_vector;
static PyObject *__pyx_n_s_get_max_genotype_alleles;
static PyObject *__pyx_n_s_get_max_genotype_ploidy;
static PyObject *__pyx_n_s_getstate;
static PyObject *__pyx_n_s_gl;
static PyObject *__pyx_n_s_gl_vector;
static PyObject *__pyx_n_s_gls;
static PyObject *__pyx_n_s_i;
static PyObject *__pyx_n_s_id;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_is_diploid_and_biallelic;
static PyObject *__pyx_n_s_items;
static PyObject *__pyx_n_s_iter;
static PyObject *__pyx_n_s_k;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_mapq;
static PyObject *__pyx_n_s_mapqs;
static PyObject *__pyx_n_s_mother_id;
static PyObject *__pyx_n_s_n;
static PyObject *__pyx_n_s_name;
static PyObject *__pyx_n_s_name_2;
static PyObject *__pyx_n_s_namedtuple;
static PyObject *__pyx_kp_s_no_default___reduce___due_to_non;
static PyObject *__pyx_n_s_nr_alleles;
static PyObject *__pyx_n_s_numeric_sample_ids;
static PyObject *__pyx_n_s_pedigree;
static PyObject *__pyx_n_s_ploidy;
static PyObject *__pyx_n_s_pos;
static PyObject *__pyx_n_s_position;
static PyObject *__pyx_n_s_positions;
static PyObject *__pyx_n_s_quality;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_readset;
static PyObject *__pyx_n_s_recombcost;
static PyObject *__pyx_n_s_reduce;
static PyObject *__pyx_n_s_reduce_cython;
static PyObject *__pyx_n_s_reduce_ex;
static PyObject *__pyx_n_s_reference_start;
static PyObject *__pyx_n_s_sample_id;
static PyObject *__pyx_n_s_send;
static PyObject *__pyx_n_s_setstate;
static PyObject *__pyx_n_s_setstate_cython;
static PyObject *__pyx_n_s_source_id;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_throw;
static PyObject *__pyx_n_s_variant;
static PyObject *__pyx_n_s_variant_index;
static PyObject *__pyx_n_s_whatshap_core;
static PyObject *__pyx_kp_s_whatshap_core_pyx;
static int __pyx_pf_8whatshap_4core_16NumericSampleIds___cinit__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_2__getitem__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, PyObject *__pyx_v_sample); /* proto */
static Py_ssize_t __pyx_pf_8whatshap_4core_16NumericSampleIds_4__len__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_6__str__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_8freeze(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_10inverse_mapping(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_12__getstate__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_14__setstate__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, PyObject *__pyx_v_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_16__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_18__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static int __pyx_pf_8whatshap_4core_4Read___cinit__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_name, int __pyx_v_mapq, int __pyx_v_source_id, int __pyx_v_sample_id, int __pyx_v_reference_start, PyObject *__pyx_v_BX_tag); /* proto */
static void __pyx_pf_8whatshap_4core_4Read_2__dealloc__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_4__repr__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_5mapqs___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_4name___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_9source_id___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_9sample_id___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_15reference_start___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_6BX_tag___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_6__iter__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static Py_ssize_t __pyx_pf_8whatshap_4core_4Read_9__len__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_11__getitem__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
static int __pyx_pf_8whatshap_4core_4Read_13__setitem__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_variant); /* proto */
static int __pyx_pf_8whatshap_4core_4Read_15__contains__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_position); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_17__getstate__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_19__setstate__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_21add_variant(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, int __pyx_v_position, int __pyx_v_allele, int __pyx_v_quality); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_23add_mapq(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, int __pyx_v_mapq); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_25sort(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_27is_sorted(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_29has_BX_tag(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_31__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4Read_33__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static int __pyx_pf_8whatshap_4core_7ReadSet___cinit__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static void __pyx_pf_8whatshap_4core_7ReadSet_2__dealloc__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_4add(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Read *__pyx_v_read); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_6__str__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_8__iter__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static Py_ssize_t __pyx_pf_8whatshap_4core_7ReadSet_11__len__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_13__getitem__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_15__getstate__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_17__setstate__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_19sort(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_21subset(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_reads_to_select); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_23get_positions(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_25__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_27__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static int __pyx_pf_8whatshap_4core_15PedigreeDPTable___cinit__(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_recombcost, struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree, bool __pyx_v_distrust_genotypes, PyObject *__pyx_v_positions); /* proto */
static void __pyx_pf_8whatshap_4core_15PedigreeDPTable_2__dealloc__(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_6get_optimal_cost(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_8get_optimal_partitioning(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static int __pyx_pf_8whatshap_4core_8Pedigree___cinit__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_numeric_sample_ids); /* proto */
static void __pyx_pf_8whatshap_4core_8Pedigree_2__dealloc__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_4add_individual(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_id, PyObject *__pyx_v_genotypes, PyObject *__pyx_v_genotype_likelihoods); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_6add_relationship(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_father_id, PyObject *__pyx_v_mother_id, PyObject *__pyx_v_child_id); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_13variant_count___get__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_8genotype(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_variant_index); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_10genotype_likelihoods(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_variant_index); /* proto */
static Py_ssize_t __pyx_pf_8whatshap_4core_8Pedigree_12__len__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_14__str__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_16__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_18__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static int __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods___cinit__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, std::vector<double>  __pyx_v_gl, unsigned int __pyx_v_ploidy, unsigned int __pyx_v_nr_alleles); /* proto */
static void __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_2__dealloc__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_4__str__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_6__getitem__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_genotype); /* proto */
static Py_ssize_t __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_8__len__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_10__iter__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_13__eq__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_other); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_15genotypes(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_17__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_19__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_binomial_coefficient(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n, int __pyx_v_k); /* proto */
static int __pyx_pf_8whatshap_4core_8Genotype___cinit__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, std::vector<uint32_t>  __pyx_v_alleles); /* proto */
static void __pyx_pf_8whatshap_4core_8Genotype_2__dealloc__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_4__str__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_6__repr__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_8is_none(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_10get_index(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_12as_vector(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_14is_homozygous(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_16is_diploid_and_biallelic(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_18get_ploidy(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_20__eq__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_22__ne__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_24__lt__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_26__getstate__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_28__setstate__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, PyObject *__pyx_v_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_30__deepcopy__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_memo); /* proto */
static Py_hash_t __pyx_pf_8whatshap_4core_8Genotype_32__hash__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_34__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_8Genotype_36__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_2get_max_genotype_ploidy(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_4get_max_genotype_alleles(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
static int __pyx_pf_8whatshap_4core_15GenotypeDPTable___cinit__(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, PyObject *__pyx_v_numeric_sample_ids, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_recombcost, struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree, PyObject *__pyx_v_positions); /* proto */
static void __pyx_pf_8whatshap_4core_15GenotypeDPTable_2__dealloc__(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_4get_genotype_likelihoods(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_pos); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_6compute_genotypes(CYTHON_UNUSED PyObject *__pyx_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_positions); /* proto */
static int __pyx_pf_8whatshap_4core_11HapChatCore___cinit__(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset); /* proto */
static void __pyx_pf_8whatshap_4core_11HapChatCore_2__dealloc__(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_4get_length(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_8get_optimal_cost(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_10get_optimal_partitioning(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static PyObject *__pyx_tp_new_8whatshap_4core_NumericSampleIds(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_Read(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_ReadSet(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_Pedigree(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_PedigreeDPTable(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_PhredGenotypeLikelihoods(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_Genotype(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_GenotypeDPTable(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core_HapChatCore(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct_1___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct_2___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_slice__5;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__6;
static PyObject *__pyx_tuple__7;
static PyObject *__pyx_tuple__8;
static PyObject *__pyx_tuple__9;
static PyObject *__pyx_tuple__10;
static PyObject *__pyx_tuple__11;
static PyObject *__pyx_tuple__12;
static PyObject *__pyx_tuple__13;
static PyObject *__pyx_tuple__14;
static PyObject *__pyx_tuple__15;
static PyObject *__pyx_tuple__16;
static PyObject *__pyx_tuple__17;
static PyObject *__pyx_tuple__18;
static PyObject *__pyx_tuple__19;
static PyObject *__pyx_tuple__20;
static PyObject *__pyx_tuple__21;
static PyObject *__pyx_tuple__23;
static PyObject *__pyx_tuple__24;
static PyObject *__pyx_tuple__25;
static PyObject *__pyx_tuple__29;
static PyObject *__pyx_codeobj__26;
static PyObject *__pyx_codeobj__27;
static PyObject *__pyx_codeobj__28;
static PyObject *__pyx_codeobj__30;
/* Late includes */

/* "whatshap/core.pyx":26
 * 	Mapping of sample names (strings) to numeric ids.
 * 	"""
 * 	def __cinit__(self):             # <<<<<<<<<<<<<<
 * 		self.mapping = {}
 * 		self.frozen = False
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_16NumericSampleIds_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_16NumericSampleIds_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
    __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
  if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds___cinit__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_16NumericSampleIds___cinit__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":27
 * 	"""
 * 	def __cinit__(self):
 * 		self.mapping = {}             # <<<<<<<<<<<<<<
 * 		self.frozen = False
 * 
 */
  __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 27, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_GIVEREF(__pyx_t_1);
  __Pyx_GOTREF(__pyx_v_self->mapping);
  __Pyx_DECREF(__pyx_v_self->mapping);
  __pyx_v_self->mapping = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":28
 * 	def __cinit__(self):
 * 		self.mapping = {}
 * 		self.frozen = False             # <<<<<<<<<<<<<<
 * 
 * 	def __getitem__(self, sample):
 */
  __pyx_v_self->frozen = 0;

  /* "whatshap/core.pyx":26
 * 	Mapping of sample names (strings) to numeric ids.
 * 	"""
 * 	def __cinit__(self):             # <<<<<<<<<<<<<<
 * 		self.mapping = {}
 * 		self.frozen = False
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":30
 * 		self.frozen = False
 * 
 * 	def __getitem__(self, sample):             # <<<<<<<<<<<<<<
 * 		if not self.frozen and sample not in self.mapping:
 * 			self.mapping[sample] = len(self.mapping)
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_3__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_sample); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_3__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_sample) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_2__getitem__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self), ((PyObject *)__pyx_v_sample));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_2__getitem__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, PyObject *__pyx_v_sample) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  Py_ssize_t __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getitem__", 0);

  /* "whatshap/core.pyx":31
 * 
 * 	def __getitem__(self, sample):
 * 		if not self.frozen and sample not in self.mapping:             # <<<<<<<<<<<<<<
 * 			self.mapping[sample] = len(self.mapping)
 * 		return self.mapping[sample]
 */
  __pyx_t_2 = ((!(__pyx_v_self->frozen != 0)) != 0);
  if (__pyx_t_2) {
  } else {
    __pyx_t_1 = __pyx_t_2;
    goto __pyx_L4_bool_binop_done;
  }
  if (unlikely(__pyx_v_self->mapping == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
    __PYX_ERR(1, 31, __pyx_L1_error)
  }
  __pyx_t_2 = (__Pyx_PyDict_ContainsTF(__pyx_v_sample, __pyx_v_self->mapping, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(1, 31, __pyx_L1_error)
  __pyx_t_3 = (__pyx_t_2 != 0);
  __pyx_t_1 = __pyx_t_3;
  __pyx_L4_bool_binop_done:;
  if (__pyx_t_1) {

    /* "whatshap/core.pyx":32
 * 	def __getitem__(self, sample):
 * 		if not self.frozen and sample not in self.mapping:
 * 			self.mapping[sample] = len(self.mapping)             # <<<<<<<<<<<<<<
 * 		return self.mapping[sample]
 * 
 */
    __pyx_t_4 = __pyx_v_self->mapping;
    __Pyx_INCREF(__pyx_t_4);
    if (unlikely(__pyx_t_4 == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
      __PYX_ERR(1, 32, __pyx_L1_error)
    }
    __pyx_t_5 = PyDict_Size(__pyx_t_4); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(1, 32, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 32, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    if (unlikely(__pyx_v_self->mapping == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
      __PYX_ERR(1, 32, __pyx_L1_error)
    }
    if (unlikely(PyDict_SetItem(__pyx_v_self->mapping, __pyx_v_sample, __pyx_t_4) < 0)) __PYX_ERR(1, 32, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

    /* "whatshap/core.pyx":31
 * 
 * 	def __getitem__(self, sample):
 * 		if not self.frozen and sample not in self.mapping:             # <<<<<<<<<<<<<<
 * 			self.mapping[sample] = len(self.mapping)
 * 		return self.mapping[sample]
 */
  }

  /* "whatshap/core.pyx":33
 * 		if not self.frozen and sample not in self.mapping:
 * 			self.mapping[sample] = len(self.mapping)
 * 		return self.mapping[sample]             # <<<<<<<<<<<<<<
 * 
 * 	def __len__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  if (unlikely(__pyx_v_self->mapping == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
    __PYX_ERR(1, 33, __pyx_L1_error)
  }
  __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_self->mapping, __pyx_v_sample); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 33, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_r = __pyx_t_4;
  __pyx_t_4 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":30
 * 		self.frozen = False
 * 
 * 	def __getitem__(self, sample):             # <<<<<<<<<<<<<<
 * 		if not self.frozen and sample not in self.mapping:
 * 			self.mapping[sample] = len(self.mapping)
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":35
 * 		return self.mapping[sample]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return len(self.mapping)
 * 
 */

/* Python wrapper */
static Py_ssize_t __pyx_pw_8whatshap_4core_16NumericSampleIds_5__len__(PyObject *__pyx_v_self); /*proto*/
static Py_ssize_t __pyx_pw_8whatshap_4core_16NumericSampleIds_5__len__(PyObject *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_4__len__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_ssize_t __pyx_pf_8whatshap_4core_16NumericSampleIds_4__len__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__len__", 0);

  /* "whatshap/core.pyx":36
 * 
 * 	def __len__(self):
 * 		return len(self.mapping)             # <<<<<<<<<<<<<<
 * 
 * 	def __str__(self):
 */
  __pyx_t_1 = __pyx_v_self->mapping;
  __Pyx_INCREF(__pyx_t_1);
  if (unlikely(__pyx_t_1 == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(1, 36, __pyx_L1_error)
  }
  __pyx_t_2 = PyDict_Size(__pyx_t_1); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(1, 36, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_r = __pyx_t_2;
  goto __pyx_L0;

  /* "whatshap/core.pyx":35
 * 		return self.mapping[sample]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return len(self.mapping)
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":38
 * 		return len(self.mapping)
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return str(self.mapping)
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_7__str__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_7__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_6__str__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_6__str__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "whatshap/core.pyx":39
 * 
 * 	def __str__(self):
 * 		return str(self.mapping)             # <<<<<<<<<<<<<<
 * 
 * 	def freeze(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyUnicode_Type)), __pyx_v_self->mapping); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 39, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":38
 * 		return len(self.mapping)
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return str(self.mapping)
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":41
 * 		return str(self.mapping)
 * 
 * 	def freeze(self):             # <<<<<<<<<<<<<<
 * 		"""No longer allow modifications"""
 * 		# TODO We should try to have a second class (FrozenNumericSampleIds) for
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_9freeze(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_16NumericSampleIds_8freeze[] = "No longer allow modifications";
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_9freeze(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("freeze (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_8freeze(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_8freeze(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("freeze", 0);

  /* "whatshap/core.pyx":45
 * 		# TODO We should try to have a second class (FrozenNumericSampleIds) for
 * 		# this or try to get rid of NumericSampleIds
 * 		self.frozen = True             # <<<<<<<<<<<<<<
 * 
 * 	def inverse_mapping(self):
 */
  __pyx_v_self->frozen = 1;

  /* "whatshap/core.pyx":41
 * 		return str(self.mapping)
 * 
 * 	def freeze(self):             # <<<<<<<<<<<<<<
 * 		"""No longer allow modifications"""
 * 		# TODO We should try to have a second class (FrozenNumericSampleIds) for
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":47
 * 		self.frozen = True
 * 
 * 	def inverse_mapping(self):             # <<<<<<<<<<<<<<
 * 		"""Returns a dict mapping numeric ids to sample names."""
 * 		return {numeric_id:name for name, numeric_id in self.mapping.items()}
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_11inverse_mapping(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_16NumericSampleIds_10inverse_mapping[] = "Returns a dict mapping numeric ids to sample names.";
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_11inverse_mapping(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("inverse_mapping (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_10inverse_mapping(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_10inverse_mapping(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  PyObject *__pyx_7genexpr__pyx_v_name = NULL;
  PyObject *__pyx_7genexpr__pyx_v_numeric_id = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  Py_ssize_t __pyx_t_4;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  int __pyx_t_8;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("inverse_mapping", 0);

  /* "whatshap/core.pyx":49
 * 	def inverse_mapping(self):
 * 		"""Returns a dict mapping numeric ids to sample names."""
 * 		return {numeric_id:name for name, numeric_id in self.mapping.items()}             # <<<<<<<<<<<<<<
 * 
 * 	def __getstate__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  { /* enter inner scope */
    __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 49, __pyx_L5_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = 0;
    if (unlikely(__pyx_v_self->mapping == Py_None)) {
      PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "items");
      __PYX_ERR(1, 49, __pyx_L5_error)
    }
    __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_self->mapping, 1, __pyx_n_s_items, (&__pyx_t_4), (&__pyx_t_5)); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 49, __pyx_L5_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_XDECREF(__pyx_t_2);
    __pyx_t_2 = __pyx_t_6;
    __pyx_t_6 = 0;
    while (1) {
      __pyx_t_8 = __Pyx_dict_iter_next(__pyx_t_2, __pyx_t_4, &__pyx_t_3, &__pyx_t_6, &__pyx_t_7, NULL, __pyx_t_5);
      if (unlikely(__pyx_t_8 == 0)) break;
      if (unlikely(__pyx_t_8 == -1)) __PYX_ERR(1, 49, __pyx_L5_error)
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_XDECREF_SET(__pyx_7genexpr__pyx_v_name, __pyx_t_6);
      __pyx_t_6 = 0;
      __Pyx_XDECREF_SET(__pyx_7genexpr__pyx_v_numeric_id, __pyx_t_7);
      __pyx_t_7 = 0;
      if (unlikely(PyDict_SetItem(__pyx_t_1, (PyObject*)__pyx_7genexpr__pyx_v_numeric_id, (PyObject*)__pyx_7genexpr__pyx_v_name))) __PYX_ERR(1, 49, __pyx_L5_error)
    }
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __Pyx_XDECREF(__pyx_7genexpr__pyx_v_name); __pyx_7genexpr__pyx_v_name = 0;
    __Pyx_XDECREF(__pyx_7genexpr__pyx_v_numeric_id); __pyx_7genexpr__pyx_v_numeric_id = 0;
    goto __pyx_L8_exit_scope;
    __pyx_L5_error:;
    __Pyx_XDECREF(__pyx_7genexpr__pyx_v_name); __pyx_7genexpr__pyx_v_name = 0;
    __Pyx_XDECREF(__pyx_7genexpr__pyx_v_numeric_id); __pyx_7genexpr__pyx_v_numeric_id = 0;
    goto __pyx_L1_error;
    __pyx_L8_exit_scope:;
  } /* exit inner scope */
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":47
 * 		self.frozen = True
 * 
 * 	def inverse_mapping(self):             # <<<<<<<<<<<<<<
 * 		"""Returns a dict mapping numeric ids to sample names."""
 * 		return {numeric_id:name for name, numeric_id in self.mapping.items()}
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.inverse_mapping", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_7genexpr__pyx_v_name);
  __Pyx_XDECREF(__pyx_7genexpr__pyx_v_numeric_id);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":51
 * 		return {numeric_id:name for name, numeric_id in self.mapping.items()}
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return (self.mapping, self.frozen)
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_13__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_13__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_12__getstate__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_12__getstate__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getstate__", 0);

  /* "whatshap/core.pyx":52
 * 
 * 	def __getstate__(self):
 * 		return (self.mapping, self.frozen)             # <<<<<<<<<<<<<<
 * 
 * 	def __setstate__(self, state):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->frozen); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 52, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 52, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_INCREF(__pyx_v_self->mapping);
  __Pyx_GIVEREF(__pyx_v_self->mapping);
  PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self->mapping);
  __Pyx_GIVEREF(__pyx_t_1);
  PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
  __pyx_t_1 = 0;
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":51
 * 		return {numeric_id:name for name, numeric_id in self.mapping.items()}
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return (self.mapping, self.frozen)
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__getstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":54
 * 		return (self.mapping, self.frozen)
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		mapping, frozen = state
 * 		self.mapping = mapping
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_15__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_15__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_14__setstate__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self), ((PyObject *)__pyx_v_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_14__setstate__(struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_v_mapping = NULL;
  PyObject *__pyx_v_frozen = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *(*__pyx_t_4)(PyObject *);
  bool __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate__", 0);

  /* "whatshap/core.pyx":55
 * 
 * 	def __setstate__(self, state):
 * 		mapping, frozen = state             # <<<<<<<<<<<<<<
 * 		self.mapping = mapping
 * 		self.frozen = frozen
 */
  if ((likely(PyTuple_CheckExact(__pyx_v_state))) || (PyList_CheckExact(__pyx_v_state))) {
    PyObject* sequence = __pyx_v_state;
    Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
    if (unlikely(size != 2)) {
      if (size > 2) __Pyx_RaiseTooManyValuesError(2);
      else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
      __PYX_ERR(1, 55, __pyx_L1_error)
    }
    #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    if (likely(PyTuple_CheckExact(sequence))) {
      __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
    } else {
      __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
    }
    __Pyx_INCREF(__pyx_t_1);
    __Pyx_INCREF(__pyx_t_2);
    #else
    __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 55, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 55, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    #endif
  } else {
    Py_ssize_t index = -1;
    __pyx_t_3 = PyObject_GetIter(__pyx_v_state); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 55, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
    index = 0; __pyx_t_1 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_1)) goto __pyx_L3_unpacking_failed;
    __Pyx_GOTREF(__pyx_t_1);
    index = 1; __pyx_t_2 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_2)) goto __pyx_L3_unpacking_failed;
    __Pyx_GOTREF(__pyx_t_2);
    if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) __PYX_ERR(1, 55, __pyx_L1_error)
    __pyx_t_4 = NULL;
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    goto __pyx_L4_unpacking_done;
    __pyx_L3_unpacking_failed:;
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
    if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
    __PYX_ERR(1, 55, __pyx_L1_error)
    __pyx_L4_unpacking_done:;
  }
  __pyx_v_mapping = __pyx_t_1;
  __pyx_t_1 = 0;
  __pyx_v_frozen = __pyx_t_2;
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":56
 * 	def __setstate__(self, state):
 * 		mapping, frozen = state
 * 		self.mapping = mapping             # <<<<<<<<<<<<<<
 * 		self.frozen = frozen
 * 
 */
  if (!(likely(PyDict_CheckExact(__pyx_v_mapping))||((__pyx_v_mapping) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "dict", Py_TYPE(__pyx_v_mapping)->tp_name), 0))) __PYX_ERR(1, 56, __pyx_L1_error)
  __pyx_t_2 = __pyx_v_mapping;
  __Pyx_INCREF(__pyx_t_2);
  __Pyx_GIVEREF(__pyx_t_2);
  __Pyx_GOTREF(__pyx_v_self->mapping);
  __Pyx_DECREF(__pyx_v_self->mapping);
  __pyx_v_self->mapping = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":57
 * 		mapping, frozen = state
 * 		self.mapping = mapping
 * 		self.frozen = frozen             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_frozen); if (unlikely((__pyx_t_5 == ((bool)-1)) && PyErr_Occurred())) __PYX_ERR(1, 57, __pyx_L1_error)
  __pyx_v_self->frozen = __pyx_t_5;

  /* "whatshap/core.pyx":54
 * 		return (self.mapping, self.frozen)
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		mapping, frozen = state
 * 		self.mapping = mapping
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__setstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_mapping);
  __Pyx_XDECREF(__pyx_v_frozen);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_17__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_17__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_16__reduce_cython__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_16__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_19__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_16NumericSampleIds_19__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_16NumericSampleIds_18__setstate_cython__(((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_16NumericSampleIds_18__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_NumericSampleIds *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.NumericSampleIds.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":61
 * 
 * cdef class Read:
 * 	def __cinit__(self, str name = None, int mapq = 0, int source_id = 0, int sample_id = 0, int reference_start = -1, str BX_tag = None):             # <<<<<<<<<<<<<<
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_4Read_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_4Read_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_name = 0;
  int __pyx_v_mapq;
  int __pyx_v_source_id;
  int __pyx_v_sample_id;
  int __pyx_v_reference_start;
  PyObject *__pyx_v_BX_tag = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_name,&__pyx_n_s_mapq,&__pyx_n_s_source_id,&__pyx_n_s_sample_id,&__pyx_n_s_reference_start,&__pyx_n_s_BX_tag,0};
    PyObject* values[6] = {0,0,0,0,0,0};
    values[0] = ((PyObject*)Py_None);
    values[5] = ((PyObject*)Py_None);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
        CYTHON_FALLTHROUGH;
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        CYTHON_FALLTHROUGH;
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_name);
          if (value) { values[0] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  1:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_mapq);
          if (value) { values[1] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_source_id);
          if (value) { values[2] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  3:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sample_id);
          if (value) { values[3] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  4:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_reference_start);
          if (value) { values[4] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  5:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_BX_tag);
          if (value) { values[5] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 61, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
        CYTHON_FALLTHROUGH;
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        CYTHON_FALLTHROUGH;
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_name = ((PyObject*)values[0]);
    if (values[1]) {
      __pyx_v_mapq = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_mapq == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 61, __pyx_L3_error)
    } else {
      __pyx_v_mapq = ((int)0);
    }
    if (values[2]) {
      __pyx_v_source_id = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_source_id == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 61, __pyx_L3_error)
    } else {
      __pyx_v_source_id = ((int)0);
    }
    if (values[3]) {
      __pyx_v_sample_id = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_sample_id == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 61, __pyx_L3_error)
    } else {
      __pyx_v_sample_id = ((int)0);
    }
    if (values[4]) {
      __pyx_v_reference_start = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_reference_start == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 61, __pyx_L3_error)
    } else {
      __pyx_v_reference_start = ((int)-1);
    }
    __pyx_v_BX_tag = ((PyObject*)values[5]);
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 61, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Read.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_name), (&PyUnicode_Type), 1, "name", 1))) __PYX_ERR(1, 61, __pyx_L1_error)
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_BX_tag), (&PyUnicode_Type), 1, "BX_tag", 1))) __PYX_ERR(1, 61, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_4Read___cinit__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), __pyx_v_name, __pyx_v_mapq, __pyx_v_source_id, __pyx_v_sample_id, __pyx_v_reference_start, __pyx_v_BX_tag);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_4Read___cinit__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_name, int __pyx_v_mapq, int __pyx_v_source_id, int __pyx_v_sample_id, int __pyx_v_reference_start, PyObject *__pyx_v_BX_tag) {
  std::string __pyx_v__name;
  std::string __pyx_v__BX_tag;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  Read *__pyx_t_6;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":62
 * cdef class Read:
 * 	def __cinit__(self, str name = None, int mapq = 0, int source_id = 0, int sample_id = 0, int reference_start = -1, str BX_tag = None):
 * 		cdef string _name = b''             # <<<<<<<<<<<<<<
 * 		cdef string _BX_tag = b''
 * 		if name is None:
 */
  __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_kp_b__3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 62, __pyx_L1_error)
  __pyx_v__name = __pyx_t_1;

  /* "whatshap/core.pyx":63
 * 	def __cinit__(self, str name = None, int mapq = 0, int source_id = 0, int sample_id = 0, int reference_start = -1, str BX_tag = None):
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''             # <<<<<<<<<<<<<<
 * 		if name is None:
 * 			self.thisptr = NULL
 */
  __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_kp_b__3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 63, __pyx_L1_error)
  __pyx_v__BX_tag = __pyx_t_1;

  /* "whatshap/core.pyx":64
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 * 		if name is None:             # <<<<<<<<<<<<<<
 * 			self.thisptr = NULL
 * 			self.ownsptr = False
 */
  __pyx_t_2 = (__pyx_v_name == ((PyObject*)Py_None));
  __pyx_t_3 = (__pyx_t_2 != 0);
  if (__pyx_t_3) {

    /* "whatshap/core.pyx":65
 * 		cdef string _BX_tag = b''
 * 		if name is None:
 * 			self.thisptr = NULL             # <<<<<<<<<<<<<<
 * 			self.ownsptr = False
 * 		else:
 */
    __pyx_v_self->thisptr = NULL;

    /* "whatshap/core.pyx":66
 * 		if name is None:
 * 			self.thisptr = NULL
 * 			self.ownsptr = False             # <<<<<<<<<<<<<<
 * 		else:
 * 			# TODO: Is this the best way to handle string arguments?
 */
    __pyx_v_self->ownsptr = 0;

    /* "whatshap/core.pyx":64
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 * 		if name is None:             # <<<<<<<<<<<<<<
 * 			self.thisptr = NULL
 * 			self.ownsptr = False
 */
    goto __pyx_L3;
  }

  /* "whatshap/core.pyx":69
 * 		else:
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')             # <<<<<<<<<<<<<<
 * 			if BX_tag is not '' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')
 */
  /*else*/ {
    if (unlikely(__pyx_v_name == Py_None)) {
      PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "encode");
      __PYX_ERR(1, 69, __pyx_L1_error)
    }
    __pyx_t_4 = PyUnicode_AsUTF8String(__pyx_v_name); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 69, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_t_4); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 69, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_v__name = __pyx_t_1;

    /* "whatshap/core.pyx":70
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not '' and BX_tag is not None:             # <<<<<<<<<<<<<<
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapq, source_id, sample_id, reference_start, _BX_tag)
 */
    __pyx_t_2 = (__pyx_v_BX_tag != __pyx_kp_u__3);
    __pyx_t_5 = (__pyx_t_2 != 0);
    if (__pyx_t_5) {
    } else {
      __pyx_t_3 = __pyx_t_5;
      goto __pyx_L5_bool_binop_done;
    }
    __pyx_t_5 = (__pyx_v_BX_tag != ((PyObject*)Py_None));
    __pyx_t_2 = (__pyx_t_5 != 0);
    __pyx_t_3 = __pyx_t_2;
    __pyx_L5_bool_binop_done:;
    if (__pyx_t_3) {

      /* "whatshap/core.pyx":71
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not '' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')             # <<<<<<<<<<<<<<
 * 			self.thisptr = new cpp.Read(_name, mapq, source_id, sample_id, reference_start, _BX_tag)
 * 			self.ownsptr = True
 */
      if (unlikely(__pyx_v_BX_tag == Py_None)) {
        PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "encode");
        __PYX_ERR(1, 71, __pyx_L1_error)
      }
      __pyx_t_4 = PyUnicode_AsUTF8String(__pyx_v_BX_tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 71, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_t_4); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 71, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      __pyx_v__BX_tag = __pyx_t_1;

      /* "whatshap/core.pyx":70
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not '' and BX_tag is not None:             # <<<<<<<<<<<<<<
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapq, source_id, sample_id, reference_start, _BX_tag)
 */
    }

    /* "whatshap/core.pyx":72
 * 			if BX_tag is not '' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapq, source_id, sample_id, reference_start, _BX_tag)             # <<<<<<<<<<<<<<
 * 			self.ownsptr = True
 * 
 */
    try {
      __pyx_t_6 = new Read(__pyx_v__name, __pyx_v_mapq, __pyx_v_source_id, __pyx_v_sample_id, __pyx_v_reference_start, __pyx_v__BX_tag);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 72, __pyx_L1_error)
    }
    __pyx_v_self->thisptr = __pyx_t_6;

    /* "whatshap/core.pyx":73
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapq, source_id, sample_id, reference_start, _BX_tag)
 * 			self.ownsptr = True             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
    __pyx_v_self->ownsptr = 1;
  }
  __pyx_L3:;

  /* "whatshap/core.pyx":61
 * 
 * cdef class Read:
 * 	def __cinit__(self, str name = None, int mapq = 0, int source_id = 0, int sample_id = 0, int reference_start = -1, str BX_tag = None):             # <<<<<<<<<<<<<<
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.Read.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":75
 * 			self.ownsptr = True
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		if self.ownsptr:
 * 			assert self.thisptr != NULL
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_4Read_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_4Read_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_4Read_2__dealloc__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_4Read_2__dealloc__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":76
 * 
 * 	def __dealloc__(self):
 * 		if self.ownsptr:             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			del self.thisptr
 */
  __pyx_t_1 = (__pyx_v_self->ownsptr != 0);
  if (__pyx_t_1) {

    /* "whatshap/core.pyx":77
 * 	def __dealloc__(self):
 * 		if self.ownsptr:
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			del self.thisptr
 * 
 */
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!Py_OptimizeFlag)) {
      if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
        PyErr_SetNone(PyExc_AssertionError);
        __PYX_ERR(1, 77, __pyx_L1_error)
      }
    }
    #endif

    /* "whatshap/core.pyx":78
 * 		if self.ownsptr:
 * 			assert self.thisptr != NULL
 * 			del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def __repr__(self):
 */
    delete __pyx_v_self->thisptr;

    /* "whatshap/core.pyx":76
 * 
 * 	def __dealloc__(self):
 * 		if self.ownsptr:             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			del self.thisptr
 */
  }

  /* "whatshap/core.pyx":75
 * 			self.ownsptr = True
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		if self.ownsptr:
 * 			assert self.thisptr != NULL
 */

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("whatshap.core.Read.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":80
 * 			del self.thisptr
 * 
 * 	def __repr__(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return 'Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})'.format(
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_5__repr__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_5__repr__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__repr__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_4__repr__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_4__repr__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  PyObject *__pyx_t_10 = NULL;
  int __pyx_t_11;
  PyObject *__pyx_t_12 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__repr__", 0);

  /* "whatshap/core.pyx":81
 * 
 * 	def __repr__(self):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		return 'Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})'.format(
 * 			self.name, self.mapqs, self.source_id, self.sample_id, self.reference_start, self.BX_tag, list(self))
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 81, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":82
 * 	def __repr__(self):
 * 		assert self.thisptr != NULL
 * 		return 'Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})'.format(             # <<<<<<<<<<<<<<
 * 			self.name, self.mapqs, self.source_id, self.sample_id, self.reference_start, self.BX_tag, list(self))
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Read_name_r_mapq_source_id_sampl, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 82, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);

  /* "whatshap/core.pyx":83
 * 		assert self.thisptr != NULL
 * 		return 'Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})'.format(
 * 			self.name, self.mapqs, self.source_id, self.sample_id, self.reference_start, self.BX_tag, list(self))             # <<<<<<<<<<<<<<
 * 
 * 	property mapqs:
 */
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_name); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_mapqs); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_source_id); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_sample_id); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reference_start); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_BX_tag); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_8);
  __pyx_t_9 = PySequence_List(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 83, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_9);
  __pyx_t_10 = NULL;
  __pyx_t_11 = 0;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_10)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_10);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
      __pyx_t_11 = 1;
    }
  }
  #if CYTHON_FAST_PYCALL
  if (PyFunction_Check(__pyx_t_2)) {
    PyObject *__pyx_temp[8] = {__pyx_t_10, __pyx_t_3, __pyx_t_4, __pyx_t_5, __pyx_t_6, __pyx_t_7, __pyx_t_8, __pyx_t_9};
    __pyx_t_1 = __Pyx_PyFunction_FastCall(__pyx_t_2, __pyx_temp+1-__pyx_t_11, 7+__pyx_t_11); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 82, __pyx_L1_error)
    __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
  } else
  #endif
  #if CYTHON_FAST_PYCCALL
  if (__Pyx_PyFastCFunction_Check(__pyx_t_2)) {
    PyObject *__pyx_temp[8] = {__pyx_t_10, __pyx_t_3, __pyx_t_4, __pyx_t_5, __pyx_t_6, __pyx_t_7, __pyx_t_8, __pyx_t_9};
    __pyx_t_1 = __Pyx_PyCFunction_FastCall(__pyx_t_2, __pyx_temp+1-__pyx_t_11, 7+__pyx_t_11); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 82, __pyx_L1_error)
    __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
  } else
  #endif
  {
    __pyx_t_12 = PyTuple_New(7+__pyx_t_11); if (unlikely(!__pyx_t_12)) __PYX_ERR(1, 82, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_12);
    if (__pyx_t_10) {
      __Pyx_GIVEREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_10); __pyx_t_10 = NULL;
    }
    __Pyx_GIVEREF(__pyx_t_3);
    PyTuple_SET_ITEM(__pyx_t_12, 0+__pyx_t_11, __pyx_t_3);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_12, 1+__pyx_t_11, __pyx_t_4);
    __Pyx_GIVEREF(__pyx_t_5);
    PyTuple_SET_ITEM(__pyx_t_12, 2+__pyx_t_11, __pyx_t_5);
    __Pyx_GIVEREF(__pyx_t_6);
    PyTuple_SET_ITEM(__pyx_t_12, 3+__pyx_t_11, __pyx_t_6);
    __Pyx_GIVEREF(__pyx_t_7);
    PyTuple_SET_ITEM(__pyx_t_12, 4+__pyx_t_11, __pyx_t_7);
    __Pyx_GIVEREF(__pyx_t_8);
    PyTuple_SET_ITEM(__pyx_t_12, 5+__pyx_t_11, __pyx_t_8);
    __Pyx_GIVEREF(__pyx_t_9);
    PyTuple_SET_ITEM(__pyx_t_12, 6+__pyx_t_11, __pyx_t_9);
    __pyx_t_3 = 0;
    __pyx_t_4 = 0;
    __pyx_t_5 = 0;
    __pyx_t_6 = 0;
    __pyx_t_7 = 0;
    __pyx_t_8 = 0;
    __pyx_t_9 = 0;
    __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_12, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 82, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":80
 * 			del self.thisptr
 * 
 * 	def __repr__(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return 'Read(name={!r}, mapq={}, source_id={}, sample_id={}, reference_start={},  BX_tag={}, variants={})'.format(
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_XDECREF(__pyx_t_12);
  __Pyx_AddTraceback("whatshap.core.Read.__repr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":86
 * 
 * 	property mapqs:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return tuple(self.thisptr.getMapqs())
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_5mapqs_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_5mapqs_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_5mapqs___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_5mapqs___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::vector<int>  __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":87
 * 	property mapqs:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return tuple(self.thisptr.getMapqs())
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 87, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":88
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return tuple(self.thisptr.getMapqs())             # <<<<<<<<<<<<<<
 * 
 * 	property name:
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getMapqs();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 88, __pyx_L1_error)
  }
  __pyx_t_2 = __pyx_convert_vector_to_py_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 88, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = __Pyx_PySequence_Tuple(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 88, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_r = __pyx_t_3;
  __pyx_t_3 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":86
 * 
 * 	property mapqs:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return tuple(self.thisptr.getMapqs())
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("whatshap.core.Read.mapqs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":91
 * 
 * 	property name:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getName().decode('utf-8')
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_4name_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_4name_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_4name___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_4name___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":92
 * 	property name:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return self.thisptr.getName().decode('utf-8')
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 92, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":93
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getName().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	property source_id:
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getName();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 93, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 93, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":91
 * 
 * 	property name:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getName().decode('utf-8')
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.name.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":96
 * 
 * 	property source_id:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSourceID()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_9source_id_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_9source_id_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_9source_id___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_9source_id___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":97
 * 	property source_id:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return self.thisptr.getSourceID()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 97, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":98
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSourceID()             # <<<<<<<<<<<<<<
 * 
 * 	property sample_id:
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getSourceID();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 98, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 98, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":96
 * 
 * 	property source_id:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSourceID()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.source_id.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":101
 * 
 * 	property sample_id:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSampleID()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_9sample_id_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_9sample_id_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_9sample_id___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_9sample_id___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":102
 * 	property sample_id:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return self.thisptr.getSampleID()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 102, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":103
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSampleID()             # <<<<<<<<<<<<<<
 * 
 * 	property reference_start:
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getSampleID();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 103, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 103, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":101
 * 
 * 	property sample_id:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getSampleID()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.sample_id.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":106
 * 
 * 	property reference_start:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getReferenceStart()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_15reference_start_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_15reference_start_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_15reference_start___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_15reference_start___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":107
 * 	property reference_start:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return self.thisptr.getReferenceStart()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 107, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":108
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getReferenceStart()             # <<<<<<<<<<<<<<
 * 
 * 	property BX_tag:
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getReferenceStart();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 108, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 108, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":106
 * 
 * 	property reference_start:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getReferenceStart()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.reference_start.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":111
 * 
 * 	property BX_tag:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getBXTag().decode('utf-8')
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_6BX_tag_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_6BX_tag_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_6BX_tag___get__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_6BX_tag___get__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":112
 * 	property BX_tag:
 * 		def __get__(self):
 * 			assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 			return self.thisptr.getBXTag().decode('utf-8')
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 112, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":113
 * 		def __get__(self):
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getBXTag().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	def __iter__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getBXTag();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 113, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 113, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":111
 * 
 * 	property BX_tag:
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			assert self.thisptr != NULL
 * 			return self.thisptr.getBXTag().decode('utf-8')
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.BX_tag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}
static PyObject *__pyx_gb_8whatshap_4core_4Read_8generator(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value); /* proto */

/* "whatshap/core.pyx":115
 * 			return self.thisptr.getBXTag().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		"""Iterate over all variants in this read"""
 * 		assert self.thisptr != NULL
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_7__iter__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_8whatshap_4core_4Read_6__iter__[] = "Iterate over all variants in this read";
#if CYTHON_UPDATE_DESCRIPTOR_DOC
struct wrapperbase __pyx_wrapperbase_8whatshap_4core_4Read_6__iter__;
#endif
static PyObject *__pyx_pw_8whatshap_4core_4Read_7__iter__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_6__iter__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_6__iter__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *__pyx_cur_scope;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__iter__", 0);
  __pyx_cur_scope = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)__pyx_tp_new_8whatshap_4core___pyx_scope_struct____iter__(__pyx_ptype_8whatshap_4core___pyx_scope_struct____iter__, __pyx_empty_tuple, NULL);
  if (unlikely(!__pyx_cur_scope)) {
    __pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)Py_None);
    __Pyx_INCREF(Py_None);
    __PYX_ERR(1, 115, __pyx_L1_error)
  } else {
    __Pyx_GOTREF(__pyx_cur_scope);
  }
  __pyx_cur_scope->__pyx_v_self = __pyx_v_self;
  __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  {
    __pyx_CoroutineObject *gen = __Pyx_Generator_New((__pyx_coroutine_body_t) __pyx_gb_8whatshap_4core_4Read_8generator, NULL, (PyObject *) __pyx_cur_scope, __pyx_n_s_iter, __pyx_n_s_Read___iter, __pyx_n_s_whatshap_core); if (unlikely(!gen)) __PYX_ERR(1, 115, __pyx_L1_error)
    __Pyx_DECREF(__pyx_cur_scope);
    __Pyx_RefNannyFinishContext();
    return (PyObject *) gen;
  }

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Read.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_DECREF(((PyObject *)__pyx_cur_scope));
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_gb_8whatshap_4core_4Read_8generator(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value) /* generator body */
{
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *__pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)__pyx_generator->closure);
  PyObject *__pyx_r = NULL;
  Py_ssize_t __pyx_t_1;
  Py_ssize_t __pyx_t_2;
  Py_ssize_t __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__", 0);
  switch (__pyx_generator->resume_label) {
    case 0: goto __pyx_L3_first_run;
    case 1: goto __pyx_L6_resume_from_yield;
    default: /* CPython raises the right error here */
    __Pyx_RefNannyFinishContext();
    return NULL;
  }
  __pyx_L3_first_run:;
  if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 115, __pyx_L1_error)

  /* "whatshap/core.pyx":117
 * 	def __iter__(self):
 * 		"""Iterate over all variants in this read"""
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		for i in range(len(self)):
 * 			yield self[i]
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_cur_scope->__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 117, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":118
 * 		"""Iterate over all variants in this read"""
 * 		assert self.thisptr != NULL
 * 		for i in range(len(self)):             # <<<<<<<<<<<<<<
 * 			yield self[i]
 * 
 */
  __pyx_t_1 = PyObject_Length(((PyObject *)__pyx_cur_scope->__pyx_v_self)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1))) __PYX_ERR(1, 118, __pyx_L1_error)
  __pyx_t_2 = __pyx_t_1;
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_cur_scope->__pyx_v_i = __pyx_t_3;

    /* "whatshap/core.pyx":119
 * 		assert self.thisptr != NULL
 * 		for i in range(len(self)):
 * 			yield self[i]             # <<<<<<<<<<<<<<
 * 
 * 	def __len__(self):
 */
    __pyx_t_4 = __Pyx_GetItemInt(((PyObject *)__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_i, Py_ssize_t, 1, PyInt_FromSsize_t, 0, 1, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 119, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_r = __pyx_t_4;
    __pyx_t_4 = 0;
    __pyx_cur_scope->__pyx_t_0 = __pyx_t_1;
    __pyx_cur_scope->__pyx_t_1 = __pyx_t_2;
    __pyx_cur_scope->__pyx_t_2 = __pyx_t_3;
    __Pyx_XGIVEREF(__pyx_r);
    __Pyx_RefNannyFinishContext();
    __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
    /* return from generator, yielding value */
    __pyx_generator->resume_label = 1;
    return __pyx_r;
    __pyx_L6_resume_from_yield:;
    __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
    __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
    __pyx_t_3 = __pyx_cur_scope->__pyx_t_2;
    if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 119, __pyx_L1_error)
  }
  CYTHON_MAYBE_UNUSED_VAR(__pyx_cur_scope);

  /* "whatshap/core.pyx":115
 * 			return self.thisptr.getBXTag().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		"""Iterate over all variants in this read"""
 * 		assert self.thisptr != NULL
 */

  /* function exit code */
  PyErr_SetNone(PyExc_StopIteration);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_r); __pyx_r = 0;
  #if !CYTHON_USE_EXC_INFO_STACK
  __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
  #endif
  __pyx_generator->resume_label = -1;
  __Pyx_Coroutine_clear((PyObject*)__pyx_generator);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":121
 * 			yield self[i]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		"""Return number of variants in this read"""
 * 		assert self.thisptr != NULL
 */

/* Python wrapper */
static Py_ssize_t __pyx_pw_8whatshap_4core_4Read_10__len__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_8whatshap_4core_4Read_9__len__[] = "Return number of variants in this read";
#if CYTHON_UPDATE_DESCRIPTOR_DOC
struct wrapperbase __pyx_wrapperbase_8whatshap_4core_4Read_9__len__;
#endif
static Py_ssize_t __pyx_pw_8whatshap_4core_4Read_10__len__(PyObject *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_9__len__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_ssize_t __pyx_pf_8whatshap_4core_4Read_9__len__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__len__", 0);

  /* "whatshap/core.pyx":123
 * 	def __len__(self):
 * 		"""Return number of variants in this read"""
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		return self.thisptr.getVariantCount()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 123, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":124
 * 		"""Return number of variants in this read"""
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.getVariantCount()             # <<<<<<<<<<<<<<
 * 
 * 	def __getitem__(self, key):
 */
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getVariantCount();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 124, __pyx_L1_error)
  }
  __pyx_r = __pyx_t_1;
  goto __pyx_L0;

  /* "whatshap/core.pyx":121
 * 			yield self[i]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		"""Return number of variants in this read"""
 * 		assert self.thisptr != NULL
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Read.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":126
 * 		return self.thisptr.getVariantCount()
 * 
 * 	def __getitem__(self, key):             # <<<<<<<<<<<<<<
 * 		"""Return Variant object at the given integer index"""
 * 		assert self.thisptr != NULL
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_12__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
static char __pyx_doc_8whatshap_4core_4Read_11__getitem__[] = "Return Variant object at the given integer index";
#if CYTHON_UPDATE_DESCRIPTOR_DOC
struct wrapperbase __pyx_wrapperbase_8whatshap_4core_4Read_11__getitem__;
#endif
static PyObject *__pyx_pw_8whatshap_4core_4Read_12__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_11__getitem__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((PyObject *)__pyx_v_key));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_11__getitem__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_key) {
  int __pyx_v_n;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getitem__", 0);
  __Pyx_INCREF(__pyx_v_key);

  /* "whatshap/core.pyx":128
 * 	def __getitem__(self, key):
 * 		"""Return Variant object at the given integer index"""
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError("Read does not support slices")
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 128, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":129
 * 		"""Return Variant object at the given integer index"""
 * 		assert self.thisptr != NULL
 * 		if isinstance(key, slice):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError("Read does not support slices")
 * 		assert isinstance(key, int)
 */
  __pyx_t_1 = PySlice_Check(__pyx_v_key); 
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (unlikely(__pyx_t_2)) {

    /* "whatshap/core.pyx":130
 * 		assert self.thisptr != NULL
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError("Read does not support slices")             # <<<<<<<<<<<<<<
 * 		assert isinstance(key, int)
 * 		cdef int n = self.thisptr.getVariantCount()
 */
    __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 130, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_Raise(__pyx_t_3, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __PYX_ERR(1, 130, __pyx_L1_error)

    /* "whatshap/core.pyx":129
 * 		"""Return Variant object at the given integer index"""
 * 		assert self.thisptr != NULL
 * 		if isinstance(key, slice):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError("Read does not support slices")
 * 		assert isinstance(key, int)
 */
  }

  /* "whatshap/core.pyx":131
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError("Read does not support slices")
 * 		assert isinstance(key, int)             # <<<<<<<<<<<<<<
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= key < n):
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    __pyx_t_2 = PyInt_Check(__pyx_v_key); 
    if (unlikely(!(__pyx_t_2 != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 131, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":132
 * 			raise NotImplementedError("Read does not support slices")
 * 		assert isinstance(key, int)
 * 		cdef int n = self.thisptr.getVariantCount()             # <<<<<<<<<<<<<<
 * 		if not (-n <= key < n):
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 */
  try {
    __pyx_t_4 = __pyx_v_self->thisptr->getVariantCount();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 132, __pyx_L1_error)
  }
  __pyx_v_n = __pyx_t_4;

  /* "whatshap/core.pyx":133
 * 		assert isinstance(key, int)
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= key < n):             # <<<<<<<<<<<<<<
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 * 		if key < 0:
 */
  __pyx_t_3 = __Pyx_PyInt_From_int((-__pyx_v_n)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 133, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_v_key, Py_LE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 133, __pyx_L1_error)
  if (__Pyx_PyObject_IsTrue(__pyx_t_5)) {
    __Pyx_DECREF(__pyx_t_5);
    __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 133, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_5 = PyObject_RichCompare(__pyx_v_key, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 133, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  }
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(1, 133, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_t_1 = ((!__pyx_t_2) != 0);
  if (unlikely(__pyx_t_1)) {

    /* "whatshap/core.pyx":134
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= key < n):
 * 			raise IndexError('Index out of bounds: {}'.format(key))             # <<<<<<<<<<<<<<
 * 		if key < 0:
 * 			key = n + key
 */
    __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Index_out_of_bounds, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 134, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_6 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) {
      __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
      if (likely(__pyx_t_6)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
        __Pyx_INCREF(__pyx_t_6);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_3, function);
      }
    }
    __pyx_t_5 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_6, __pyx_v_key) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_key);
    __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
    if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 134, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_5); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 134, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_Raise(__pyx_t_3, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __PYX_ERR(1, 134, __pyx_L1_error)

    /* "whatshap/core.pyx":133
 * 		assert isinstance(key, int)
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= key < n):             # <<<<<<<<<<<<<<
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 * 		if key < 0:
 */
  }

  /* "whatshap/core.pyx":135
 * 		if not (-n <= key < n):
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 * 		if key < 0:             # <<<<<<<<<<<<<<
 * 			key = n + key
 * 		return Variant(
 */
  __pyx_t_3 = PyObject_RichCompare(__pyx_v_key, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 135, __pyx_L1_error)
  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(1, 135, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (__pyx_t_1) {

    /* "whatshap/core.pyx":136
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 * 		if key < 0:
 * 			key = n + key             # <<<<<<<<<<<<<<
 * 		return Variant(
 * 			position=self.thisptr.getPosition(key),
 */
    __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 136, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_v_key); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 136, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF_SET(__pyx_v_key, __pyx_t_5);
    __pyx_t_5 = 0;

    /* "whatshap/core.pyx":135
 * 		if not (-n <= key < n):
 * 			raise IndexError('Index out of bounds: {}'.format(key))
 * 		if key < 0:             # <<<<<<<<<<<<<<
 * 			key = n + key
 * 		return Variant(
 */
  }

  /* "whatshap/core.pyx":137
 * 		if key < 0:
 * 			key = n + key
 * 		return Variant(             # <<<<<<<<<<<<<<
 * 			position=self.thisptr.getPosition(key),
 * 			allele=self.thisptr.getAllele(key),
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_Variant); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 137, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);

  /* "whatshap/core.pyx":138
 * 			key = n + key
 * 		return Variant(
 * 			position=self.thisptr.getPosition(key),             # <<<<<<<<<<<<<<
 * 			allele=self.thisptr.getAllele(key),
 * 			quality=self.thisptr.getVariantQuality(key)
 */
  __pyx_t_3 = __Pyx_PyDict_NewPresized(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 138, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_v_key); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 138, __pyx_L1_error)
  try {
    __pyx_t_7 = __pyx_v_self->thisptr->getPosition(__pyx_t_4);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 138, __pyx_L1_error)
  }
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_t_7); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 138, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_position, __pyx_t_6) < 0) __PYX_ERR(1, 138, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "whatshap/core.pyx":139
 * 		return Variant(
 * 			position=self.thisptr.getPosition(key),
 * 			allele=self.thisptr.getAllele(key),             # <<<<<<<<<<<<<<
 * 			quality=self.thisptr.getVariantQuality(key)
 * 		)
 */
  __pyx_t_7 = __Pyx_PyInt_As_int(__pyx_v_key); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 139, __pyx_L1_error)
  try {
    __pyx_t_4 = __pyx_v_self->thisptr->getAllele(__pyx_t_7);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 139, __pyx_L1_error)
  }
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_t_4); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 139, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_allele, __pyx_t_6) < 0) __PYX_ERR(1, 138, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "whatshap/core.pyx":140
 * 			position=self.thisptr.getPosition(key),
 * 			allele=self.thisptr.getAllele(key),
 * 			quality=self.thisptr.getVariantQuality(key)             # <<<<<<<<<<<<<<
 * 		)
 * 
 */
  __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_v_key); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 140, __pyx_L1_error)
  try {
    __pyx_t_7 = __pyx_v_self->thisptr->getVariantQuality(__pyx_t_4);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 140, __pyx_L1_error)
  }
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_t_7); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 140, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_quality, __pyx_t_6) < 0) __PYX_ERR(1, 138, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "whatshap/core.pyx":137
 * 		if key < 0:
 * 			key = n + key
 * 		return Variant(             # <<<<<<<<<<<<<<
 * 			position=self.thisptr.getPosition(key),
 * 			allele=self.thisptr.getAllele(key),
 */
  __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_empty_tuple, __pyx_t_3); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 137, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_r = __pyx_t_6;
  __pyx_t_6 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":126
 * 		return self.thisptr.getVariantCount()
 * 
 * 	def __getitem__(self, key):             # <<<<<<<<<<<<<<
 * 		"""Return Variant object at the given integer index"""
 * 		assert self.thisptr != NULL
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("whatshap.core.Read.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_key);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":143
 * 		)
 * 
 * 	def __setitem__(self, index, variant):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		cdef int n = self.thisptr.getVariantCount()
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_4Read_14__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_variant); /*proto*/
static int __pyx_pw_8whatshap_4core_4Read_14__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_variant) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setitem__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_13__setitem__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((PyObject *)__pyx_v_index), ((PyObject *)__pyx_v_variant));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_4Read_13__setitem__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_variant) {
  int __pyx_v_n;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setitem__", 0);
  __Pyx_INCREF(__pyx_v_index);

  /* "whatshap/core.pyx":144
 * 
 * 	def __setitem__(self, index, variant):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= index < n):
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 144, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":145
 * 	def __setitem__(self, index, variant):
 * 		assert self.thisptr != NULL
 * 		cdef int n = self.thisptr.getVariantCount()             # <<<<<<<<<<<<<<
 * 		if not (-n <= index < n):
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 */
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->getVariantCount();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 145, __pyx_L1_error)
  }
  __pyx_v_n = __pyx_t_1;

  /* "whatshap/core.pyx":146
 * 		assert self.thisptr != NULL
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= index < n):             # <<<<<<<<<<<<<<
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 * 		if index < 0:
 */
  __pyx_t_2 = __Pyx_PyInt_From_int((-__pyx_v_n)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 146, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, __pyx_v_index, Py_LE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 146, __pyx_L1_error)
  if (__Pyx_PyObject_IsTrue(__pyx_t_3)) {
    __Pyx_DECREF(__pyx_t_3);
    __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 146, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_3 = PyObject_RichCompare(__pyx_v_index, __pyx_t_4, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 146, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(1, 146, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_6 = ((!__pyx_t_5) != 0);
  if (unlikely(__pyx_t_6)) {

    /* "whatshap/core.pyx":147
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= index < n):
 * 			raise IndexError('Index out of bounds: {}'.format(index))             # <<<<<<<<<<<<<<
 * 		if index < 0:
 * 			index = n + index
 */
    __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Index_out_of_bounds, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 147, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
      __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
      if (likely(__pyx_t_4)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
        __Pyx_INCREF(__pyx_t_4);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_2, function);
      }
    }
    __pyx_t_3 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_4, __pyx_v_index) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_index);
    __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 147, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IndexError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 147, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_Raise(__pyx_t_2, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __PYX_ERR(1, 147, __pyx_L1_error)

    /* "whatshap/core.pyx":146
 * 		assert self.thisptr != NULL
 * 		cdef int n = self.thisptr.getVariantCount()
 * 		if not (-n <= index < n):             # <<<<<<<<<<<<<<
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 * 		if index < 0:
 */
  }

  /* "whatshap/core.pyx":148
 * 		if not (-n <= index < n):
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 * 		if index < 0:             # <<<<<<<<<<<<<<
 * 			index = n + index
 * 		if not isinstance(variant, Variant):
 */
  __pyx_t_2 = PyObject_RichCompare(__pyx_v_index, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 148, __pyx_L1_error)
  __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(1, 148, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (__pyx_t_6) {

    /* "whatshap/core.pyx":149
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 * 		if index < 0:
 * 			index = n + index             # <<<<<<<<<<<<<<
 * 		if not isinstance(variant, Variant):
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))
 */
    __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 149, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = PyNumber_Add(__pyx_t_2, __pyx_v_index); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 149, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __Pyx_DECREF_SET(__pyx_v_index, __pyx_t_3);
    __pyx_t_3 = 0;

    /* "whatshap/core.pyx":148
 * 		if not (-n <= index < n):
 * 			raise IndexError('Index out of bounds: {}'.format(index))
 * 		if index < 0:             # <<<<<<<<<<<<<<
 * 			index = n + index
 * 		if not isinstance(variant, Variant):
 */
  }

  /* "whatshap/core.pyx":150
 * 		if index < 0:
 * 			index = n + index
 * 		if not isinstance(variant, Variant):             # <<<<<<<<<<<<<<
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))
 * 		self.thisptr.setPosition(index, variant.position)
 */
  __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_Variant); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 150, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_6 = PyObject_IsInstance(__pyx_v_variant, __pyx_t_3); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(1, 150, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_5 = ((!(__pyx_t_6 != 0)) != 0);
  if (unlikely(__pyx_t_5)) {

    /* "whatshap/core.pyx":151
 * 			index = n + index
 * 		if not isinstance(variant, Variant):
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))             # <<<<<<<<<<<<<<
 * 		self.thisptr.setPosition(index, variant.position)
 * 		self.thisptr.setAllele(index, variant.allele)
 */
    __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Expected_instance_of_Variant_but, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 151, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
      __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
      if (likely(__pyx_t_4)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
        __Pyx_INCREF(__pyx_t_4);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_2, function);
      }
    }
    __pyx_t_3 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_4, ((PyObject *)Py_TYPE(__pyx_v_variant))) : __Pyx_PyObject_CallOneArg(__pyx_t_2, ((PyObject *)Py_TYPE(__pyx_v_variant)));
    __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 151, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 151, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_Raise(__pyx_t_2, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __PYX_ERR(1, 151, __pyx_L1_error)

    /* "whatshap/core.pyx":150
 * 		if index < 0:
 * 			index = n + index
 * 		if not isinstance(variant, Variant):             # <<<<<<<<<<<<<<
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))
 * 		self.thisptr.setPosition(index, variant.position)
 */
  }

  /* "whatshap/core.pyx":152
 * 		if not isinstance(variant, Variant):
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))
 * 		self.thisptr.setPosition(index, variant.position)             # <<<<<<<<<<<<<<
 * 		self.thisptr.setAllele(index, variant.allele)
 * 		self.thisptr.setVariantQuality(index, variant.quality)
 */
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_index); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 152, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_variant, __pyx_n_s_position); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 152, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_7 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 152, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  try {
    __pyx_v_self->thisptr->setPosition(__pyx_t_1, __pyx_t_7);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 152, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":153
 * 			raise ValueError('Expected instance of Variant, but found {}'.format(type(variant)))
 * 		self.thisptr.setPosition(index, variant.position)
 * 		self.thisptr.setAllele(index, variant.allele)             # <<<<<<<<<<<<<<
 * 		self.thisptr.setVariantQuality(index, variant.quality)
 * 
 */
  __pyx_t_7 = __Pyx_PyInt_As_int(__pyx_v_index); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 153, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_variant, __pyx_n_s_allele); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 153, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 153, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  try {
    __pyx_v_self->thisptr->setAllele(__pyx_t_7, __pyx_t_1);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 153, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":154
 * 		self.thisptr.setPosition(index, variant.position)
 * 		self.thisptr.setAllele(index, variant.allele)
 * 		self.thisptr.setVariantQuality(index, variant.quality)             # <<<<<<<<<<<<<<
 * 
 * 	def __contains__(self, position):
 */
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_v_index); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 154, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_variant, __pyx_n_s_quality); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 154, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_7 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 154, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  try {
    __pyx_v_self->thisptr->setVariantQuality(__pyx_t_1, __pyx_t_7);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 154, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":143
 * 		)
 * 
 * 	def __setitem__(self, index, variant):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		cdef int n = self.thisptr.getVariantCount()
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.Read.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_index);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":156
 * 		self.thisptr.setVariantQuality(index, variant.quality)
 * 
 * 	def __contains__(self, position):             # <<<<<<<<<<<<<<
 * 		"""Return whether this read contains a variant at the given position.
 * 		A linear search is used.
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_4Read_16__contains__(PyObject *__pyx_v_self, PyObject *__pyx_v_position); /*proto*/
static char __pyx_doc_8whatshap_4core_4Read_15__contains__[] = "Return whether this read contains a variant at the given position.\n\t\tA linear search is used.\n\t\t";
#if CYTHON_UPDATE_DESCRIPTOR_DOC
struct wrapperbase __pyx_wrapperbase_8whatshap_4core_4Read_15__contains__;
#endif
static int __pyx_pw_8whatshap_4core_4Read_16__contains__(PyObject *__pyx_v_self, PyObject *__pyx_v_position) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__contains__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_15__contains__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((PyObject *)__pyx_v_position));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_4Read_15__contains__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_position) {
  PyObject *__pyx_v_variant = NULL;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  PyObject *(*__pyx_t_4)(PyObject *);
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__contains__", 0);

  /* "whatshap/core.pyx":160
 * 		A linear search is used.
 * 		"""
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		assert isinstance(position, int)
 * 		for variant in self:
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 160, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":161
 * 		"""
 * 		assert self.thisptr != NULL
 * 		assert isinstance(position, int)             # <<<<<<<<<<<<<<
 * 		for variant in self:
 * 			if variant.position == position:
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    __pyx_t_1 = PyInt_Check(__pyx_v_position); 
    if (unlikely(!(__pyx_t_1 != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 161, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":162
 * 		assert self.thisptr != NULL
 * 		assert isinstance(position, int)
 * 		for variant in self:             # <<<<<<<<<<<<<<
 * 			if variant.position == position:
 * 				return True
 */
  if (likely(PyList_CheckExact(((PyObject *)__pyx_v_self))) || PyTuple_CheckExact(((PyObject *)__pyx_v_self))) {
    __pyx_t_2 = ((PyObject *)__pyx_v_self); __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
  } else {
    __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 162, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 162, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_4)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 162, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 162, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      } else {
        if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 162, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 162, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      }
    } else {
      __pyx_t_5 = __pyx_t_4(__pyx_t_2);
      if (unlikely(!__pyx_t_5)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 162, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_5);
    }
    __Pyx_XDECREF_SET(__pyx_v_variant, __pyx_t_5);
    __pyx_t_5 = 0;

    /* "whatshap/core.pyx":163
 * 		assert isinstance(position, int)
 * 		for variant in self:
 * 			if variant.position == position:             # <<<<<<<<<<<<<<
 * 				return True
 * 		return False
 */
    __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_variant, __pyx_n_s_position); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 163, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_v_position, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 163, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(1, 163, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    if (__pyx_t_1) {

      /* "whatshap/core.pyx":164
 * 		for variant in self:
 * 			if variant.position == position:
 * 				return True             # <<<<<<<<<<<<<<
 * 		return False
 * 
 */
      __pyx_r = 1;
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      goto __pyx_L0;

      /* "whatshap/core.pyx":163
 * 		assert isinstance(position, int)
 * 		for variant in self:
 * 			if variant.position == position:             # <<<<<<<<<<<<<<
 * 				return True
 * 		return False
 */
    }

    /* "whatshap/core.pyx":162
 * 		assert self.thisptr != NULL
 * 		assert isinstance(position, int)
 * 		for variant in self:             # <<<<<<<<<<<<<<
 * 			if variant.position == position:
 * 				return True
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "whatshap/core.pyx":165
 * 			if variant.position == position:
 * 				return True
 * 		return False             # <<<<<<<<<<<<<<
 * 
 * 	def __getstate__(self):
 */
  __pyx_r = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":156
 * 		self.thisptr.setVariantQuality(index, variant.quality)
 * 
 * 	def __contains__(self, position):             # <<<<<<<<<<<<<<
 * 		"""Return whether this read contains a variant at the given position.
 * 		A linear search is used.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("whatshap.core.Read.__contains__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_variant);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":167
 * 		return False
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		mapqs = [mapq for mapq in self.mapqs]
 * 		variants = [(var.position, var.allele, var.quality) for var in self]
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_18__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_18__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_17__getstate__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_17__getstate__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_v_mapqs = NULL;
  PyObject *__pyx_v_variants = NULL;
  PyObject *__pyx_8genexpr1__pyx_v_mapq = NULL;
  PyObject *__pyx_8genexpr2__pyx_v_var = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  Py_ssize_t __pyx_t_4;
  PyObject *(*__pyx_t_5)(PyObject *);
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getstate__", 0);

  /* "whatshap/core.pyx":168
 * 
 * 	def __getstate__(self):
 * 		mapqs = [mapq for mapq in self.mapqs]             # <<<<<<<<<<<<<<
 * 		variants = [(var.position, var.allele, var.quality) for var in self]
 * 		return (mapqs, self.name, self.source_id, self.sample_id, self.reference_start, self.BX_tag, variants)
 */
  { /* enter inner scope */
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 168, __pyx_L5_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_mapqs); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 168, __pyx_L5_error)
    __Pyx_GOTREF(__pyx_t_2);
    if (likely(PyList_CheckExact(__pyx_t_2)) || PyTuple_CheckExact(__pyx_t_2)) {
      __pyx_t_3 = __pyx_t_2; __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0;
      __pyx_t_5 = NULL;
    } else {
      __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 168, __pyx_L5_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_5 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 168, __pyx_L5_error)
    }
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    for (;;) {
      if (likely(!__pyx_t_5)) {
        if (likely(PyList_CheckExact(__pyx_t_3))) {
          if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 168, __pyx_L5_error)
          #else
          __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 168, __pyx_L5_error)
          __Pyx_GOTREF(__pyx_t_2);
          #endif
        } else {
          if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 168, __pyx_L5_error)
          #else
          __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 168, __pyx_L5_error)
          __Pyx_GOTREF(__pyx_t_2);
          #endif
        }
      } else {
        __pyx_t_2 = __pyx_t_5(__pyx_t_3);
        if (unlikely(!__pyx_t_2)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 168, __pyx_L5_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_2);
      }
      __Pyx_XDECREF_SET(__pyx_8genexpr1__pyx_v_mapq, __pyx_t_2);
      __pyx_t_2 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_8genexpr1__pyx_v_mapq))) __PYX_ERR(1, 168, __pyx_L5_error)
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_mapq); __pyx_8genexpr1__pyx_v_mapq = 0;
    goto __pyx_L8_exit_scope;
    __pyx_L5_error:;
    __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_mapq); __pyx_8genexpr1__pyx_v_mapq = 0;
    goto __pyx_L1_error;
    __pyx_L8_exit_scope:;
  } /* exit inner scope */
  __pyx_v_mapqs = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":169
 * 	def __getstate__(self):
 * 		mapqs = [mapq for mapq in self.mapqs]
 * 		variants = [(var.position, var.allele, var.quality) for var in self]             # <<<<<<<<<<<<<<
 * 		return (mapqs, self.name, self.source_id, self.sample_id, self.reference_start, self.BX_tag, variants)
 * 
 */
  { /* enter inner scope */
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 169, __pyx_L11_error)
    __Pyx_GOTREF(__pyx_t_1);
    if (likely(PyList_CheckExact(((PyObject *)__pyx_v_self))) || PyTuple_CheckExact(((PyObject *)__pyx_v_self))) {
      __pyx_t_3 = ((PyObject *)__pyx_v_self); __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0;
      __pyx_t_5 = NULL;
    } else {
      __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_5 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 169, __pyx_L11_error)
    }
    for (;;) {
      if (likely(!__pyx_t_5)) {
        if (likely(PyList_CheckExact(__pyx_t_3))) {
          if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 169, __pyx_L11_error)
          #else
          __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 169, __pyx_L11_error)
          __Pyx_GOTREF(__pyx_t_2);
          #endif
        } else {
          if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 169, __pyx_L11_error)
          #else
          __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 169, __pyx_L11_error)
          __Pyx_GOTREF(__pyx_t_2);
          #endif
        }
      } else {
        __pyx_t_2 = __pyx_t_5(__pyx_t_3);
        if (unlikely(!__pyx_t_2)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 169, __pyx_L11_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_2);
      }
      __Pyx_XDECREF_SET(__pyx_8genexpr2__pyx_v_var, __pyx_t_2);
      __pyx_t_2 = 0;
      __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_8genexpr2__pyx_v_var, __pyx_n_s_position); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_8genexpr2__pyx_v_var, __pyx_n_s_allele); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_8genexpr2__pyx_v_var, __pyx_n_s_quality); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_GOTREF(__pyx_t_7);
      __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_GOTREF(__pyx_t_8);
      __Pyx_GIVEREF(__pyx_t_2);
      PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
      __Pyx_GIVEREF(__pyx_t_6);
      PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_6);
      __Pyx_GIVEREF(__pyx_t_7);
      PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7);
      __pyx_t_2 = 0;
      __pyx_t_6 = 0;
      __pyx_t_7 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_8))) __PYX_ERR(1, 169, __pyx_L11_error)
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_var); __pyx_8genexpr2__pyx_v_var = 0;
    goto __pyx_L14_exit_scope;
    __pyx_L11_error:;
    __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_var); __pyx_8genexpr2__pyx_v_var = 0;
    goto __pyx_L1_error;
    __pyx_L14_exit_scope:;
  } /* exit inner scope */
  __pyx_v_variants = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":170
 * 		mapqs = [mapq for mapq in self.mapqs]
 * 		variants = [(var.position, var.allele, var.quality) for var in self]
 * 		return (mapqs, self.name, self.source_id, self.sample_id, self.reference_start, self.BX_tag, variants)             # <<<<<<<<<<<<<<
 * 
 * 	def __setstate__(self, state):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_name); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_source_id); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_sample_id); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_8);
  __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_reference_start); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_BX_tag); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_t_2 = PyTuple_New(7); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 170, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_INCREF(__pyx_v_mapqs);
  __Pyx_GIVEREF(__pyx_v_mapqs);
  PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_mapqs);
  __Pyx_GIVEREF(__pyx_t_1);
  PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
  __Pyx_GIVEREF(__pyx_t_3);
  PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_3);
  __Pyx_GIVEREF(__pyx_t_8);
  PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8);
  __Pyx_GIVEREF(__pyx_t_7);
  PyTuple_SET_ITEM(__pyx_t_2, 4, __pyx_t_7);
  __Pyx_GIVEREF(__pyx_t_6);
  PyTuple_SET_ITEM(__pyx_t_2, 5, __pyx_t_6);
  __Pyx_INCREF(__pyx_v_variants);
  __Pyx_GIVEREF(__pyx_v_variants);
  PyTuple_SET_ITEM(__pyx_t_2, 6, __pyx_v_variants);
  __pyx_t_1 = 0;
  __pyx_t_3 = 0;
  __pyx_t_8 = 0;
  __pyx_t_7 = 0;
  __pyx_t_6 = 0;
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":167
 * 		return False
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		mapqs = [mapq for mapq in self.mapqs]
 * 		variants = [(var.position, var.allele, var.quality) for var in self]
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_AddTraceback("whatshap.core.Read.__getstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_mapqs);
  __Pyx_XDECREF(__pyx_v_variants);
  __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_mapq);
  __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_var);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":172
 * 		return (mapqs, self.name, self.source_id, self.sample_id, self.reference_start, self.BX_tag, variants)
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		mapqs, name, source_id, sample_id, reference_start, BX_tag, variants = state
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_20__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_20__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_19__setstate__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((PyObject *)__pyx_v_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_19__setstate__(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_v_mapqs = NULL;
  PyObject *__pyx_v_name = NULL;
  PyObject *__pyx_v_source_id = NULL;
  PyObject *__pyx_v_sample_id = NULL;
  PyObject *__pyx_v_reference_start = NULL;
  PyObject *__pyx_v_BX_tag = NULL;
  PyObject *__pyx_v_variants = NULL;
  std::string __pyx_v__name;
  std::string __pyx_v__BX_tag;
  PyObject *__pyx_v_mapq = NULL;
  PyObject *__pyx_v_pos = NULL;
  PyObject *__pyx_v_allele = NULL;
  PyObject *__pyx_v_quality = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  PyObject *(*__pyx_t_9)(PyObject *);
  std::string __pyx_t_10;
  int __pyx_t_11;
  int __pyx_t_12;
  int __pyx_t_13;
  int __pyx_t_14;
  Py_ssize_t __pyx_t_15;
  int __pyx_t_16;
  int __pyx_t_17;
  int __pyx_t_18;
  Read *__pyx_t_19;
  PyObject *(*__pyx_t_20)(PyObject *);
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate__", 0);

  /* "whatshap/core.pyx":173
 * 
 * 	def __setstate__(self, state):
 * 		mapqs, name, source_id, sample_id, reference_start, BX_tag, variants = state             # <<<<<<<<<<<<<<
 * 
 * 		# TODO: Duplicated code from __cinit__ is ugly, but cinit cannot be used here directly
 */
  if ((likely(PyTuple_CheckExact(__pyx_v_state))) || (PyList_CheckExact(__pyx_v_state))) {
    PyObject* sequence = __pyx_v_state;
    Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
    if (unlikely(size != 7)) {
      if (size > 7) __Pyx_RaiseTooManyValuesError(7);
      else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
      __PYX_ERR(1, 173, __pyx_L1_error)
    }
    #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    if (likely(PyTuple_CheckExact(sequence))) {
      __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
      __pyx_t_3 = PyTuple_GET_ITEM(sequence, 2); 
      __pyx_t_4 = PyTuple_GET_ITEM(sequence, 3); 
      __pyx_t_5 = PyTuple_GET_ITEM(sequence, 4); 
      __pyx_t_6 = PyTuple_GET_ITEM(sequence, 5); 
      __pyx_t_7 = PyTuple_GET_ITEM(sequence, 6); 
    } else {
      __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
      __pyx_t_3 = PyList_GET_ITEM(sequence, 2); 
      __pyx_t_4 = PyList_GET_ITEM(sequence, 3); 
      __pyx_t_5 = PyList_GET_ITEM(sequence, 4); 
      __pyx_t_6 = PyList_GET_ITEM(sequence, 5); 
      __pyx_t_7 = PyList_GET_ITEM(sequence, 6); 
    }
    __Pyx_INCREF(__pyx_t_1);
    __Pyx_INCREF(__pyx_t_2);
    __Pyx_INCREF(__pyx_t_3);
    __Pyx_INCREF(__pyx_t_4);
    __Pyx_INCREF(__pyx_t_5);
    __Pyx_INCREF(__pyx_t_6);
    __Pyx_INCREF(__pyx_t_7);
    #else
    {
      Py_ssize_t i;
      PyObject** temps[7] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_3,&__pyx_t_4,&__pyx_t_5,&__pyx_t_6,&__pyx_t_7};
      for (i=0; i < 7; i++) {
        PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) __PYX_ERR(1, 173, __pyx_L1_error)
        __Pyx_GOTREF(item);
        *(temps[i]) = item;
      }
    }
    #endif
  } else {
    Py_ssize_t index = -1;
    PyObject** temps[7] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_3,&__pyx_t_4,&__pyx_t_5,&__pyx_t_6,&__pyx_t_7};
    __pyx_t_8 = PyObject_GetIter(__pyx_v_state); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 173, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_8);
    __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
    for (index=0; index < 7; index++) {
      PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L3_unpacking_failed;
      __Pyx_GOTREF(item);
      *(temps[index]) = item;
    }
    if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 7) < 0) __PYX_ERR(1, 173, __pyx_L1_error)
    __pyx_t_9 = NULL;
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    goto __pyx_L4_unpacking_done;
    __pyx_L3_unpacking_failed:;
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __pyx_t_9 = NULL;
    if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
    __PYX_ERR(1, 173, __pyx_L1_error)
    __pyx_L4_unpacking_done:;
  }
  __pyx_v_mapqs = __pyx_t_1;
  __pyx_t_1 = 0;
  __pyx_v_name = __pyx_t_2;
  __pyx_t_2 = 0;
  __pyx_v_source_id = __pyx_t_3;
  __pyx_t_3 = 0;
  __pyx_v_sample_id = __pyx_t_4;
  __pyx_t_4 = 0;
  __pyx_v_reference_start = __pyx_t_5;
  __pyx_t_5 = 0;
  __pyx_v_BX_tag = __pyx_t_6;
  __pyx_t_6 = 0;
  __pyx_v_variants = __pyx_t_7;
  __pyx_t_7 = 0;

  /* "whatshap/core.pyx":176
 * 
 * 		# TODO: Duplicated code from __cinit__ is ugly, but cinit cannot be used here directly
 * 		cdef string _name = b''             # <<<<<<<<<<<<<<
 * 		cdef string _BX_tag = b''
 * 		if name is None:
 */
  __pyx_t_10 = __pyx_convert_string_from_py_std__in_string(__pyx_kp_b__3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 176, __pyx_L1_error)
  __pyx_v__name = __pyx_t_10;

  /* "whatshap/core.pyx":177
 * 		# TODO: Duplicated code from __cinit__ is ugly, but cinit cannot be used here directly
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''             # <<<<<<<<<<<<<<
 * 		if name is None:
 * 			self.thisptr = NULL
 */
  __pyx_t_10 = __pyx_convert_string_from_py_std__in_string(__pyx_kp_b__3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 177, __pyx_L1_error)
  __pyx_v__BX_tag = __pyx_t_10;

  /* "whatshap/core.pyx":178
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 * 		if name is None:             # <<<<<<<<<<<<<<
 * 			self.thisptr = NULL
 * 			self.ownsptr = False
 */
  __pyx_t_11 = (__pyx_v_name == Py_None);
  __pyx_t_12 = (__pyx_t_11 != 0);
  if (__pyx_t_12) {

    /* "whatshap/core.pyx":179
 * 		cdef string _BX_tag = b''
 * 		if name is None:
 * 			self.thisptr = NULL             # <<<<<<<<<<<<<<
 * 			self.ownsptr = False
 * 		else:
 */
    __pyx_v_self->thisptr = NULL;

    /* "whatshap/core.pyx":180
 * 		if name is None:
 * 			self.thisptr = NULL
 * 			self.ownsptr = False             # <<<<<<<<<<<<<<
 * 		else:
 * 			# TODO: Is this the best way to handle string arguments?
 */
    __pyx_v_self->ownsptr = 0;

    /* "whatshap/core.pyx":178
 * 		cdef string _name = b''
 * 		cdef string _BX_tag = b''
 * 		if name is None:             # <<<<<<<<<<<<<<
 * 			self.thisptr = NULL
 * 			self.ownsptr = False
 */
    goto __pyx_L5;
  }

  /* "whatshap/core.pyx":183
 * 		else:
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')             # <<<<<<<<<<<<<<
 * 			if BX_tag is not b'' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')
 */
  /*else*/ {
    __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_name, __pyx_n_s_encode); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 183, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_5 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_6))) {
      __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
      if (likely(__pyx_t_5)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
        __Pyx_INCREF(__pyx_t_5);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_6, function);
      }
    }
    __pyx_t_7 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_6, __pyx_t_5, __pyx_kp_u_UTF_8) : __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_kp_u_UTF_8);
    __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 183, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_10 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 183, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __pyx_v__name = __pyx_t_10;

    /* "whatshap/core.pyx":184
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not b'' and BX_tag is not None:             # <<<<<<<<<<<<<<
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapqs[0] if len(mapqs) > 0 else 0, source_id, sample_id, reference_start, _BX_tag)
 */
    __pyx_t_11 = (__pyx_v_BX_tag != __pyx_kp_b__3);
    __pyx_t_13 = (__pyx_t_11 != 0);
    if (__pyx_t_13) {
    } else {
      __pyx_t_12 = __pyx_t_13;
      goto __pyx_L7_bool_binop_done;
    }
    __pyx_t_13 = (__pyx_v_BX_tag != Py_None);
    __pyx_t_11 = (__pyx_t_13 != 0);
    __pyx_t_12 = __pyx_t_11;
    __pyx_L7_bool_binop_done:;
    if (__pyx_t_12) {

      /* "whatshap/core.pyx":185
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not b'' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')             # <<<<<<<<<<<<<<
 * 			self.thisptr = new cpp.Read(_name, mapqs[0] if len(mapqs) > 0 else 0, source_id, sample_id, reference_start, _BX_tag)
 * 			self.ownsptr = True
 */
      __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_BX_tag, __pyx_n_s_encode); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 185, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_5 = NULL;
      if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_6))) {
        __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_6);
        if (likely(__pyx_t_5)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
          __Pyx_INCREF(__pyx_t_5);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_6, function);
        }
      }
      __pyx_t_7 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_6, __pyx_t_5, __pyx_kp_u_UTF_8) : __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_kp_u_UTF_8);
      __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
      if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 185, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_10 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 185, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_v__BX_tag = __pyx_t_10;

      /* "whatshap/core.pyx":184
 * 			# TODO: Is this the best way to handle string arguments?
 * 			_name = name.encode('UTF-8')
 * 			if BX_tag is not b'' and BX_tag is not None:             # <<<<<<<<<<<<<<
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapqs[0] if len(mapqs) > 0 else 0, source_id, sample_id, reference_start, _BX_tag)
 */
    }

    /* "whatshap/core.pyx":186
 * 			if BX_tag is not b'' and BX_tag is not None:
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapqs[0] if len(mapqs) > 0 else 0, source_id, sample_id, reference_start, _BX_tag)             # <<<<<<<<<<<<<<
 * 			self.ownsptr = True
 * 
 */
    __pyx_t_15 = PyObject_Length(__pyx_v_mapqs); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(1, 186, __pyx_L1_error)
    if (((__pyx_t_15 > 0) != 0)) {
      __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_mapqs, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_t_7); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 186, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_14 = __pyx_t_16;
    } else {
      __pyx_t_14 = 0;
    }
    __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_v_source_id); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 186, __pyx_L1_error)
    __pyx_t_17 = __Pyx_PyInt_As_int(__pyx_v_sample_id); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 186, __pyx_L1_error)
    __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_v_reference_start); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 186, __pyx_L1_error)
    try {
      __pyx_t_19 = new Read(__pyx_v__name, __pyx_t_14, __pyx_t_16, __pyx_t_17, __pyx_t_18, __pyx_v__BX_tag);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 186, __pyx_L1_error)
    }
    __pyx_v_self->thisptr = __pyx_t_19;

    /* "whatshap/core.pyx":187
 * 				_BX_tag = BX_tag.encode('UTF-8')
 * 			self.thisptr = new cpp.Read(_name, mapqs[0] if len(mapqs) > 0 else 0, source_id, sample_id, reference_start, _BX_tag)
 * 			self.ownsptr = True             # <<<<<<<<<<<<<<
 * 
 * 		for mapq in mapqs[1:]:
 */
    __pyx_v_self->ownsptr = 1;
  }
  __pyx_L5:;

  /* "whatshap/core.pyx":189
 * 			self.ownsptr = True
 * 
 * 		for mapq in mapqs[1:]:             # <<<<<<<<<<<<<<
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:
 */
  __pyx_t_7 = __Pyx_PyObject_GetSlice(__pyx_v_mapqs, 1, 0, NULL, NULL, &__pyx_slice__5, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 189, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  if (likely(PyList_CheckExact(__pyx_t_7)) || PyTuple_CheckExact(__pyx_t_7)) {
    __pyx_t_6 = __pyx_t_7; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0;
    __pyx_t_20 = NULL;
  } else {
    __pyx_t_15 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 189, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_20 = Py_TYPE(__pyx_t_6)->tp_iternext; if (unlikely(!__pyx_t_20)) __PYX_ERR(1, 189, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  for (;;) {
    if (likely(!__pyx_t_20)) {
      if (likely(PyList_CheckExact(__pyx_t_6))) {
        if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(1, 189, __pyx_L1_error)
        #else
        __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 189, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        #endif
      } else {
        if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(1, 189, __pyx_L1_error)
        #else
        __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 189, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        #endif
      }
    } else {
      __pyx_t_7 = __pyx_t_20(__pyx_t_6);
      if (unlikely(!__pyx_t_7)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 189, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_7);
    }
    __Pyx_XDECREF_SET(__pyx_v_mapq, __pyx_t_7);
    __pyx_t_7 = 0;

    /* "whatshap/core.pyx":190
 * 
 * 		for mapq in mapqs[1:]:
 * 			self.add_mapq(mapq)             # <<<<<<<<<<<<<<
 * 		for (pos, allele, quality) in variants:
 * 			self.add_variant(pos, allele, quality)
 */
    __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_add_mapq); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 190, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_4 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_5))) {
      __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_5);
      if (likely(__pyx_t_4)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
        __Pyx_INCREF(__pyx_t_4);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_5, function);
      }
    }
    __pyx_t_7 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_5, __pyx_t_4, __pyx_v_mapq) : __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_mapq);
    __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 190, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

    /* "whatshap/core.pyx":189
 * 			self.ownsptr = True
 * 
 * 		for mapq in mapqs[1:]:             # <<<<<<<<<<<<<<
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:
 */
  }
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "whatshap/core.pyx":191
 * 		for mapq in mapqs[1:]:
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:             # <<<<<<<<<<<<<<
 * 			self.add_variant(pos, allele, quality)
 * 
 */
  if (likely(PyList_CheckExact(__pyx_v_variants)) || PyTuple_CheckExact(__pyx_v_variants)) {
    __pyx_t_6 = __pyx_v_variants; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0;
    __pyx_t_20 = NULL;
  } else {
    __pyx_t_15 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_v_variants); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 191, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_20 = Py_TYPE(__pyx_t_6)->tp_iternext; if (unlikely(!__pyx_t_20)) __PYX_ERR(1, 191, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_20)) {
      if (likely(PyList_CheckExact(__pyx_t_6))) {
        if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(1, 191, __pyx_L1_error)
        #else
        __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 191, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        #endif
      } else {
        if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(1, 191, __pyx_L1_error)
        #else
        __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 191, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        #endif
      }
    } else {
      __pyx_t_7 = __pyx_t_20(__pyx_t_6);
      if (unlikely(!__pyx_t_7)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 191, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_7);
    }
    if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
      PyObject* sequence = __pyx_t_7;
      Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
      if (unlikely(size != 3)) {
        if (size > 3) __Pyx_RaiseTooManyValuesError(3);
        else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
        __PYX_ERR(1, 191, __pyx_L1_error)
      }
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      if (likely(PyTuple_CheckExact(sequence))) {
        __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); 
        __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1); 
        __pyx_t_3 = PyTuple_GET_ITEM(sequence, 2); 
      } else {
        __pyx_t_5 = PyList_GET_ITEM(sequence, 0); 
        __pyx_t_4 = PyList_GET_ITEM(sequence, 1); 
        __pyx_t_3 = PyList_GET_ITEM(sequence, 2); 
      }
      __Pyx_INCREF(__pyx_t_5);
      __Pyx_INCREF(__pyx_t_4);
      __Pyx_INCREF(__pyx_t_3);
      #else
      __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 191, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 191, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_3 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 191, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      #endif
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    } else {
      Py_ssize_t index = -1;
      __pyx_t_2 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 191, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_9 = Py_TYPE(__pyx_t_2)->tp_iternext;
      index = 0; __pyx_t_5 = __pyx_t_9(__pyx_t_2); if (unlikely(!__pyx_t_5)) goto __pyx_L13_unpacking_failed;
      __Pyx_GOTREF(__pyx_t_5);
      index = 1; __pyx_t_4 = __pyx_t_9(__pyx_t_2); if (unlikely(!__pyx_t_4)) goto __pyx_L13_unpacking_failed;
      __Pyx_GOTREF(__pyx_t_4);
      index = 2; __pyx_t_3 = __pyx_t_9(__pyx_t_2); if (unlikely(!__pyx_t_3)) goto __pyx_L13_unpacking_failed;
      __Pyx_GOTREF(__pyx_t_3);
      if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_2), 3) < 0) __PYX_ERR(1, 191, __pyx_L1_error)
      __pyx_t_9 = NULL;
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      goto __pyx_L14_unpacking_done;
      __pyx_L13_unpacking_failed:;
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_t_9 = NULL;
      if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
      __PYX_ERR(1, 191, __pyx_L1_error)
      __pyx_L14_unpacking_done:;
    }
    __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_5);
    __pyx_t_5 = 0;
    __Pyx_XDECREF_SET(__pyx_v_allele, __pyx_t_4);
    __pyx_t_4 = 0;
    __Pyx_XDECREF_SET(__pyx_v_quality, __pyx_t_3);
    __pyx_t_3 = 0;

    /* "whatshap/core.pyx":192
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:
 * 			self.add_variant(pos, allele, quality)             # <<<<<<<<<<<<<<
 * 
 * 	def add_variant(self, int position, int allele, int quality):
 */
    __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_add_variant); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 192, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = NULL;
    __pyx_t_18 = 0;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) {
      __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
      if (likely(__pyx_t_4)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
        __Pyx_INCREF(__pyx_t_4);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_3, function);
        __pyx_t_18 = 1;
      }
    }
    #if CYTHON_FAST_PYCALL
    if (PyFunction_Check(__pyx_t_3)) {
      PyObject *__pyx_temp[4] = {__pyx_t_4, __pyx_v_pos, __pyx_v_allele, __pyx_v_quality};
      __pyx_t_7 = __Pyx_PyFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_18, 3+__pyx_t_18); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 192, __pyx_L1_error)
      __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
      __Pyx_GOTREF(__pyx_t_7);
    } else
    #endif
    #if CYTHON_FAST_PYCCALL
    if (__Pyx_PyFastCFunction_Check(__pyx_t_3)) {
      PyObject *__pyx_temp[4] = {__pyx_t_4, __pyx_v_pos, __pyx_v_allele, __pyx_v_quality};
      __pyx_t_7 = __Pyx_PyCFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_18, 3+__pyx_t_18); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 192, __pyx_L1_error)
      __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
      __Pyx_GOTREF(__pyx_t_7);
    } else
    #endif
    {
      __pyx_t_5 = PyTuple_New(3+__pyx_t_18); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 192, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      if (__pyx_t_4) {
        __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL;
      }
      __Pyx_INCREF(__pyx_v_pos);
      __Pyx_GIVEREF(__pyx_v_pos);
      PyTuple_SET_ITEM(__pyx_t_5, 0+__pyx_t_18, __pyx_v_pos);
      __Pyx_INCREF(__pyx_v_allele);
      __Pyx_GIVEREF(__pyx_v_allele);
      PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_18, __pyx_v_allele);
      __Pyx_INCREF(__pyx_v_quality);
      __Pyx_GIVEREF(__pyx_v_quality);
      PyTuple_SET_ITEM(__pyx_t_5, 2+__pyx_t_18, __pyx_v_quality);
      __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 192, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

    /* "whatshap/core.pyx":191
 * 		for mapq in mapqs[1:]:
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:             # <<<<<<<<<<<<<<
 * 			self.add_variant(pos, allele, quality)
 * 
 */
  }
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "whatshap/core.pyx":172
 * 		return (mapqs, self.name, self.source_id, self.sample_id, self.reference_start, self.BX_tag, variants)
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		mapqs, name, source_id, sample_id, reference_start, BX_tag, variants = state
 * 
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_AddTraceback("whatshap.core.Read.__setstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_mapqs);
  __Pyx_XDECREF(__pyx_v_name);
  __Pyx_XDECREF(__pyx_v_source_id);
  __Pyx_XDECREF(__pyx_v_sample_id);
  __Pyx_XDECREF(__pyx_v_reference_start);
  __Pyx_XDECREF(__pyx_v_BX_tag);
  __Pyx_XDECREF(__pyx_v_variants);
  __Pyx_XDECREF(__pyx_v_mapq);
  __Pyx_XDECREF(__pyx_v_pos);
  __Pyx_XDECREF(__pyx_v_allele);
  __Pyx_XDECREF(__pyx_v_quality);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":194
 * 			self.add_variant(pos, allele, quality)
 * 
 * 	def add_variant(self, int position, int allele, int quality):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addVariant(position, allele, quality)
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_22add_variant(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_22add_variant(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_v_position;
  int __pyx_v_allele;
  int __pyx_v_quality;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add_variant (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_position,&__pyx_n_s_allele,&__pyx_n_s_quality,0};
    PyObject* values[3] = {0,0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_position)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_allele)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add_variant", 1, 3, 3, 1); __PYX_ERR(1, 194, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_quality)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add_variant", 1, 3, 3, 2); __PYX_ERR(1, 194, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add_variant") < 0)) __PYX_ERR(1, 194, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
      values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
    }
    __pyx_v_position = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_position == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 194, __pyx_L3_error)
    __pyx_v_allele = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_allele == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 194, __pyx_L3_error)
    __pyx_v_quality = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_quality == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 194, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("add_variant", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 194, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Read.add_variant", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_21add_variant(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), __pyx_v_position, __pyx_v_allele, __pyx_v_quality);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_21add_variant(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, int __pyx_v_position, int __pyx_v_allele, int __pyx_v_quality) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("add_variant", 0);

  /* "whatshap/core.pyx":195
 * 
 * 	def add_variant(self, int position, int allele, int quality):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		self.thisptr.addVariant(position, allele, quality)
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 195, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":196
 * 	def add_variant(self, int position, int allele, int quality):
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addVariant(position, allele, quality)             # <<<<<<<<<<<<<<
 * 
 * 	def add_mapq(self, int mapq):
 */
  try {
    __pyx_v_self->thisptr->addVariant(__pyx_v_position, __pyx_v_allele, __pyx_v_quality);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 196, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":194
 * 			self.add_variant(pos, allele, quality)
 * 
 * 	def add_variant(self, int position, int allele, int quality):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addVariant(position, allele, quality)
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Read.add_variant", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":198
 * 		self.thisptr.addVariant(position, allele, quality)
 * 
 * 	def add_mapq(self, int mapq):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addMapq(mapq)
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_24add_mapq(PyObject *__pyx_v_self, PyObject *__pyx_arg_mapq); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_24add_mapq(PyObject *__pyx_v_self, PyObject *__pyx_arg_mapq) {
  int __pyx_v_mapq;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add_mapq (wrapper)", 0);
  assert(__pyx_arg_mapq); {
    __pyx_v_mapq = __Pyx_PyInt_As_int(__pyx_arg_mapq); if (unlikely((__pyx_v_mapq == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 198, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Read.add_mapq", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_23add_mapq(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((int)__pyx_v_mapq));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_23add_mapq(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, int __pyx_v_mapq) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("add_mapq", 0);

  /* "whatshap/core.pyx":199
 * 
 * 	def add_mapq(self, int mapq):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		self.thisptr.addMapq(mapq)
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 199, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":200
 * 	def add_mapq(self, int mapq):
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addMapq(mapq)             # <<<<<<<<<<<<<<
 * 
 * 	def sort(self):
 */
  try {
    __pyx_v_self->thisptr->addMapq(__pyx_v_mapq);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 200, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":198
 * 		self.thisptr.addVariant(position, allele, quality)
 * 
 * 	def add_mapq(self, int mapq):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.addMapq(mapq)
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Read.add_mapq", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":202
 * 		self.thisptr.addMapq(mapq)
 * 
 * 	def sort(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.sortVariants()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_26sort(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_26sort(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("sort (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_25sort(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_25sort(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("sort", 0);

  /* "whatshap/core.pyx":203
 * 
 * 	def sort(self):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		self.thisptr.sortVariants()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 203, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":204
 * 	def sort(self):
 * 		assert self.thisptr != NULL
 * 		self.thisptr.sortVariants()             # <<<<<<<<<<<<<<
 * 
 * 	def is_sorted(self):
 */
  try {
    __pyx_v_self->thisptr->sortVariants();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 204, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":202
 * 		self.thisptr.addMapq(mapq)
 * 
 * 	def sort(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		self.thisptr.sortVariants()
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Read.sort", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":206
 * 		self.thisptr.sortVariants()
 * 
 * 	def is_sorted(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.isSorted()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_28is_sorted(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_28is_sorted(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("is_sorted (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_27is_sorted(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_27is_sorted(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("is_sorted", 0);

  /* "whatshap/core.pyx":207
 * 
 * 	def is_sorted(self):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		return self.thisptr.isSorted()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 207, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":208
 * 	def is_sorted(self):
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.isSorted()             # <<<<<<<<<<<<<<
 * 
 * 	def has_BX_tag(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->isSorted();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 208, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 208, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":206
 * 		self.thisptr.sortVariants()
 * 
 * 	def is_sorted(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.isSorted()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.is_sorted", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":210
 * 		return self.thisptr.isSorted()
 * 
 * 	def has_BX_tag(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.hasBXTag()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_30has_BX_tag(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_30has_BX_tag(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("has_BX_tag (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_29has_BX_tag(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_29has_BX_tag(struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("has_BX_tag", 0);

  /* "whatshap/core.pyx":211
 * 
 * 	def has_BX_tag(self):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		return self.thisptr.hasBXTag()
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 211, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":212
 * 	def has_BX_tag(self):
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.hasBXTag()             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->hasBXTag();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 212, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 212, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":210
 * 		return self.thisptr.isSorted()
 * 
 * 	def has_BX_tag(self):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		return self.thisptr.hasBXTag()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Read.has_BX_tag", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_32__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_32__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_31__reduce_cython__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_31__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Read.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_4Read_34__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_4Read_34__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4Read_33__setstate_cython__(((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4Read_33__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Read *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Read.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":216
 * 
 * cdef class ReadSet:
 * 	def __cinit__(self):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.ReadSet()
 * 
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_7ReadSet_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_7ReadSet_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
    __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
  if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet___cinit__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_7ReadSet___cinit__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  ReadSet *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":217
 * cdef class ReadSet:
 * 	def __cinit__(self):
 * 		self.thisptr = new cpp.ReadSet()             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  try {
    __pyx_t_1 = new ReadSet();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 217, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_1;

  /* "whatshap/core.pyx":216
 * 
 * cdef class ReadSet:
 * 	def __cinit__(self):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.ReadSet()
 * 
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.ReadSet.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":219
 * 		self.thisptr = new cpp.ReadSet()
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_7ReadSet_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_7ReadSet_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_7ReadSet_2__dealloc__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_7ReadSet_2__dealloc__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":220
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def add(self, Read read):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":219
 * 		self.thisptr = new cpp.ReadSet()
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":222
 * 		del self.thisptr
 * 
 * 	def add(self, Read read):             # <<<<<<<<<<<<<<
 * 		"""Adds a read to the set.
 * 		WARNING: this will internally create a copy of the wrapped C++ Read object,
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_5add(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
static char __pyx_doc_8whatshap_4core_7ReadSet_4add[] = "Adds a read to the set.\n\t\tWARNING: this will internally create a copy of the wrapped C++ Read object,\n\t\tso that subsequent changes to the Read don't affect the\n\t\tnewly created copy that is added to the ReadSet.";
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_5add(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_8whatshap_4core_Read, 1, "read", 0))) __PYX_ERR(1, 222, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_4add(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_Read *)__pyx_v_read));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_4add(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Read *__pyx_v_read) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  Read *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("add", 0);

  /* "whatshap/core.pyx":227
 * 		so that subsequent changes to the Read don't affect the
 * 		newly created copy that is added to the ReadSet."""
 * 		self.thisptr.add(new cpp.Read(read.thisptr[0]))             # <<<<<<<<<<<<<<
 * 
 * 	def __str__(self):
 */
  try {
    __pyx_t_1 = new Read((__pyx_v_read->thisptr[0]));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 227, __pyx_L1_error)
  }
  try {
    __pyx_v_self->thisptr->add(__pyx_t_1);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 227, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":222
 * 		del self.thisptr
 * 
 * 	def add(self, Read read):             # <<<<<<<<<<<<<<
 * 		"""Adds a read to the set.
 * 		WARNING: this will internally create a copy of the wrapped C++ Read object,
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.ReadSet.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":229
 * 		self.thisptr.add(new cpp.Read(read.thisptr[0]))
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_7__str__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_7__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_6__str__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_6__str__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "whatshap/core.pyx":230
 * 
 * 	def __str__(self):
 * 		return self.thisptr.toString().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	def __iter__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->toString();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 230, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 230, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":229
 * 		self.thisptr.add(new cpp.Read(read.thisptr[0]))
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}
static PyObject *__pyx_gb_8whatshap_4core_7ReadSet_10generator1(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value); /* proto */

/* "whatshap/core.pyx":232
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for i in range(self.thisptr.size()):
 * 			yield self[i]
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_9__iter__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_9__iter__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_8__iter__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_8__iter__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *__pyx_cur_scope;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__iter__", 0);
  __pyx_cur_scope = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)__pyx_tp_new_8whatshap_4core___pyx_scope_struct_1___iter__(__pyx_ptype_8whatshap_4core___pyx_scope_struct_1___iter__, __pyx_empty_tuple, NULL);
  if (unlikely(!__pyx_cur_scope)) {
    __pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)Py_None);
    __Pyx_INCREF(Py_None);
    __PYX_ERR(1, 232, __pyx_L1_error)
  } else {
    __Pyx_GOTREF(__pyx_cur_scope);
  }
  __pyx_cur_scope->__pyx_v_self = __pyx_v_self;
  __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  {
    __pyx_CoroutineObject *gen = __Pyx_Generator_New((__pyx_coroutine_body_t) __pyx_gb_8whatshap_4core_7ReadSet_10generator1, NULL, (PyObject *) __pyx_cur_scope, __pyx_n_s_iter, __pyx_n_s_ReadSet___iter, __pyx_n_s_whatshap_core); if (unlikely(!gen)) __PYX_ERR(1, 232, __pyx_L1_error)
    __Pyx_DECREF(__pyx_cur_scope);
    __Pyx_RefNannyFinishContext();
    return (PyObject *) gen;
  }

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.ReadSet.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_DECREF(((PyObject *)__pyx_cur_scope));
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_gb_8whatshap_4core_7ReadSet_10generator1(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value) /* generator body */
{
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *__pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)__pyx_generator->closure);
  PyObject *__pyx_r = NULL;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__", 0);
  switch (__pyx_generator->resume_label) {
    case 0: goto __pyx_L3_first_run;
    case 1: goto __pyx_L6_resume_from_yield;
    default: /* CPython raises the right error here */
    __Pyx_RefNannyFinishContext();
    return NULL;
  }
  __pyx_L3_first_run:;
  if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 232, __pyx_L1_error)

  /* "whatshap/core.pyx":233
 * 
 * 	def __iter__(self):
 * 		for i in range(self.thisptr.size()):             # <<<<<<<<<<<<<<
 * 			yield self[i]
 * 
 */
  try {
    __pyx_t_1 = __pyx_cur_scope->__pyx_v_self->thisptr->size();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 233, __pyx_L1_error)
  }
  __pyx_t_2 = __pyx_t_1;
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_cur_scope->__pyx_v_i = __pyx_t_3;

    /* "whatshap/core.pyx":234
 * 	def __iter__(self):
 * 		for i in range(self.thisptr.size()):
 * 			yield self[i]             # <<<<<<<<<<<<<<
 * 
 * 	def __len__(self):
 */
    __pyx_t_4 = __Pyx_GetItemInt(((PyObject *)__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_i, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 234, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_r = __pyx_t_4;
    __pyx_t_4 = 0;
    __pyx_cur_scope->__pyx_t_0 = __pyx_t_1;
    __pyx_cur_scope->__pyx_t_1 = __pyx_t_2;
    __pyx_cur_scope->__pyx_t_2 = __pyx_t_3;
    __Pyx_XGIVEREF(__pyx_r);
    __Pyx_RefNannyFinishContext();
    __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
    /* return from generator, yielding value */
    __pyx_generator->resume_label = 1;
    return __pyx_r;
    __pyx_L6_resume_from_yield:;
    __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
    __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
    __pyx_t_3 = __pyx_cur_scope->__pyx_t_2;
    if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 234, __pyx_L1_error)
  }
  CYTHON_MAYBE_UNUSED_VAR(__pyx_cur_scope);

  /* "whatshap/core.pyx":232
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for i in range(self.thisptr.size()):
 * 			yield self[i]
 */

  /* function exit code */
  PyErr_SetNone(PyExc_StopIteration);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_r); __pyx_r = 0;
  #if !CYTHON_USE_EXC_INFO_STACK
  __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
  #endif
  __pyx_generator->resume_label = -1;
  __Pyx_Coroutine_clear((PyObject*)__pyx_generator);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":236
 * 			yield self[i]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

/* Python wrapper */
static Py_ssize_t __pyx_pw_8whatshap_4core_7ReadSet_12__len__(PyObject *__pyx_v_self); /*proto*/
static Py_ssize_t __pyx_pw_8whatshap_4core_7ReadSet_12__len__(PyObject *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_11__len__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_ssize_t __pyx_pf_8whatshap_4core_7ReadSet_11__len__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__len__", 0);

  /* "whatshap/core.pyx":237
 * 
 * 	def __len__(self):
 * 		return self.thisptr.size()             # <<<<<<<<<<<<<<
 * 
 * 	def __getitem__(self, key):
 */
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->size();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 237, __pyx_L1_error)
  }
  __pyx_r = __pyx_t_1;
  goto __pyx_L0;

  /* "whatshap/core.pyx":236
 * 			yield self[i]
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.ReadSet.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":239
 * 		return self.thisptr.size()
 * 
 * 	def __getitem__(self, key):             # <<<<<<<<<<<<<<
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError('ReadSet does not support slices')
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_14__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_14__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_13__getitem__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self), ((PyObject *)__pyx_v_key));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_13__getitem__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_key) {
  std::string __pyx_v_name;
  Read *__pyx_v_cread;
  struct __pyx_obj_8whatshap_4core_Read *__pyx_v_read = 0;
  PyObject *__pyx_v_source_id = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  std::string __pyx_t_4;
  int __pyx_t_5;
  Read *__pyx_t_6;
  int __pyx_t_7;
  Py_ssize_t __pyx_t_8;
  PyObject *__pyx_t_9 = NULL;
  PyObject *__pyx_t_10 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getitem__", 0);

  /* "whatshap/core.pyx":240
 * 
 * 	def __getitem__(self, key):
 * 		if isinstance(key, slice):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError('ReadSet does not support slices')
 * 		cdef string name = b''
 */
  __pyx_t_1 = PySlice_Check(__pyx_v_key); 
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (unlikely(__pyx_t_2)) {

    /* "whatshap/core.pyx":241
 * 	def __getitem__(self, key):
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError('ReadSet does not support slices')             # <<<<<<<<<<<<<<
 * 		cdef string name = b''
 * 		cdef cpp.Read* cread = NULL
 */
    __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 241, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_Raise(__pyx_t_3, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __PYX_ERR(1, 241, __pyx_L1_error)

    /* "whatshap/core.pyx":240
 * 
 * 	def __getitem__(self, key):
 * 		if isinstance(key, slice):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError('ReadSet does not support slices')
 * 		cdef string name = b''
 */
  }

  /* "whatshap/core.pyx":242
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError('ReadSet does not support slices')
 * 		cdef string name = b''             # <<<<<<<<<<<<<<
 * 		cdef cpp.Read* cread = NULL
 * 		cdef Read read = Read()
 */
  __pyx_t_4 = __pyx_convert_string_from_py_std__in_string(__pyx_kp_b__3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 242, __pyx_L1_error)
  __pyx_v_name = __pyx_t_4;

  /* "whatshap/core.pyx":243
 * 			raise NotImplementedError('ReadSet does not support slices')
 * 		cdef string name = b''
 * 		cdef cpp.Read* cread = NULL             # <<<<<<<<<<<<<<
 * 		cdef Read read = Read()
 * 		if isinstance(key, int):
 */
  __pyx_v_cread = NULL;

  /* "whatshap/core.pyx":244
 * 		cdef string name = b''
 * 		cdef cpp.Read* cread = NULL
 * 		cdef Read read = Read()             # <<<<<<<<<<<<<<
 * 		if isinstance(key, int):
 * 			read.thisptr = self.thisptr.get(key)
 */
  __pyx_t_3 = __Pyx_PyObject_CallNoArg(((PyObject *)__pyx_ptype_8whatshap_4core_Read)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 244, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_v_read = ((struct __pyx_obj_8whatshap_4core_Read *)__pyx_t_3);
  __pyx_t_3 = 0;

  /* "whatshap/core.pyx":245
 * 		cdef cpp.Read* cread = NULL
 * 		cdef Read read = Read()
 * 		if isinstance(key, int):             # <<<<<<<<<<<<<<
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):
 */
  __pyx_t_2 = PyInt_Check(__pyx_v_key); 
  __pyx_t_1 = (__pyx_t_2 != 0);
  if (__pyx_t_1) {

    /* "whatshap/core.pyx":246
 * 		cdef Read read = Read()
 * 		if isinstance(key, int):
 * 			read.thisptr = self.thisptr.get(key)             # <<<<<<<<<<<<<<
 * 		elif isinstance(key, str):
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 */
    __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_v_key); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 246, __pyx_L1_error)
    try {
      __pyx_t_6 = __pyx_v_self->thisptr->get(__pyx_t_5);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 246, __pyx_L1_error)
    }
    __pyx_v_read->thisptr = __pyx_t_6;

    /* "whatshap/core.pyx":245
 * 		cdef cpp.Read* cread = NULL
 * 		cdef Read read = Read()
 * 		if isinstance(key, int):             # <<<<<<<<<<<<<<
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):
 */
    goto __pyx_L4;
  }

  /* "whatshap/core.pyx":247
 * 		if isinstance(key, int):
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 */
  __pyx_t_1 = PyUnicode_Check(__pyx_v_key); 
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (unlikely(__pyx_t_2)) {

    /* "whatshap/core.pyx":248
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')             # <<<<<<<<<<<<<<
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 * 			source_id = key[0]
 */
    __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 248, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_Raise(__pyx_t_3, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __PYX_ERR(1, 248, __pyx_L1_error)

    /* "whatshap/core.pyx":247
 * 		if isinstance(key, int):
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):             # <<<<<<<<<<<<<<
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 */
  }

  /* "whatshap/core.pyx":249
 * 		elif isinstance(key, str):
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):             # <<<<<<<<<<<<<<
 * 			source_id = key[0]
 * 			name = key[1].encode('UTF-8')
 */
  __pyx_t_1 = PyTuple_Check(__pyx_v_key); 
  __pyx_t_7 = (__pyx_t_1 != 0);
  if (__pyx_t_7) {
  } else {
    __pyx_t_2 = __pyx_t_7;
    goto __pyx_L5_bool_binop_done;
  }
  __pyx_t_8 = PyObject_Length(__pyx_v_key); if (unlikely(__pyx_t_8 == ((Py_ssize_t)-1))) __PYX_ERR(1, 249, __pyx_L1_error)
  __pyx_t_7 = ((__pyx_t_8 == 2) != 0);
  if (__pyx_t_7) {
  } else {
    __pyx_t_2 = __pyx_t_7;
    goto __pyx_L5_bool_binop_done;
  }
  __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_key, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 249, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_7 = PyInt_Check(__pyx_t_3); 
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_1 = (__pyx_t_7 != 0);
  if (__pyx_t_1) {
  } else {
    __pyx_t_2 = __pyx_t_1;
    goto __pyx_L5_bool_binop_done;
  }
  __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_key, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 249, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_1 = PyUnicode_Check(__pyx_t_3); 
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_7 = (__pyx_t_1 != 0);
  __pyx_t_2 = __pyx_t_7;
  __pyx_L5_bool_binop_done:;
  if (__pyx_t_2) {

    /* "whatshap/core.pyx":250
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 * 			source_id = key[0]             # <<<<<<<<<<<<<<
 * 			name = key[1].encode('UTF-8')
 * 			cread = self.thisptr.getByName(name, source_id)
 */
    __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_key, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 250, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_v_source_id = __pyx_t_3;
    __pyx_t_3 = 0;

    /* "whatshap/core.pyx":251
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 * 			source_id = key[0]
 * 			name = key[1].encode('UTF-8')             # <<<<<<<<<<<<<<
 * 			cread = self.thisptr.getByName(name, source_id)
 * 			if cread == NULL:
 */
    __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_key, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 251, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_9);
    __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_encode); if (unlikely(!__pyx_t_10)) __PYX_ERR(1, 251, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_10);
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    __pyx_t_9 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_10))) {
      __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_10);
      if (likely(__pyx_t_9)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
        __Pyx_INCREF(__pyx_t_9);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_10, function);
      }
    }
    __pyx_t_3 = (__pyx_t_9) ? __Pyx_PyObject_Call2Args(__pyx_t_10, __pyx_t_9, __pyx_kp_u_UTF_8) : __Pyx_PyObject_CallOneArg(__pyx_t_10, __pyx_kp_u_UTF_8);
    __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
    if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 251, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
    __pyx_t_4 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 251, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_v_name = __pyx_t_4;

    /* "whatshap/core.pyx":252
 * 			source_id = key[0]
 * 			name = key[1].encode('UTF-8')
 * 			cread = self.thisptr.getByName(name, source_id)             # <<<<<<<<<<<<<<
 * 			if cread == NULL:
 * 				raise KeyError(key)
 */
    __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_v_source_id); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 252, __pyx_L1_error)
    try {
      __pyx_t_6 = __pyx_v_self->thisptr->getByName(__pyx_v_name, __pyx_t_5);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 252, __pyx_L1_error)
    }
    __pyx_v_cread = __pyx_t_6;

    /* "whatshap/core.pyx":253
 * 			name = key[1].encode('UTF-8')
 * 			cread = self.thisptr.getByName(name, source_id)
 * 			if cread == NULL:             # <<<<<<<<<<<<<<
 * 				raise KeyError(key)
 * 			else:
 */
    __pyx_t_2 = ((__pyx_v_cread == NULL) != 0);
    if (unlikely(__pyx_t_2)) {

      /* "whatshap/core.pyx":254
 * 			cread = self.thisptr.getByName(name, source_id)
 * 			if cread == NULL:
 * 				raise KeyError(key)             # <<<<<<<<<<<<<<
 * 			else:
 * 				read.thisptr = cread
 */
      __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_KeyError, __pyx_v_key); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 254, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_Raise(__pyx_t_3, 0, 0, 0);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __PYX_ERR(1, 254, __pyx_L1_error)

      /* "whatshap/core.pyx":253
 * 			name = key[1].encode('UTF-8')
 * 			cread = self.thisptr.getByName(name, source_id)
 * 			if cread == NULL:             # <<<<<<<<<<<<<<
 * 				raise KeyError(key)
 * 			else:
 */
    }

    /* "whatshap/core.pyx":256
 * 				raise KeyError(key)
 * 			else:
 * 				read.thisptr = cread             # <<<<<<<<<<<<<<
 * 		else:
 * 			assert False, 'Invalid key: {}'.format(key)
 */
    /*else*/ {
      __pyx_v_read->thisptr = __pyx_v_cread;
    }

    /* "whatshap/core.pyx":249
 * 		elif isinstance(key, str):
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):             # <<<<<<<<<<<<<<
 * 			source_id = key[0]
 * 			name = key[1].encode('UTF-8')
 */
    goto __pyx_L4;
  }

  /* "whatshap/core.pyx":258
 * 				read.thisptr = cread
 * 		else:
 * 			assert False, 'Invalid key: {}'.format(key)             # <<<<<<<<<<<<<<
 * 		return read
 * 
 */
  /*else*/ {
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!Py_OptimizeFlag)) {
      if (unlikely(!0)) {
        __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Invalid_key, __pyx_n_s_format); if (unlikely(!__pyx_t_10)) __PYX_ERR(1, 258, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_10);
        __pyx_t_9 = NULL;
        if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_10))) {
          __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_10);
          if (likely(__pyx_t_9)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
            __Pyx_INCREF(__pyx_t_9);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_10, function);
          }
        }
        __pyx_t_3 = (__pyx_t_9) ? __Pyx_PyObject_Call2Args(__pyx_t_10, __pyx_t_9, __pyx_v_key) : __Pyx_PyObject_CallOneArg(__pyx_t_10, __pyx_v_key);
        __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
        if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 258, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
        __pyx_t_10 = PyTuple_Pack(1, __pyx_t_3); if (unlikely(!__pyx_t_10)) __PYX_ERR(1, 258, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_10);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        PyErr_SetObject(PyExc_AssertionError, __pyx_t_10);
        __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
        __PYX_ERR(1, 258, __pyx_L1_error)
      }
    }
    #endif
  }
  __pyx_L4:;

  /* "whatshap/core.pyx":259
 * 		else:
 * 			assert False, 'Invalid key: {}'.format(key)
 * 		return read             # <<<<<<<<<<<<<<
 * 
 * 	def __getstate__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(((PyObject *)__pyx_v_read));
  __pyx_r = ((PyObject *)__pyx_v_read);
  goto __pyx_L0;

  /* "whatshap/core.pyx":239
 * 		return self.thisptr.size()
 * 
 * 	def __getitem__(self, key):             # <<<<<<<<<<<<<<
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError('ReadSet does not support slices')
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF((PyObject *)__pyx_v_read);
  __Pyx_XDECREF(__pyx_v_source_id);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":261
 * 		return read
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return ([read for read in self])
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_16__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_16__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_15__getstate__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_15__getstate__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  PyObject *__pyx_8genexpr3__pyx_v_read = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  PyObject *(*__pyx_t_4)(PyObject *);
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getstate__", 0);

  /* "whatshap/core.pyx":262
 * 
 * 	def __getstate__(self):
 * 		return ([read for read in self])             # <<<<<<<<<<<<<<
 * 
 * 	def __setstate__(self, state):
 */
  __Pyx_XDECREF(__pyx_r);
  { /* enter inner scope */
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 262, __pyx_L5_error)
    __Pyx_GOTREF(__pyx_t_1);
    if (likely(PyList_CheckExact(((PyObject *)__pyx_v_self))) || PyTuple_CheckExact(((PyObject *)__pyx_v_self))) {
      __pyx_t_2 = ((PyObject *)__pyx_v_self); __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
      __pyx_t_4 = NULL;
    } else {
      __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 262, __pyx_L5_error)
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 262, __pyx_L5_error)
    }
    for (;;) {
      if (likely(!__pyx_t_4)) {
        if (likely(PyList_CheckExact(__pyx_t_2))) {
          if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 262, __pyx_L5_error)
          #else
          __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 262, __pyx_L5_error)
          __Pyx_GOTREF(__pyx_t_5);
          #endif
        } else {
          if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 262, __pyx_L5_error)
          #else
          __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 262, __pyx_L5_error)
          __Pyx_GOTREF(__pyx_t_5);
          #endif
        }
      } else {
        __pyx_t_5 = __pyx_t_4(__pyx_t_2);
        if (unlikely(!__pyx_t_5)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 262, __pyx_L5_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_5);
      }
      __Pyx_XDECREF_SET(__pyx_8genexpr3__pyx_v_read, __pyx_t_5);
      __pyx_t_5 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_8genexpr3__pyx_v_read))) __PYX_ERR(1, 262, __pyx_L5_error)
    }
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_read); __pyx_8genexpr3__pyx_v_read = 0;
    goto __pyx_L8_exit_scope;
    __pyx_L5_error:;
    __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_read); __pyx_8genexpr3__pyx_v_read = 0;
    goto __pyx_L1_error;
    __pyx_L8_exit_scope:;
  } /* exit inner scope */
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":261
 * 		return read
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return ([read for read in self])
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__getstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_8genexpr3__pyx_v_read);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":264
 * 		return ([read for read in self])
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.ReadSet()
 * 		for read in state:
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_18__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_18__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_17__setstate__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self), ((PyObject *)__pyx_v_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_17__setstate__(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_v_read = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  ReadSet *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  PyObject *(*__pyx_t_4)(PyObject *);
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate__", 0);

  /* "whatshap/core.pyx":265
 * 
 * 	def __setstate__(self, state):
 * 		self.thisptr = new cpp.ReadSet()             # <<<<<<<<<<<<<<
 * 		for read in state:
 * 			self.add(read)
 */
  try {
    __pyx_t_1 = new ReadSet();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 265, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_1;

  /* "whatshap/core.pyx":266
 * 	def __setstate__(self, state):
 * 		self.thisptr = new cpp.ReadSet()
 * 		for read in state:             # <<<<<<<<<<<<<<
 * 			self.add(read)
 * 
 */
  if (likely(PyList_CheckExact(__pyx_v_state)) || PyTuple_CheckExact(__pyx_v_state)) {
    __pyx_t_2 = __pyx_v_state; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
  } else {
    __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_state); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 266, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 266, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_4)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 266, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 266, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      } else {
        if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 266, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 266, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      }
    } else {
      __pyx_t_5 = __pyx_t_4(__pyx_t_2);
      if (unlikely(!__pyx_t_5)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 266, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_5);
    }
    __Pyx_XDECREF_SET(__pyx_v_read, __pyx_t_5);
    __pyx_t_5 = 0;

    /* "whatshap/core.pyx":267
 * 		self.thisptr = new cpp.ReadSet()
 * 		for read in state:
 * 			self.add(read)             # <<<<<<<<<<<<<<
 * 
 * 	#def get_by_name(self, name):
 */
    __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_add); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 267, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_7 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_6))) {
      __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
      if (likely(__pyx_t_7)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
        __Pyx_INCREF(__pyx_t_7);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_6, function);
      }
    }
    __pyx_t_5 = (__pyx_t_7) ? __Pyx_PyObject_Call2Args(__pyx_t_6, __pyx_t_7, __pyx_v_read) : __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_v_read);
    __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
    if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 267, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;

    /* "whatshap/core.pyx":266
 * 	def __setstate__(self, state):
 * 		self.thisptr = new cpp.ReadSet()
 * 		for read in state:             # <<<<<<<<<<<<<<
 * 			self.add(read)
 * 
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "whatshap/core.pyx":264
 * 		return ([read for read in self])
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.ReadSet()
 * 		for read in state:
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__setstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_read);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":279
 * 			#return read
 * 
 * 	def sort(self):             # <<<<<<<<<<<<<<
 * 		"""Sort contained reads by the position of the first variant they contain. Note that
 * 		this is not necessarily the variant with the lowest position, unless sort() has been
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_20sort(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_7ReadSet_19sort[] = "Sort contained reads by the position of the first variant they contain. Note that\n\t\tthis is not necessarily the variant with the lowest position, unless sort() has been\n\t\tcalled on all contained reads. Ties are resolved by comparing the read name.";
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_20sort(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("sort (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_19sort(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_19sort(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("sort", 0);

  /* "whatshap/core.pyx":283
 * 		this is not necessarily the variant with the lowest position, unless sort() has been
 * 		called on all contained reads. Ties are resolved by comparing the read name."""
 * 		self.thisptr.sort()             # <<<<<<<<<<<<<<
 * 
 * 	def subset(self, reads_to_select):
 */
  try {
    __pyx_v_self->thisptr->sort();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 283, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":279
 * 			#return read
 * 
 * 	def sort(self):             # <<<<<<<<<<<<<<
 * 		"""Sort contained reads by the position of the first variant they contain. Note that
 * 		this is not necessarily the variant with the lowest position, unless sort() has been
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.ReadSet.sort", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":285
 * 		self.thisptr.sort()
 * 
 * 	def subset(self, reads_to_select):             # <<<<<<<<<<<<<<
 * 		# TODO: is there a way of avoiding to unecessarily creating/destroying a ReadSet object?
 * 		cdef cpp.IndexSet* index_set = new cpp.IndexSet()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_22subset(PyObject *__pyx_v_self, PyObject *__pyx_v_reads_to_select); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_22subset(PyObject *__pyx_v_self, PyObject *__pyx_v_reads_to_select) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("subset (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_21subset(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self), ((PyObject *)__pyx_v_reads_to_select));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_21subset(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, PyObject *__pyx_v_reads_to_select) {
  IndexSet *__pyx_v_index_set;
  int __pyx_v_i;
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_result = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  IndexSet *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  PyObject *(*__pyx_t_4)(PyObject *);
  PyObject *__pyx_t_5 = NULL;
  int __pyx_t_6;
  ReadSet *__pyx_t_7;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("subset", 0);

  /* "whatshap/core.pyx":287
 * 	def subset(self, reads_to_select):
 * 		# TODO: is there a way of avoiding to unecessarily creating/destroying a ReadSet object?
 * 		cdef cpp.IndexSet* index_set = new cpp.IndexSet()             # <<<<<<<<<<<<<<
 * 		cdef int i
 * 		for i in reads_to_select:
 */
  try {
    __pyx_t_1 = new IndexSet();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 287, __pyx_L1_error)
  }
  __pyx_v_index_set = __pyx_t_1;

  /* "whatshap/core.pyx":289
 * 		cdef cpp.IndexSet* index_set = new cpp.IndexSet()
 * 		cdef int i
 * 		for i in reads_to_select:             # <<<<<<<<<<<<<<
 * 			index_set.add(i)
 * 		result = ReadSet()
 */
  if (likely(PyList_CheckExact(__pyx_v_reads_to_select)) || PyTuple_CheckExact(__pyx_v_reads_to_select)) {
    __pyx_t_2 = __pyx_v_reads_to_select; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
  } else {
    __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_reads_to_select); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 289, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 289, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_4)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 289, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 289, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      } else {
        if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(1, 289, __pyx_L1_error)
        #else
        __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 289, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_5);
        #endif
      }
    } else {
      __pyx_t_5 = __pyx_t_4(__pyx_t_2);
      if (unlikely(!__pyx_t_5)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 289, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_5);
    }
    __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 289, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_v_i = __pyx_t_6;

    /* "whatshap/core.pyx":290
 * 		cdef int i
 * 		for i in reads_to_select:
 * 			index_set.add(i)             # <<<<<<<<<<<<<<
 * 		result = ReadSet()
 * 		del result.thisptr
 */
    try {
      __pyx_v_index_set->add(__pyx_v_i);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 290, __pyx_L1_error)
    }

    /* "whatshap/core.pyx":289
 * 		cdef cpp.IndexSet* index_set = new cpp.IndexSet()
 * 		cdef int i
 * 		for i in reads_to_select:             # <<<<<<<<<<<<<<
 * 			index_set.add(i)
 * 		result = ReadSet()
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "whatshap/core.pyx":291
 * 		for i in reads_to_select:
 * 			index_set.add(i)
 * 		result = ReadSet()             # <<<<<<<<<<<<<<
 * 		del result.thisptr
 * 		result.thisptr = self.thisptr.subset(index_set)
 */
  __pyx_t_2 = __Pyx_PyObject_CallNoArg(((PyObject *)__pyx_ptype_8whatshap_4core_ReadSet)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 291, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_v_result = ((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":292
 * 			index_set.add(i)
 * 		result = ReadSet()
 * 		del result.thisptr             # <<<<<<<<<<<<<<
 * 		result.thisptr = self.thisptr.subset(index_set)
 * 		del index_set
 */
  delete __pyx_v_result->thisptr;

  /* "whatshap/core.pyx":293
 * 		result = ReadSet()
 * 		del result.thisptr
 * 		result.thisptr = self.thisptr.subset(index_set)             # <<<<<<<<<<<<<<
 * 		del index_set
 * 		return result
 */
  try {
    __pyx_t_7 = __pyx_v_self->thisptr->subset(__pyx_v_index_set);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 293, __pyx_L1_error)
  }
  __pyx_v_result->thisptr = __pyx_t_7;

  /* "whatshap/core.pyx":294
 * 		del result.thisptr
 * 		result.thisptr = self.thisptr.subset(index_set)
 * 		del index_set             # <<<<<<<<<<<<<<
 * 		return result
 * 
 */
  delete __pyx_v_index_set;

  /* "whatshap/core.pyx":295
 * 		result.thisptr = self.thisptr.subset(index_set)
 * 		del index_set
 * 		return result             # <<<<<<<<<<<<<<
 * 
 * 	def get_positions(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(((PyObject *)__pyx_v_result));
  __pyx_r = ((PyObject *)__pyx_v_result);
  goto __pyx_L0;

  /* "whatshap/core.pyx":285
 * 		self.thisptr.sort()
 * 
 * 	def subset(self, reads_to_select):             # <<<<<<<<<<<<<<
 * 		# TODO: is there a way of avoiding to unecessarily creating/destroying a ReadSet object?
 * 		cdef cpp.IndexSet* index_set = new cpp.IndexSet()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("whatshap.core.ReadSet.subset", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF((PyObject *)__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":297
 * 		return result
 * 
 * 	def get_positions(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[unsigned int]* v = self.thisptr.get_positions()
 * 		result = list(v[0])
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_24get_positions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_24get_positions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_positions (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_23get_positions(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_23get_positions(struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  std::vector<unsigned int>  *__pyx_v_v;
  PyObject *__pyx_v_result = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_positions", 0);

  /* "whatshap/core.pyx":298
 * 
 * 	def get_positions(self):
 * 		cdef vector[unsigned int]* v = self.thisptr.get_positions()             # <<<<<<<<<<<<<<
 * 		result = list(v[0])
 * 		del v
 */
  __pyx_v_v = __pyx_v_self->thisptr->get_positions();

  /* "whatshap/core.pyx":299
 * 	def get_positions(self):
 * 		cdef vector[unsigned int]* v = self.thisptr.get_positions()
 * 		result = list(v[0])             # <<<<<<<<<<<<<<
 * 		del v
 * 		return result
 */
  __pyx_t_1 = __pyx_convert_vector_to_py_unsigned_int((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 299, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = PySequence_List(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 299, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_result = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":300
 * 		cdef vector[unsigned int]* v = self.thisptr.get_positions()
 * 		result = list(v[0])
 * 		del v             # <<<<<<<<<<<<<<
 * 		return result
 * 
 */
  delete __pyx_v_v;

  /* "whatshap/core.pyx":301
 * 		result = list(v[0])
 * 		del v
 * 		return result             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_result);
  __pyx_r = __pyx_v_result;
  goto __pyx_L0;

  /* "whatshap/core.pyx":297
 * 		return result
 * 
 * 	def get_positions(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[unsigned int]* v = self.thisptr.get_positions()
 * 		result = list(v[0])
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.ReadSet.get_positions", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_26__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_26__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_25__reduce_cython__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_25__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_28__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_7ReadSet_28__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_7ReadSet_27__setstate_cython__(((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_7ReadSet_27__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.ReadSet.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":305
 * 
 * cdef class PedigreeDPTable:
 * 	def __cinit__(self, ReadSet readset, recombcost, Pedigree pedigree, bool distrust_genotypes = False, positions = None):             # <<<<<<<<<<<<<<
 * 		"""Build the DP table from the given read set which is assumed to be sorted;
 * 		that is, the variants in each read must be sorted by position and the reads
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_15PedigreeDPTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_15PedigreeDPTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset = 0;
  PyObject *__pyx_v_recombcost = 0;
  struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree = 0;
  bool __pyx_v_distrust_genotypes;
  PyObject *__pyx_v_positions = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_readset,&__pyx_n_s_recombcost,&__pyx_n_s_pedigree,&__pyx_n_s_distrust_genotypes,&__pyx_n_s_positions,0};
    PyObject* values[5] = {0,0,0,0,0};
    values[4] = ((PyObject *)Py_None);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        CYTHON_FALLTHROUGH;
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_readset)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_recombcost)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 1); __PYX_ERR(1, 305, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pedigree)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, 2); __PYX_ERR(1, 305, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  3:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_distrust_genotypes);
          if (value) { values[3] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  4:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_positions);
          if (value) { values[4] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 305, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        CYTHON_FALLTHROUGH;
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_readset = ((struct __pyx_obj_8whatshap_4core_ReadSet *)values[0]);
    __pyx_v_recombcost = values[1];
    __pyx_v_pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)values[2]);
    if (values[3]) {
      __pyx_v_distrust_genotypes = __Pyx_PyObject_IsTrue(values[3]); if (unlikely((__pyx_v_distrust_genotypes == ((bool)-1)) && PyErr_Occurred())) __PYX_ERR(1, 305, __pyx_L3_error)
    } else {
      __pyx_v_distrust_genotypes = ((bool)0);
    }
    __pyx_v_positions = values[4];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 305, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_readset), __pyx_ptype_8whatshap_4core_ReadSet, 1, "readset", 0))) __PYX_ERR(1, 305, __pyx_L1_error)
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_pedigree), __pyx_ptype_8whatshap_4core_Pedigree, 1, "pedigree", 0))) __PYX_ERR(1, 305, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable___cinit__(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self), __pyx_v_readset, __pyx_v_recombcost, __pyx_v_pedigree, __pyx_v_distrust_genotypes, __pyx_v_positions);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_15PedigreeDPTable___cinit__(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_recombcost, struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree, bool __pyx_v_distrust_genotypes, PyObject *__pyx_v_positions) {
  std::vector<unsigned int>  *__pyx_v_c_positions;
  PyObject *__pyx_v_pos = NULL;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  std::vector<unsigned int>  *__pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  Py_ssize_t __pyx_t_5;
  PyObject *(*__pyx_t_6)(PyObject *);
  PyObject *__pyx_t_7 = NULL;
  unsigned int __pyx_t_8;
  std::vector<unsigned int>  __pyx_t_9;
  PedigreeDPTable *__pyx_t_10;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":310
 * 		in the read set must also be sorted (by position of their left-most variant).
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL             # <<<<<<<<<<<<<<
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 */
  __pyx_v_c_positions = NULL;

  /* "whatshap/core.pyx":311
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:             # <<<<<<<<<<<<<<
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 */
  __pyx_t_1 = (__pyx_v_positions != Py_None);
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (__pyx_t_2) {

    /* "whatshap/core.pyx":312
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()             # <<<<<<<<<<<<<<
 * 			for pos in positions:
 * 				c_positions.push_back(pos)
 */
    try {
      __pyx_t_3 = new std::vector<unsigned int> ();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 312, __pyx_L1_error)
    }
    __pyx_v_c_positions = __pyx_t_3;

    /* "whatshap/core.pyx":313
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:             # <<<<<<<<<<<<<<
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.PedigreeDPTable(readset.thisptr, recombcost, pedigree.thisptr, distrust_genotypes, c_positions)
 */
    if (likely(PyList_CheckExact(__pyx_v_positions)) || PyTuple_CheckExact(__pyx_v_positions)) {
      __pyx_t_4 = __pyx_v_positions; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
      __pyx_t_6 = NULL;
    } else {
      __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_positions); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 313, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext; if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 313, __pyx_L1_error)
    }
    for (;;) {
      if (likely(!__pyx_t_6)) {
        if (likely(PyList_CheckExact(__pyx_t_4))) {
          if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(1, 313, __pyx_L1_error)
          #else
          __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 313, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          #endif
        } else {
          if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(1, 313, __pyx_L1_error)
          #else
          __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 313, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          #endif
        }
      } else {
        __pyx_t_7 = __pyx_t_6(__pyx_t_4);
        if (unlikely(!__pyx_t_7)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 313, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_7);
      }
      __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_7);
      __pyx_t_7 = 0;

      /* "whatshap/core.pyx":314
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 * 				c_positions.push_back(pos)             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.PedigreeDPTable(readset.thisptr, recombcost, pedigree.thisptr, distrust_genotypes, c_positions)
 * 		self.pedigree = pedigree
 */
      __pyx_t_8 = __Pyx_PyInt_As_unsigned_int(__pyx_v_pos); if (unlikely((__pyx_t_8 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 314, __pyx_L1_error)
      try {
        __pyx_v_c_positions->push_back(__pyx_t_8);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 314, __pyx_L1_error)
      }

      /* "whatshap/core.pyx":313
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:             # <<<<<<<<<<<<<<
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.PedigreeDPTable(readset.thisptr, recombcost, pedigree.thisptr, distrust_genotypes, c_positions)
 */
    }
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

    /* "whatshap/core.pyx":311
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:             # <<<<<<<<<<<<<<
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 */
  }

  /* "whatshap/core.pyx":315
 * 			for pos in positions:
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.PedigreeDPTable(readset.thisptr, recombcost, pedigree.thisptr, distrust_genotypes, c_positions)             # <<<<<<<<<<<<<<
 * 		self.pedigree = pedigree
 * 
 */
  __pyx_t_9 = __pyx_convert_vector_from_py_unsigned_int(__pyx_v_recombcost); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 315, __pyx_L1_error)
  try {
    __pyx_t_10 = new PedigreeDPTable(__pyx_v_readset->thisptr, __pyx_t_9, __pyx_v_pedigree->thisptr, __pyx_v_distrust_genotypes, __pyx_v_c_positions);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 315, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_10;

  /* "whatshap/core.pyx":316
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.PedigreeDPTable(readset.thisptr, recombcost, pedigree.thisptr, distrust_genotypes, c_positions)
 * 		self.pedigree = pedigree             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  __Pyx_INCREF(((PyObject *)__pyx_v_pedigree));
  __Pyx_GIVEREF(((PyObject *)__pyx_v_pedigree));
  __Pyx_GOTREF(__pyx_v_self->pedigree);
  __Pyx_DECREF(((PyObject *)__pyx_v_self->pedigree));
  __pyx_v_self->pedigree = __pyx_v_pedigree;

  /* "whatshap/core.pyx":305
 * 
 * cdef class PedigreeDPTable:
 * 	def __cinit__(self, ReadSet readset, recombcost, Pedigree pedigree, bool distrust_genotypes = False, positions = None):             # <<<<<<<<<<<<<<
 * 		"""Build the DP table from the given read set which is assumed to be sorted;
 * 		that is, the variants in each read must be sorted by position and the reads
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_pos);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":318
 * 		self.pedigree = pedigree
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_15PedigreeDPTable_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_15PedigreeDPTable_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_15PedigreeDPTable_2__dealloc__(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_15PedigreeDPTable_2__dealloc__(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":319
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def get_super_reads(self):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":318
 * 		self.pedigree = pedigree
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":321
 * 		del self.thisptr
 * 
 * 	def get_super_reads(self):             # <<<<<<<<<<<<<<
 * 		"""Obtain optimal-score haplotypes. Returns a triple (mother, father, child)
 * 		IMPORTANT: The ReadSet given at construction time must not have been altered.
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_5get_super_reads(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_15PedigreeDPTable_4get_super_reads[] = "Obtain optimal-score haplotypes. Returns a triple (mother, father, child)\n\t\tIMPORTANT: The ReadSet given at construction time must not have been altered.\n\t\tDPTable retained a pointer to this set and will access it again. If it has\n\t\tbeen altered, behavior is undefined.\n\t\tTODO: Change that.\n\t\t";
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_5get_super_reads(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_super_reads (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self) {
  std::vector<ReadSet *>  *__pyx_v_read_sets;
  std::vector<ReadSet *> ::size_type __pyx_v_i;
  std::vector<unsigned int>  *__pyx_v_transmission_vector_ptr;
  PyObject *__pyx_v_results = NULL;
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_rs = NULL;
  PyObject *__pyx_v_python_transmission_vector = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::vector<ReadSet *>  *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  Py_ssize_t __pyx_t_3;
  Py_ssize_t __pyx_t_4;
  std::vector<ReadSet *> ::size_type __pyx_t_5;
  ReadSet *__pyx_t_6;
  std::vector<unsigned int>  *__pyx_t_7;
  std::vector<ReadSet *> ::size_type __pyx_t_8;
  std::vector<ReadSet *> ::size_type __pyx_t_9;
  int __pyx_t_10;
  PyObject *__pyx_t_11 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_super_reads", 0);

  /* "whatshap/core.pyx":328
 * 		TODO: Change that.
 * 		"""
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()             # <<<<<<<<<<<<<<
 * 
 * 		for i in range(len(self.pedigree)):
 */
  try {
    __pyx_t_1 = new std::vector<ReadSet *> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 328, __pyx_L1_error)
  }
  __pyx_v_read_sets = __pyx_t_1;

  /* "whatshap/core.pyx":330
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 * 
 * 		for i in range(len(self.pedigree)):             # <<<<<<<<<<<<<<
 * 			read_sets.push_back(new cpp.ReadSet())
 * 		transmission_vector_ptr = new vector[unsigned int]()
 */
  __pyx_t_2 = ((PyObject *)__pyx_v_self->pedigree);
  __Pyx_INCREF(__pyx_t_2);
  __pyx_t_3 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 330, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_4 = __pyx_t_3;
  for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
    __pyx_v_i = __pyx_t_5;

    /* "whatshap/core.pyx":331
 * 
 * 		for i in range(len(self.pedigree)):
 * 			read_sets.push_back(new cpp.ReadSet())             # <<<<<<<<<<<<<<
 * 		transmission_vector_ptr = new vector[unsigned int]()
 * 		self.thisptr.get_super_reads(read_sets, transmission_vector_ptr)
 */
    try {
      __pyx_t_6 = new ReadSet();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 331, __pyx_L1_error)
    }
    try {
      __pyx_v_read_sets->push_back(__pyx_t_6);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 331, __pyx_L1_error)
    }
  }

  /* "whatshap/core.pyx":332
 * 		for i in range(len(self.pedigree)):
 * 			read_sets.push_back(new cpp.ReadSet())
 * 		transmission_vector_ptr = new vector[unsigned int]()             # <<<<<<<<<<<<<<
 * 		self.thisptr.get_super_reads(read_sets, transmission_vector_ptr)
 * 
 */
  try {
    __pyx_t_7 = new std::vector<unsigned int> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 332, __pyx_L1_error)
  }
  __pyx_v_transmission_vector_ptr = __pyx_t_7;

  /* "whatshap/core.pyx":333
 * 			read_sets.push_back(new cpp.ReadSet())
 * 		transmission_vector_ptr = new vector[unsigned int]()
 * 		self.thisptr.get_super_reads(read_sets, transmission_vector_ptr)             # <<<<<<<<<<<<<<
 * 
 * 		results = []
 */
  try {
    __pyx_v_self->thisptr->get_super_reads(__pyx_v_read_sets, __pyx_v_transmission_vector_ptr);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 333, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":335
 * 		self.thisptr.get_super_reads(read_sets, transmission_vector_ptr)
 * 
 * 		results = []             # <<<<<<<<<<<<<<
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()
 */
  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 335, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_v_results = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":336
 * 
 * 		results = []
 * 		for i in range(read_sets.size()):             # <<<<<<<<<<<<<<
 * 			rs = ReadSet()
 * 			del rs.thisptr
 */
  __pyx_t_5 = __pyx_v_read_sets->size();
  __pyx_t_8 = __pyx_t_5;
  for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
    __pyx_v_i = __pyx_t_9;

    /* "whatshap/core.pyx":337
 * 		results = []
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()             # <<<<<<<<<<<<<<
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]
 */
    __pyx_t_2 = __Pyx_PyObject_CallNoArg(((PyObject *)__pyx_ptype_8whatshap_4core_ReadSet)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 337, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_XDECREF_SET(__pyx_v_rs, ((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_t_2));
    __pyx_t_2 = 0;

    /* "whatshap/core.pyx":338
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()
 * 			del rs.thisptr             # <<<<<<<<<<<<<<
 * 			rs.thisptr = deref(read_sets)[i]
 * 			results.append(rs)
 */
    delete __pyx_v_rs->thisptr;

    /* "whatshap/core.pyx":339
 * 			rs = ReadSet()
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]             # <<<<<<<<<<<<<<
 * 			results.append(rs)
 * 
 */
    __pyx_v_rs->thisptr = ((*__pyx_v_read_sets)[__pyx_v_i]);

    /* "whatshap/core.pyx":340
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]
 * 			results.append(rs)             # <<<<<<<<<<<<<<
 * 
 * 		python_transmission_vector = list(transmission_vector_ptr[0])
 */
    __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_results, ((PyObject *)__pyx_v_rs)); if (unlikely(__pyx_t_10 == ((int)-1))) __PYX_ERR(1, 340, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":342
 * 			results.append(rs)
 * 
 * 		python_transmission_vector = list(transmission_vector_ptr[0])             # <<<<<<<<<<<<<<
 * 		del transmission_vector_ptr
 * 		return results, python_transmission_vector
 */
  __pyx_t_2 = __pyx_convert_vector_to_py_unsigned_int((__pyx_v_transmission_vector_ptr[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 342, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_11 = PySequence_List(__pyx_t_2); if (unlikely(!__pyx_t_11)) __PYX_ERR(1, 342, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_11);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_v_python_transmission_vector = ((PyObject*)__pyx_t_11);
  __pyx_t_11 = 0;

  /* "whatshap/core.pyx":343
 * 
 * 		python_transmission_vector = list(transmission_vector_ptr[0])
 * 		del transmission_vector_ptr             # <<<<<<<<<<<<<<
 * 		return results, python_transmission_vector
 * 
 */
  delete __pyx_v_transmission_vector_ptr;

  /* "whatshap/core.pyx":344
 * 		python_transmission_vector = list(transmission_vector_ptr[0])
 * 		del transmission_vector_ptr
 * 		return results, python_transmission_vector             # <<<<<<<<<<<<<<
 * 
 * 	def get_optimal_cost(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) __PYX_ERR(1, 344, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_11);
  __Pyx_INCREF(__pyx_v_results);
  __Pyx_GIVEREF(__pyx_v_results);
  PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_results);
  __Pyx_INCREF(__pyx_v_python_transmission_vector);
  __Pyx_GIVEREF(__pyx_v_python_transmission_vector);
  PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_v_python_transmission_vector);
  __pyx_r = __pyx_t_11;
  __pyx_t_11 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":321
 * 		del self.thisptr
 * 
 * 	def get_super_reads(self):             # <<<<<<<<<<<<<<
 * 		"""Obtain optimal-score haplotypes. Returns a triple (mother, father, child)
 * 		IMPORTANT: The ReadSet given at construction time must not have been altered.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_11);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.get_super_reads", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_results);
  __Pyx_XDECREF((PyObject *)__pyx_v_rs);
  __Pyx_XDECREF(__pyx_v_python_transmission_vector);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":346
 * 		return results, python_transmission_vector
 * 
 * 	def get_optimal_cost(self):             # <<<<<<<<<<<<<<
 * 		"""Returns the cost resulting from solving the Minimum Error Correction (MEC) problem."""
 * 		return self.thisptr.get_optimal_score()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_7get_optimal_cost(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_15PedigreeDPTable_6get_optimal_cost[] = "Returns the cost resulting from solving the Minimum Error Correction (MEC) problem.";
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_7get_optimal_cost(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_optimal_cost (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable_6get_optimal_cost(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_6get_optimal_cost(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_optimal_cost", 0);

  /* "whatshap/core.pyx":348
 * 	def get_optimal_cost(self):
 * 		"""Returns the cost resulting from solving the Minimum Error Correction (MEC) problem."""
 * 		return self.thisptr.get_optimal_score()             # <<<<<<<<<<<<<<
 * 
 * 	def get_optimal_partitioning(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_optimal_score();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 348, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 348, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":346
 * 		return results, python_transmission_vector
 * 
 * 	def get_optimal_cost(self):             # <<<<<<<<<<<<<<
 * 		"""Returns the cost resulting from solving the Minimum Error Correction (MEC) problem."""
 * 		return self.thisptr.get_optimal_score()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.get_optimal_cost", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":350
 * 		return self.thisptr.get_optimal_score()
 * 
 * 	def get_optimal_partitioning(self):             # <<<<<<<<<<<<<<
 * 		"""Returns a list of the same size as the read set, where each entry is either 0 or 1,
 * 		telling whether the corresponding read is in partition 0 or in partition 1,"""
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_9get_optimal_partitioning(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_8whatshap_4core_15PedigreeDPTable_8get_optimal_partitioning[] = "Returns a list of the same size as the read set, where each entry is either 0 or 1,\n\t\ttelling whether the corresponding read is in partition 0 or in partition 1,";
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_9get_optimal_partitioning(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_optimal_partitioning (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable_8get_optimal_partitioning(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_8get_optimal_partitioning(struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self) {
  std::vector<bool>  *__pyx_v_p;
  PyObject *__pyx_v_result = NULL;
  bool __pyx_8genexpr4__pyx_v_x;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  std::vector<bool> ::iterator __pyx_t_2;
  std::vector<bool>  *__pyx_t_3;
  bool __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_optimal_partitioning", 0);

  /* "whatshap/core.pyx":353
 * 		"""Returns a list of the same size as the read set, where each entry is either 0 or 1,
 * 		telling whether the corresponding read is in partition 0 or in partition 1,"""
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()             # <<<<<<<<<<<<<<
 * 		result = [0 if x else 1 for x in p[0]]
 * 		del p
 */
  __pyx_v_p = __pyx_v_self->thisptr->get_optimal_partitioning();

  /* "whatshap/core.pyx":354
 * 		telling whether the corresponding read is in partition 0 or in partition 1,"""
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = [0 if x else 1 for x in p[0]]             # <<<<<<<<<<<<<<
 * 		del p
 * 		return result
 */
  { /* enter inner scope */
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 354, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = &(__pyx_v_p[0]);
    __pyx_t_2 = __pyx_t_3->begin();
    for (;;) {
      if (!(__pyx_t_2 != __pyx_t_3->end())) break;
      __pyx_t_4 = *__pyx_t_2;
      ++__pyx_t_2;
      __pyx_8genexpr4__pyx_v_x = __pyx_t_4;
      if ((__pyx_8genexpr4__pyx_v_x != 0)) {
        __Pyx_INCREF(__pyx_int_0);
        __pyx_t_5 = __pyx_int_0;
      } else {
        __Pyx_INCREF(__pyx_int_1);
        __pyx_t_5 = __pyx_int_1;
      }
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(1, 354, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    }
  } /* exit inner scope */
  __pyx_v_result = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":355
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = [0 if x else 1 for x in p[0]]
 * 		del p             # <<<<<<<<<<<<<<
 * 		return result
 * 
 */
  delete __pyx_v_p;

  /* "whatshap/core.pyx":356
 * 		result = [0 if x else 1 for x in p[0]]
 * 		del p
 * 		return result             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_result);
  __pyx_r = __pyx_v_result;
  goto __pyx_L0;

  /* "whatshap/core.pyx":350
 * 		return self.thisptr.get_optimal_score()
 * 
 * 	def get_optimal_partitioning(self):             # <<<<<<<<<<<<<<
 * 		"""Returns a list of the same size as the read set, where each entry is either 0 or 1,
 * 		telling whether the corresponding read is in partition 0 or in partition 1,"""
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.get_optimal_partitioning", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_11__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_11__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable_10__reduce_cython__(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_13__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_15PedigreeDPTable_13__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15PedigreeDPTable_12__setstate_cython__(((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15PedigreeDPTable_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PedigreeDPTable *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.PedigreeDPTable.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":360
 * 
 * cdef class Pedigree:
 * 	def __cinit__(self, numeric_sample_ids):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.Pedigree()
 * 		self.numeric_sample_ids = numeric_sample_ids
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_8Pedigree_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_8Pedigree_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_numeric_sample_ids = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_numeric_sample_ids,0};
    PyObject* values[1] = {0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_numeric_sample_ids)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 360, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
    }
    __pyx_v_numeric_sample_ids = values[0];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 360, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Pedigree.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree___cinit__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), __pyx_v_numeric_sample_ids);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_8Pedigree___cinit__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_numeric_sample_ids) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  Pedigree *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":361
 * cdef class Pedigree:
 * 	def __cinit__(self, numeric_sample_ids):
 * 		self.thisptr = new cpp.Pedigree()             # <<<<<<<<<<<<<<
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 */
  try {
    __pyx_t_1 = new Pedigree();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 361, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_1;

  /* "whatshap/core.pyx":362
 * 	def __cinit__(self, numeric_sample_ids):
 * 		self.thisptr = new cpp.Pedigree()
 * 		self.numeric_sample_ids = numeric_sample_ids             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  if (!(likely(((__pyx_v_numeric_sample_ids) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_numeric_sample_ids, __pyx_ptype_8whatshap_4core_NumericSampleIds))))) __PYX_ERR(1, 362, __pyx_L1_error)
  __pyx_t_2 = __pyx_v_numeric_sample_ids;
  __Pyx_INCREF(__pyx_t_2);
  __Pyx_GIVEREF(__pyx_t_2);
  __Pyx_GOTREF(__pyx_v_self->numeric_sample_ids);
  __Pyx_DECREF(((PyObject *)__pyx_v_self->numeric_sample_ids));
  __pyx_v_self->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":360
 * 
 * cdef class Pedigree:
 * 	def __cinit__(self, numeric_sample_ids):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.Pedigree()
 * 		self.numeric_sample_ids = numeric_sample_ids
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Pedigree.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":364
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_8Pedigree_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_8Pedigree_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_8Pedigree_2__dealloc__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_8Pedigree_2__dealloc__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":365
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def add_individual(self, id, genotypes, genotype_likelihoods=None):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":364
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":367
 * 		del self.thisptr
 * 
 * 	def add_individual(self, id, genotypes, genotype_likelihoods=None):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.Genotype*] gt_vector
 * 		for gt in genotypes:
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_5add_individual(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_5add_individual(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_id = 0;
  PyObject *__pyx_v_genotypes = 0;
  PyObject *__pyx_v_genotype_likelihoods = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add_individual (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_id,&__pyx_n_s_genotypes,&__pyx_n_s_genotype_likelihoods,0};
    PyObject* values[3] = {0,0,0};
    values[2] = ((PyObject *)Py_None);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_id)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_genotypes)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add_individual", 0, 2, 3, 1); __PYX_ERR(1, 367, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_genotype_likelihoods);
          if (value) { values[2] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add_individual") < 0)) __PYX_ERR(1, 367, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_id = values[0];
    __pyx_v_genotypes = values[1];
    __pyx_v_genotype_likelihoods = values[2];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("add_individual", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 367, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Pedigree.add_individual", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_4add_individual(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), __pyx_v_id, __pyx_v_genotypes, __pyx_v_genotype_likelihoods);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_4add_individual(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_id, PyObject *__pyx_v_genotypes, PyObject *__pyx_v_genotype_likelihoods) {
  std::vector<Genotype *>  __pyx_v_gt_vector;
  PyObject *__pyx_v_gt = NULL;
  std::vector<PhredGenotypeLikelihoods *>  __pyx_v_gl_vector;
  PyObject *__pyx_v_gl = NULL;
  CYTHON_UNUSED PyObject *__pyx_v__ = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  PyObject *(*__pyx_t_3)(PyObject *);
  PyObject *__pyx_t_4 = NULL;
  Genotype *__pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  PhredGenotypeLikelihoods *__pyx_t_8;
  unsigned int __pyx_t_9;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("add_individual", 0);

  /* "whatshap/core.pyx":369
 * 	def add_individual(self, id, genotypes, genotype_likelihoods=None):
 * 		cdef vector[cpp.Genotype*] gt_vector
 * 		for gt in genotypes:             # <<<<<<<<<<<<<<
 * 			gt_vector.push_back(new cpp.Genotype((<Genotype?>gt).thisptr[0]))
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 */
  if (likely(PyList_CheckExact(__pyx_v_genotypes)) || PyTuple_CheckExact(__pyx_v_genotypes)) {
    __pyx_t_1 = __pyx_v_genotypes; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
    __pyx_t_3 = NULL;
  } else {
    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_genotypes); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 369, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 369, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_3)) {
      if (likely(PyList_CheckExact(__pyx_t_1))) {
        if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 369, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 369, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      } else {
        if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 369, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 369, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      }
    } else {
      __pyx_t_4 = __pyx_t_3(__pyx_t_1);
      if (unlikely(!__pyx_t_4)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 369, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_4);
    }
    __Pyx_XDECREF_SET(__pyx_v_gt, __pyx_t_4);
    __pyx_t_4 = 0;

    /* "whatshap/core.pyx":370
 * 		cdef vector[cpp.Genotype*] gt_vector
 * 		for gt in genotypes:
 * 			gt_vector.push_back(new cpp.Genotype((<Genotype?>gt).thisptr[0]))             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 * 		if genotype_likelihoods:
 */
    if (!(likely(__Pyx_TypeTest(__pyx_v_gt, __pyx_ptype_8whatshap_4core_Genotype)))) __PYX_ERR(1, 370, __pyx_L1_error)
    try {
      __pyx_t_5 = new Genotype((((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_gt)->thisptr[0]));
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 370, __pyx_L1_error)
    }
    try {
      __pyx_v_gt_vector.push_back(__pyx_t_5);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 370, __pyx_L1_error)
    }

    /* "whatshap/core.pyx":369
 * 	def add_individual(self, id, genotypes, genotype_likelihoods=None):
 * 		cdef vector[cpp.Genotype*] gt_vector
 * 		for gt in genotypes:             # <<<<<<<<<<<<<<
 * 			gt_vector.push_back(new cpp.Genotype((<Genotype?>gt).thisptr[0]))
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 */
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":372
 * 			gt_vector.push_back(new cpp.Genotype((<Genotype?>gt).thisptr[0]))
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 * 		if genotype_likelihoods:             # <<<<<<<<<<<<<<
 * 			for gl in genotype_likelihoods:
 * 				if gl is None:
 */
  __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_genotype_likelihoods); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(1, 372, __pyx_L1_error)
  if (__pyx_t_6) {

    /* "whatshap/core.pyx":373
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 * 		if genotype_likelihoods:
 * 			for gl in genotype_likelihoods:             # <<<<<<<<<<<<<<
 * 				if gl is None:
 * 					gl_vector.push_back(NULL)
 */
    if (likely(PyList_CheckExact(__pyx_v_genotype_likelihoods)) || PyTuple_CheckExact(__pyx_v_genotype_likelihoods)) {
      __pyx_t_1 = __pyx_v_genotype_likelihoods; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
      __pyx_t_3 = NULL;
    } else {
      __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_genotype_likelihoods); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 373, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 373, __pyx_L1_error)
    }
    for (;;) {
      if (likely(!__pyx_t_3)) {
        if (likely(PyList_CheckExact(__pyx_t_1))) {
          if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 373, __pyx_L1_error)
          #else
          __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 373, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          #endif
        } else {
          if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 373, __pyx_L1_error)
          #else
          __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 373, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          #endif
        }
      } else {
        __pyx_t_4 = __pyx_t_3(__pyx_t_1);
        if (unlikely(!__pyx_t_4)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 373, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_4);
      }
      __Pyx_XDECREF_SET(__pyx_v_gl, __pyx_t_4);
      __pyx_t_4 = 0;

      /* "whatshap/core.pyx":374
 * 		if genotype_likelihoods:
 * 			for gl in genotype_likelihoods:
 * 				if gl is None:             # <<<<<<<<<<<<<<
 * 					gl_vector.push_back(NULL)
 * 				else:
 */
      __pyx_t_6 = (__pyx_v_gl == Py_None);
      __pyx_t_7 = (__pyx_t_6 != 0);
      if (__pyx_t_7) {

        /* "whatshap/core.pyx":375
 * 			for gl in genotype_likelihoods:
 * 				if gl is None:
 * 					gl_vector.push_back(NULL)             # <<<<<<<<<<<<<<
 * 				else:
 * 					gl_vector.push_back(new cpp.PhredGenotypeLikelihoods((<PhredGenotypeLikelihoods?>gl).thisptr[0]) )
 */
        try {
          __pyx_v_gl_vector.push_back(NULL);
        } catch(...) {
          __Pyx_CppExn2PyErr();
          __PYX_ERR(1, 375, __pyx_L1_error)
        }

        /* "whatshap/core.pyx":374
 * 		if genotype_likelihoods:
 * 			for gl in genotype_likelihoods:
 * 				if gl is None:             # <<<<<<<<<<<<<<
 * 					gl_vector.push_back(NULL)
 * 				else:
 */
        goto __pyx_L8;
      }

      /* "whatshap/core.pyx":377
 * 					gl_vector.push_back(NULL)
 * 				else:
 * 					gl_vector.push_back(new cpp.PhredGenotypeLikelihoods((<PhredGenotypeLikelihoods?>gl).thisptr[0]) )             # <<<<<<<<<<<<<<
 * 		else:
 * 			for _ in genotypes:
 */
      /*else*/ {
        if (!(likely(__Pyx_TypeTest(__pyx_v_gl, __pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods)))) __PYX_ERR(1, 377, __pyx_L1_error)
        try {
          __pyx_t_8 = new PhredGenotypeLikelihoods((((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_gl)->thisptr[0]));
        } catch(...) {
          __Pyx_CppExn2PyErr();
          __PYX_ERR(1, 377, __pyx_L1_error)
        }
        try {
          __pyx_v_gl_vector.push_back(__pyx_t_8);
        } catch(...) {
          __Pyx_CppExn2PyErr();
          __PYX_ERR(1, 377, __pyx_L1_error)
        }
      }
      __pyx_L8:;

      /* "whatshap/core.pyx":373
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 * 		if genotype_likelihoods:
 * 			for gl in genotype_likelihoods:             # <<<<<<<<<<<<<<
 * 				if gl is None:
 * 					gl_vector.push_back(NULL)
 */
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

    /* "whatshap/core.pyx":372
 * 			gt_vector.push_back(new cpp.Genotype((<Genotype?>gt).thisptr[0]))
 * 		cdef vector[cpp.PhredGenotypeLikelihoods*] gl_vector
 * 		if genotype_likelihoods:             # <<<<<<<<<<<<<<
 * 			for gl in genotype_likelihoods:
 * 				if gl is None:
 */
    goto __pyx_L5;
  }

  /* "whatshap/core.pyx":379
 * 					gl_vector.push_back(new cpp.PhredGenotypeLikelihoods((<PhredGenotypeLikelihoods?>gl).thisptr[0]) )
 * 		else:
 * 			for _ in genotypes:             # <<<<<<<<<<<<<<
 * 				gl_vector.push_back(NULL)
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)
 */
  /*else*/ {
    if (likely(PyList_CheckExact(__pyx_v_genotypes)) || PyTuple_CheckExact(__pyx_v_genotypes)) {
      __pyx_t_1 = __pyx_v_genotypes; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
      __pyx_t_3 = NULL;
    } else {
      __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_genotypes); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 379, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 379, __pyx_L1_error)
    }
    for (;;) {
      if (likely(!__pyx_t_3)) {
        if (likely(PyList_CheckExact(__pyx_t_1))) {
          if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 379, __pyx_L1_error)
          #else
          __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 379, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          #endif
        } else {
          if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 379, __pyx_L1_error)
          #else
          __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 379, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          #endif
        }
      } else {
        __pyx_t_4 = __pyx_t_3(__pyx_t_1);
        if (unlikely(!__pyx_t_4)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 379, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_4);
      }
      __Pyx_XDECREF_SET(__pyx_v__, __pyx_t_4);
      __pyx_t_4 = 0;

      /* "whatshap/core.pyx":380
 * 		else:
 * 			for _ in genotypes:
 * 				gl_vector.push_back(NULL)             # <<<<<<<<<<<<<<
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)
 * 
 */
      try {
        __pyx_v_gl_vector.push_back(NULL);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 380, __pyx_L1_error)
      }

      /* "whatshap/core.pyx":379
 * 					gl_vector.push_back(new cpp.PhredGenotypeLikelihoods((<PhredGenotypeLikelihoods?>gl).thisptr[0]) )
 * 		else:
 * 			for _ in genotypes:             # <<<<<<<<<<<<<<
 * 				gl_vector.push_back(NULL)
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)
 */
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }
  __pyx_L5:;

  /* "whatshap/core.pyx":381
 * 			for _ in genotypes:
 * 				gl_vector.push_back(NULL)
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)             # <<<<<<<<<<<<<<
 * 
 * 	def add_relationship(self, father_id, mother_id, child_id):
 */
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 381, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_9 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_9 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 381, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  try {
    __pyx_v_self->thisptr->addIndividual(__pyx_t_9, __pyx_v_gt_vector, __pyx_v_gl_vector);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 381, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":367
 * 		del self.thisptr
 * 
 * 	def add_individual(self, id, genotypes, genotype_likelihoods=None):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.Genotype*] gt_vector
 * 		for gt in genotypes:
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.Pedigree.add_individual", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_gt);
  __Pyx_XDECREF(__pyx_v_gl);
  __Pyx_XDECREF(__pyx_v__);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":383
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)
 * 
 * 	def add_relationship(self, father_id, mother_id, child_id):             # <<<<<<<<<<<<<<
 * 		self.thisptr.addRelationship(self.numeric_sample_ids[father_id], self.numeric_sample_ids[mother_id], self.numeric_sample_ids[child_id])
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_7add_relationship(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_7add_relationship(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_father_id = 0;
  PyObject *__pyx_v_mother_id = 0;
  PyObject *__pyx_v_child_id = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("add_relationship (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_father_id,&__pyx_n_s_mother_id,&__pyx_n_s_child_id,0};
    PyObject* values[3] = {0,0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_father_id)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_mother_id)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add_relationship", 1, 3, 3, 1); __PYX_ERR(1, 383, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_child_id)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("add_relationship", 1, 3, 3, 2); __PYX_ERR(1, 383, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "add_relationship") < 0)) __PYX_ERR(1, 383, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
      values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
    }
    __pyx_v_father_id = values[0];
    __pyx_v_mother_id = values[1];
    __pyx_v_child_id = values[2];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("add_relationship", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 383, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Pedigree.add_relationship", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_6add_relationship(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), __pyx_v_father_id, __pyx_v_mother_id, __pyx_v_child_id);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_6add_relationship(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_father_id, PyObject *__pyx_v_mother_id, PyObject *__pyx_v_child_id) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  unsigned int __pyx_t_2;
  unsigned int __pyx_t_3;
  unsigned int __pyx_t_4;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("add_relationship", 0);

  /* "whatshap/core.pyx":384
 * 
 * 	def add_relationship(self, father_id, mother_id, child_id):
 * 		self.thisptr.addRelationship(self.numeric_sample_ids[father_id], self.numeric_sample_ids[mother_id], self.numeric_sample_ids[child_id])             # <<<<<<<<<<<<<<
 * 
 * 	property variant_count:
 */
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_father_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_mother_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_child_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_4 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 384, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  try {
    __pyx_v_self->thisptr->addRelationship(__pyx_t_2, __pyx_t_3, __pyx_t_4);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 384, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":383
 * 		self.thisptr.addIndividual(self.numeric_sample_ids[id], gt_vector, gl_vector)
 * 
 * 	def add_relationship(self, father_id, mother_id, child_id):             # <<<<<<<<<<<<<<
 * 		self.thisptr.addRelationship(self.numeric_sample_ids[father_id], self.numeric_sample_ids[mother_id], self.numeric_sample_ids[child_id])
 * 
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Pedigree.add_relationship", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":388
 * 	property variant_count:
 * 		"""Number of variants stored for each individual."""
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			return self.thisptr.get_variant_count()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_13variant_count_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_13variant_count_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_13variant_count___get__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_13variant_count___get__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  unsigned int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "whatshap/core.pyx":389
 * 		"""Number of variants stored for each individual."""
 * 		def __get__(self):
 * 			return self.thisptr.get_variant_count()             # <<<<<<<<<<<<<<
 * 
 * 	def genotype(self, sample_id, unsigned int variant_index):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_variant_count();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 389, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_unsigned_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 389, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":388
 * 	property variant_count:
 * 		"""Number of variants stored for each individual."""
 * 		def __get__(self):             # <<<<<<<<<<<<<<
 * 			return self.thisptr.get_variant_count()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Pedigree.variant_count.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":391
 * 			return self.thisptr.get_variant_count()
 * 
 * 	def genotype(self, sample_id, unsigned int variant_index):             # <<<<<<<<<<<<<<
 * 		cdef const cpp.Genotype* gt = self.thisptr.get_genotype_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		return Genotype(gt[0].as_vector())
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_9genotype(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_9genotype(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_sample_id = 0;
  unsigned int __pyx_v_variant_index;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("genotype (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_sample_id,&__pyx_n_s_variant_index,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sample_id)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_variant_index)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("genotype", 1, 2, 2, 1); __PYX_ERR(1, 391, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "genotype") < 0)) __PYX_ERR(1, 391, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_sample_id = values[0];
    __pyx_v_variant_index = __Pyx_PyInt_As_unsigned_int(values[1]); if (unlikely((__pyx_v_variant_index == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 391, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("genotype", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 391, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Pedigree.genotype", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_8genotype(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), __pyx_v_sample_id, __pyx_v_variant_index);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_8genotype(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_variant_index) {
  Genotype const *__pyx_v_gt;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  unsigned int __pyx_t_2;
  Genotype const *__pyx_t_3;
  std::vector<uint32_t>  __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("genotype", 0);

  /* "whatshap/core.pyx":392
 * 
 * 	def genotype(self, sample_id, unsigned int variant_index):
 * 		cdef const cpp.Genotype* gt = self.thisptr.get_genotype_by_id(self.numeric_sample_ids[sample_id], variant_index)             # <<<<<<<<<<<<<<
 * 		return Genotype(gt[0].as_vector())
 * 
 */
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_sample_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 392, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 392, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  try {
    __pyx_t_3 = __pyx_v_self->thisptr->get_genotype_by_id(__pyx_t_2, __pyx_v_variant_index);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 392, __pyx_L1_error)
  }
  __pyx_v_gt = __pyx_t_3;

  /* "whatshap/core.pyx":393
 * 	def genotype(self, sample_id, unsigned int variant_index):
 * 		cdef const cpp.Genotype* gt = self.thisptr.get_genotype_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		return Genotype(gt[0].as_vector())             # <<<<<<<<<<<<<<
 * 
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_4 = (__pyx_v_gt[0]).as_vector();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 393, __pyx_L1_error)
  }
  __pyx_t_1 = __pyx_convert_vector_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 393, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_5 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_8whatshap_4core_Genotype), __pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 393, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_r = __pyx_t_5;
  __pyx_t_5 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":391
 * 			return self.thisptr.get_variant_count()
 * 
 * 	def genotype(self, sample_id, unsigned int variant_index):             # <<<<<<<<<<<<<<
 * 		cdef const cpp.Genotype* gt = self.thisptr.get_genotype_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		return Genotype(gt[0].as_vector())
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("whatshap.core.Pedigree.genotype", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":395
 * 		return Genotype(gt[0].as_vector())
 * 
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):             # <<<<<<<<<<<<<<
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		if gl == NULL:
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_11genotype_likelihoods(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_11genotype_likelihoods(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_sample_id = 0;
  unsigned int __pyx_v_variant_index;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("genotype_likelihoods (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_sample_id,&__pyx_n_s_variant_index,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sample_id)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_variant_index)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("genotype_likelihoods", 1, 2, 2, 1); __PYX_ERR(1, 395, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "genotype_likelihoods") < 0)) __PYX_ERR(1, 395, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_sample_id = values[0];
    __pyx_v_variant_index = __Pyx_PyInt_As_unsigned_int(values[1]); if (unlikely((__pyx_v_variant_index == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 395, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("genotype_likelihoods", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 395, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Pedigree.genotype_likelihoods", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_10genotype_likelihoods(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), __pyx_v_sample_id, __pyx_v_variant_index);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_10genotype_likelihoods(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_variant_index) {
  PhredGenotypeLikelihoods const *__pyx_v_gl;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  unsigned int __pyx_t_2;
  PhredGenotypeLikelihoods const *__pyx_t_3;
  int __pyx_t_4;
  std::vector<double>  __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("genotype_likelihoods", 0);

  /* "whatshap/core.pyx":396
 * 
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)             # <<<<<<<<<<<<<<
 * 		if gl == NULL:
 * 			return None
 */
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_sample_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 396, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 396, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  try {
    __pyx_t_3 = __pyx_v_self->thisptr->get_genotype_likelihoods_by_id(__pyx_t_2, __pyx_v_variant_index);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 396, __pyx_L1_error)
  }
  __pyx_v_gl = __pyx_t_3;

  /* "whatshap/core.pyx":397
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		if gl == NULL:             # <<<<<<<<<<<<<<
 * 			return None
 * 		else:
 */
  __pyx_t_4 = ((__pyx_v_gl == NULL) != 0);
  if (__pyx_t_4) {

    /* "whatshap/core.pyx":398
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		if gl == NULL:
 * 			return None             # <<<<<<<<<<<<<<
 * 		else:
 * 			return PhredGenotypeLikelihoods(gl[0].as_vector(), gl[0].get_ploidy(), gl[0].get_nr_alleles())
 */
    __Pyx_XDECREF(__pyx_r);
    __pyx_r = Py_None; __Pyx_INCREF(Py_None);
    goto __pyx_L0;

    /* "whatshap/core.pyx":397
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		if gl == NULL:             # <<<<<<<<<<<<<<
 * 			return None
 * 		else:
 */
  }

  /* "whatshap/core.pyx":400
 * 			return None
 * 		else:
 * 			return PhredGenotypeLikelihoods(gl[0].as_vector(), gl[0].get_ploidy(), gl[0].get_nr_alleles())             # <<<<<<<<<<<<<<
 * 
 * 	def __len__(self):
 */
  /*else*/ {
    __Pyx_XDECREF(__pyx_r);
    try {
      __pyx_t_5 = (__pyx_v_gl[0]).as_vector();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 400, __pyx_L1_error)
    }
    __pyx_t_1 = __pyx_convert_vector_to_py_double(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 400, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    try {
      __pyx_t_2 = (__pyx_v_gl[0]).get_ploidy();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 400, __pyx_L1_error)
    }
    __pyx_t_6 = __Pyx_PyInt_From_unsigned_int(__pyx_t_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 400, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    try {
      __pyx_t_2 = (__pyx_v_gl[0]).get_nr_alleles();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 400, __pyx_L1_error)
    }
    __pyx_t_7 = __Pyx_PyInt_From_unsigned_int(__pyx_t_2); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 400, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 400, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_8);
    __Pyx_GIVEREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
    __Pyx_GIVEREF(__pyx_t_6);
    PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_6);
    __Pyx_GIVEREF(__pyx_t_7);
    PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7);
    __pyx_t_1 = 0;
    __pyx_t_6 = 0;
    __pyx_t_7 = 0;
    __pyx_t_7 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods), __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 400, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __pyx_r = __pyx_t_7;
    __pyx_t_7 = 0;
    goto __pyx_L0;
  }

  /* "whatshap/core.pyx":395
 * 		return Genotype(gt[0].as_vector())
 * 
 * 	def genotype_likelihoods(self, sample_id, unsigned int variant_index):             # <<<<<<<<<<<<<<
 * 		cdef const cpp.PhredGenotypeLikelihoods* gl = self.thisptr.get_genotype_likelihoods_by_id(self.numeric_sample_ids[sample_id], variant_index)
 * 		if gl == NULL:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_AddTraceback("whatshap.core.Pedigree.genotype_likelihoods", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":402
 * 			return PhredGenotypeLikelihoods(gl[0].as_vector(), gl[0].get_ploidy(), gl[0].get_nr_alleles())
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

/* Python wrapper */
static Py_ssize_t __pyx_pw_8whatshap_4core_8Pedigree_13__len__(PyObject *__pyx_v_self); /*proto*/
static Py_ssize_t __pyx_pw_8whatshap_4core_8Pedigree_13__len__(PyObject *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_12__len__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_ssize_t __pyx_pf_8whatshap_4core_8Pedigree_12__len__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__", 0);

  /* "whatshap/core.pyx":403
 * 
 * 	def __len__(self):
 * 		return self.thisptr.size()             # <<<<<<<<<<<<<<
 * 
 * 	def __str__(self):
 */
  __pyx_r = __pyx_v_self->thisptr->size();
  goto __pyx_L0;

  /* "whatshap/core.pyx":402
 * 			return PhredGenotypeLikelihoods(gl[0].as_vector(), gl[0].get_ploidy(), gl[0].get_nr_alleles())
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

  /* function exit code */
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":405
 * 		return self.thisptr.size()
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_15__str__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_15__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_14__str__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_14__str__(struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "whatshap/core.pyx":406
 * 
 * 	def __str__(self):
 * 		return self.thisptr.toString().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->toString();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 406, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 406, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":405
 * 		return self.thisptr.size()
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Pedigree.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_17__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_17__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_16__reduce_cython__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_16__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Pedigree.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_19__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Pedigree_19__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Pedigree_18__setstate_cython__(((struct __pyx_obj_8whatshap_4core_Pedigree *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Pedigree_18__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Pedigree.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":410
 * 
 * cdef class PhredGenotypeLikelihoods:
 * 	def __cinit__(self, vector[double] gl, unsigned int ploidy=2, unsigned int nr_alleles=2):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.PhredGenotypeLikelihoods(gl, ploidy, nr_alleles)
 * 
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  std::vector<double>  __pyx_v_gl;
  unsigned int __pyx_v_ploidy;
  unsigned int __pyx_v_nr_alleles;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_gl,&__pyx_n_s_ploidy,&__pyx_n_s_nr_alleles,0};
    PyObject* values[3] = {0,0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_gl)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_ploidy);
          if (value) { values[1] = value; kw_args--; }
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_nr_alleles);
          if (value) { values[2] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 410, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_gl = __pyx_convert_vector_from_py_double(values[0]); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 410, __pyx_L3_error)
    if (values[1]) {
      __pyx_v_ploidy = __Pyx_PyInt_As_unsigned_int(values[1]); if (unlikely((__pyx_v_ploidy == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 410, __pyx_L3_error)
    } else {
      __pyx_v_ploidy = ((unsigned int)2);
    }
    if (values[2]) {
      __pyx_v_nr_alleles = __Pyx_PyInt_As_unsigned_int(values[2]); if (unlikely((__pyx_v_nr_alleles == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 410, __pyx_L3_error)
    } else {
      __pyx_v_nr_alleles = ((unsigned int)2);
    }
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 410, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods___cinit__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self), __pyx_v_gl, __pyx_v_ploidy, __pyx_v_nr_alleles);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods___cinit__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, std::vector<double>  __pyx_v_gl, unsigned int __pyx_v_ploidy, unsigned int __pyx_v_nr_alleles) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PhredGenotypeLikelihoods *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":411
 * cdef class PhredGenotypeLikelihoods:
 * 	def __cinit__(self, vector[double] gl, unsigned int ploidy=2, unsigned int nr_alleles=2):
 * 		self.thisptr = new cpp.PhredGenotypeLikelihoods(gl, ploidy, nr_alleles)             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  try {
    __pyx_t_1 = new PhredGenotypeLikelihoods(__pyx_v_gl, __pyx_v_ploidy, __pyx_v_nr_alleles);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 411, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_1;

  /* "whatshap/core.pyx":410
 * 
 * cdef class PhredGenotypeLikelihoods:
 * 	def __cinit__(self, vector[double] gl, unsigned int ploidy=2, unsigned int nr_alleles=2):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.PhredGenotypeLikelihoods(gl, ploidy, nr_alleles)
 * 
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":413
 * 		self.thisptr = new cpp.PhredGenotypeLikelihoods(gl, ploidy, nr_alleles)
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_2__dealloc__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_2__dealloc__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":414
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def __str__(self):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":413
 * 		self.thisptr = new cpp.PhredGenotypeLikelihoods(gl, ploidy, nr_alleles)
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":416
 * 		del self.thisptr
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_5__str__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_5__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_4__str__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_4__str__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "whatshap/core.pyx":417
 * 
 * 	def __str__(self):
 * 		return self.thisptr.toString().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	def __getitem__(self, Genotype genotype):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->toString();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 417, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 417, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":416
 * 		del self.thisptr
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":419
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __getitem__(self, Genotype genotype):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		assert genotype.is_diploid_and_biallelic()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_genotype); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_genotype) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_genotype), __pyx_ptype_8whatshap_4core_Genotype, 1, "genotype", 0))) __PYX_ERR(1, 419, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_6__getitem__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_genotype));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_6__getitem__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_genotype) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  double __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getitem__", 0);

  /* "whatshap/core.pyx":420
 * 
 * 	def __getitem__(self, Genotype genotype):
 * 		assert self.thisptr != NULL             # <<<<<<<<<<<<<<
 * 		assert genotype.is_diploid_and_biallelic()
 * 		return self.thisptr.get(genotype.thisptr[0])
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_self->thisptr != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 420, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":421
 * 	def __getitem__(self, Genotype genotype):
 * 		assert self.thisptr != NULL
 * 		assert genotype.is_diploid_and_biallelic()             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get(genotype.thisptr[0])
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_genotype), __pyx_n_s_is_diploid_and_biallelic); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 421, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
      __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
      if (likely(__pyx_t_3)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
        __Pyx_INCREF(__pyx_t_3);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_2, function);
      }
    }
    __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
    __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
    if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 421, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(1, 421, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (unlikely(!__pyx_t_4)) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(1, 421, __pyx_L1_error)
    }
  }
  #endif

  /* "whatshap/core.pyx":422
 * 		assert self.thisptr != NULL
 * 		assert genotype.is_diploid_and_biallelic()
 * 		return self.thisptr.get(genotype.thisptr[0])             # <<<<<<<<<<<<<<
 * 
 * 	def __len__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_5 = __pyx_v_self->thisptr->get((__pyx_v_genotype->thisptr[0]));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 422, __pyx_L1_error)
  }
  __pyx_t_1 = PyFloat_FromDouble(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 422, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":419
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __getitem__(self, Genotype genotype):             # <<<<<<<<<<<<<<
 * 		assert self.thisptr != NULL
 * 		assert genotype.is_diploid_and_biallelic()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":424
 * 		return self.thisptr.get(genotype.thisptr[0])
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

/* Python wrapper */
static Py_ssize_t __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_9__len__(PyObject *__pyx_v_self); /*proto*/
static Py_ssize_t __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_9__len__(PyObject *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_8__len__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_ssize_t __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_8__len__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  Py_ssize_t __pyx_r;
  __Pyx_RefNannyDeclarations
  unsigned int __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__len__", 0);

  /* "whatshap/core.pyx":425
 * 
 * 	def __len__(self):
 * 		return self.thisptr.size()             # <<<<<<<<<<<<<<
 * 
 * 	def __iter__(self):
 */
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->size();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 425, __pyx_L1_error)
  }
  __pyx_r = __pyx_t_1;
  goto __pyx_L0;

  /* "whatshap/core.pyx":424
 * 		return self.thisptr.get(genotype.thisptr[0])
 * 
 * 	def __len__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.size()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}
static PyObject *__pyx_gb_8whatshap_4core_24PhredGenotypeLikelihoods_12generator2(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value); /* proto */

/* "whatshap/core.pyx":427
 * 		return self.thisptr.size()
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for genotype in self.genotypes():
 * 			yield self[genotype]
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_11__iter__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_11__iter__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_10__iter__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_10__iter__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *__pyx_cur_scope;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__iter__", 0);
  __pyx_cur_scope = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)__pyx_tp_new_8whatshap_4core___pyx_scope_struct_2___iter__(__pyx_ptype_8whatshap_4core___pyx_scope_struct_2___iter__, __pyx_empty_tuple, NULL);
  if (unlikely(!__pyx_cur_scope)) {
    __pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)Py_None);
    __Pyx_INCREF(Py_None);
    __PYX_ERR(1, 427, __pyx_L1_error)
  } else {
    __Pyx_GOTREF(__pyx_cur_scope);
  }
  __pyx_cur_scope->__pyx_v_self = __pyx_v_self;
  __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  __Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
  {
    __pyx_CoroutineObject *gen = __Pyx_Generator_New((__pyx_coroutine_body_t) __pyx_gb_8whatshap_4core_24PhredGenotypeLikelihoods_12generator2, NULL, (PyObject *) __pyx_cur_scope, __pyx_n_s_iter, __pyx_n_s_PhredGenotypeLikelihoods___iter, __pyx_n_s_whatshap_core); if (unlikely(!gen)) __PYX_ERR(1, 427, __pyx_L1_error)
    __Pyx_DECREF(__pyx_cur_scope);
    __Pyx_RefNannyFinishContext();
    return (PyObject *) gen;
  }

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_DECREF(((PyObject *)__pyx_cur_scope));
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_gb_8whatshap_4core_24PhredGenotypeLikelihoods_12generator2(__pyx_CoroutineObject *__pyx_generator, CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject *__pyx_sent_value) /* generator body */
{
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *__pyx_cur_scope = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)__pyx_generator->closure);
  PyObject *__pyx_r = NULL;
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  Py_ssize_t __pyx_t_4;
  PyObject *(*__pyx_t_5)(PyObject *);
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__iter__", 0);
  switch (__pyx_generator->resume_label) {
    case 0: goto __pyx_L3_first_run;
    case 1: goto __pyx_L6_resume_from_yield;
    default: /* CPython raises the right error here */
    __Pyx_RefNannyFinishContext();
    return NULL;
  }
  __pyx_L3_first_run:;
  if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 427, __pyx_L1_error)

  /* "whatshap/core.pyx":428
 * 
 * 	def __iter__(self):
 * 		for genotype in self.genotypes():             # <<<<<<<<<<<<<<
 * 			yield self[genotype]
 * 
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_cur_scope->__pyx_v_self), __pyx_n_s_genotypes); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 428, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 428, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
    __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
    __pyx_t_5 = NULL;
  } else {
    __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 428, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 428, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  for (;;) {
    if (likely(!__pyx_t_5)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 428, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 428, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      } else {
        if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(1, 428, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 428, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      }
    } else {
      __pyx_t_1 = __pyx_t_5(__pyx_t_2);
      if (unlikely(!__pyx_t_1)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 428, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_1);
    }
    __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_genotype);
    __Pyx_XDECREF_SET(__pyx_cur_scope->__pyx_v_genotype, __pyx_t_1);
    __Pyx_GIVEREF(__pyx_t_1);
    __pyx_t_1 = 0;

    /* "whatshap/core.pyx":429
 * 	def __iter__(self):
 * 		for genotype in self.genotypes():
 * 			yield self[genotype]             # <<<<<<<<<<<<<<
 * 
 * 	def __eq__(self, PhredGenotypeLikelihoods other):
 */
    __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_genotype); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 429, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_r = __pyx_t_1;
    __pyx_t_1 = 0;
    __Pyx_XGIVEREF(__pyx_t_2);
    __pyx_cur_scope->__pyx_t_0 = __pyx_t_2;
    __pyx_cur_scope->__pyx_t_1 = __pyx_t_4;
    __pyx_cur_scope->__pyx_t_2 = __pyx_t_5;
    __Pyx_XGIVEREF(__pyx_r);
    __Pyx_RefNannyFinishContext();
    __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
    /* return from generator, yielding value */
    __pyx_generator->resume_label = 1;
    return __pyx_r;
    __pyx_L6_resume_from_yield:;
    __pyx_t_2 = __pyx_cur_scope->__pyx_t_0;
    __pyx_cur_scope->__pyx_t_0 = 0;
    __Pyx_XGOTREF(__pyx_t_2);
    __pyx_t_4 = __pyx_cur_scope->__pyx_t_1;
    __pyx_t_5 = __pyx_cur_scope->__pyx_t_2;
    if (unlikely(!__pyx_sent_value)) __PYX_ERR(1, 429, __pyx_L1_error)

    /* "whatshap/core.pyx":428
 * 
 * 	def __iter__(self):
 * 		for genotype in self.genotypes():             # <<<<<<<<<<<<<<
 * 			yield self[genotype]
 * 
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  CYTHON_MAYBE_UNUSED_VAR(__pyx_cur_scope);

  /* "whatshap/core.pyx":427
 * 		return self.thisptr.size()
 * 
 * 	def __iter__(self):             # <<<<<<<<<<<<<<
 * 		for genotype in self.genotypes():
 * 			yield self[genotype]
 */

  /* function exit code */
  PyErr_SetNone(PyExc_StopIteration);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_r); __pyx_r = 0;
  #if !CYTHON_USE_EXC_INFO_STACK
  __Pyx_Coroutine_ResetAndClearException(__pyx_generator);
  #endif
  __pyx_generator->resume_label = -1;
  __Pyx_Coroutine_clear((PyObject*)__pyx_generator);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":431
 * 			yield self[genotype]
 * 
 * 	def __eq__(self, PhredGenotypeLikelihoods other):             # <<<<<<<<<<<<<<
 * 		if self.genotypes() != other.genotypes():
 * 			return False
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_14__eq__(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_14__eq__(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__eq__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods, 1, "other", 0))) __PYX_ERR(1, 431, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_13__eq__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_other));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_13__eq__(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_other) {
  PyObject *__pyx_v_genotype = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  Py_ssize_t __pyx_t_6;
  PyObject *(*__pyx_t_7)(PyObject *);
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__eq__", 0);

  /* "whatshap/core.pyx":432
 * 
 * 	def __eq__(self, PhredGenotypeLikelihoods other):
 * 		if self.genotypes() != other.genotypes():             # <<<<<<<<<<<<<<
 * 			return False
 * 		for genotype in self.genotypes():
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_genotypes); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_other), __pyx_n_s_genotypes); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_4 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) {
    __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
    if (likely(__pyx_t_4)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
      __Pyx_INCREF(__pyx_t_4);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_3, function);
    }
  }
  __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4) : __Pyx_PyObject_CallNoArg(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
  if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(1, 432, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (__pyx_t_5) {

    /* "whatshap/core.pyx":433
 * 	def __eq__(self, PhredGenotypeLikelihoods other):
 * 		if self.genotypes() != other.genotypes():
 * 			return False             # <<<<<<<<<<<<<<
 * 		for genotype in self.genotypes():
 * 			if self[genotype] != other[genotype]:
 */
    __Pyx_XDECREF(__pyx_r);
    __Pyx_INCREF(Py_False);
    __pyx_r = Py_False;
    goto __pyx_L0;

    /* "whatshap/core.pyx":432
 * 
 * 	def __eq__(self, PhredGenotypeLikelihoods other):
 * 		if self.genotypes() != other.genotypes():             # <<<<<<<<<<<<<<
 * 			return False
 * 		for genotype in self.genotypes():
 */
  }

  /* "whatshap/core.pyx":434
 * 		if self.genotypes() != other.genotypes():
 * 			return False
 * 		for genotype in self.genotypes():             # <<<<<<<<<<<<<<
 * 			if self[genotype] != other[genotype]:
 * 				return False
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_genotypes); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 434, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_1 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_1)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_1);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_3 = (__pyx_t_1) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_1) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 434, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (likely(PyList_CheckExact(__pyx_t_3)) || PyTuple_CheckExact(__pyx_t_3)) {
    __pyx_t_2 = __pyx_t_3; __Pyx_INCREF(__pyx_t_2); __pyx_t_6 = 0;
    __pyx_t_7 = NULL;
  } else {
    __pyx_t_6 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 434, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_7 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 434, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  for (;;) {
    if (likely(!__pyx_t_7)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_6 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_3); __pyx_t_6++; if (unlikely(0 < 0)) __PYX_ERR(1, 434, __pyx_L1_error)
        #else
        __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 434, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        #endif
      } else {
        if (__pyx_t_6 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_6); __Pyx_INCREF(__pyx_t_3); __pyx_t_6++; if (unlikely(0 < 0)) __PYX_ERR(1, 434, __pyx_L1_error)
        #else
        __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 434, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        #endif
      }
    } else {
      __pyx_t_3 = __pyx_t_7(__pyx_t_2);
      if (unlikely(!__pyx_t_3)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(1, 434, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_3);
    }
    __Pyx_XDECREF_SET(__pyx_v_genotype, __pyx_t_3);
    __pyx_t_3 = 0;

    /* "whatshap/core.pyx":435
 * 			return False
 * 		for genotype in self.genotypes():
 * 			if self[genotype] != other[genotype]:             # <<<<<<<<<<<<<<
 * 				return False
 * 		return True
 */
    __pyx_t_3 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self), __pyx_v_genotype); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 435, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_other), __pyx_v_genotype); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 435, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_t_1, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 435, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(1, 435, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (__pyx_t_5) {

      /* "whatshap/core.pyx":436
 * 		for genotype in self.genotypes():
 * 			if self[genotype] != other[genotype]:
 * 				return False             # <<<<<<<<<<<<<<
 * 		return True
 * 
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      goto __pyx_L0;

      /* "whatshap/core.pyx":435
 * 			return False
 * 		for genotype in self.genotypes():
 * 			if self[genotype] != other[genotype]:             # <<<<<<<<<<<<<<
 * 				return False
 * 		return True
 */
    }

    /* "whatshap/core.pyx":434
 * 		if self.genotypes() != other.genotypes():
 * 			return False
 * 		for genotype in self.genotypes():             # <<<<<<<<<<<<<<
 * 			if self[genotype] != other[genotype]:
 * 				return False
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "whatshap/core.pyx":437
 * 			if self[genotype] != other[genotype]:
 * 				return False
 * 		return True             # <<<<<<<<<<<<<<
 * 
 * 	def genotypes(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(Py_True);
  __pyx_r = Py_True;
  goto __pyx_L0;

  /* "whatshap/core.pyx":431
 * 			yield self[genotype]
 * 
 * 	def __eq__(self, PhredGenotypeLikelihoods other):             # <<<<<<<<<<<<<<
 * 		if self.genotypes() != other.genotypes():
 * 			return False
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__eq__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_genotype);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":439
 * 		return True
 * 
 * 	def genotypes(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.Genotype]* genotypes = new vector[cpp.Genotype]()
 * 		self.thisptr.get_genotypes(deref(genotypes))
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_16genotypes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_16genotypes(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("genotypes (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_15genotypes(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_15genotypes(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  std::vector<Genotype>  *__pyx_v_genotypes;
  PyObject *__pyx_v_result = NULL;
  Genotype __pyx_8genexpr5__pyx_v_genotype;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::vector<Genotype>  *__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  std::vector<Genotype> ::iterator __pyx_t_3;
  Genotype __pyx_t_4;
  std::vector<uint32_t>  __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("genotypes", 0);

  /* "whatshap/core.pyx":440
 * 
 * 	def genotypes(self):
 * 		cdef vector[cpp.Genotype]* genotypes = new vector[cpp.Genotype]()             # <<<<<<<<<<<<<<
 * 		self.thisptr.get_genotypes(deref(genotypes))
 * 		result = [Genotype(genotype.as_vector()) for genotype in genotypes[0]]
 */
  try {
    __pyx_t_1 = new std::vector<Genotype> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 440, __pyx_L1_error)
  }
  __pyx_v_genotypes = __pyx_t_1;

  /* "whatshap/core.pyx":441
 * 	def genotypes(self):
 * 		cdef vector[cpp.Genotype]* genotypes = new vector[cpp.Genotype]()
 * 		self.thisptr.get_genotypes(deref(genotypes))             # <<<<<<<<<<<<<<
 * 		result = [Genotype(genotype.as_vector()) for genotype in genotypes[0]]
 * 		del genotypes
 */
  try {
    __pyx_v_self->thisptr->get_genotypes((*__pyx_v_genotypes));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 441, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":442
 * 		cdef vector[cpp.Genotype]* genotypes = new vector[cpp.Genotype]()
 * 		self.thisptr.get_genotypes(deref(genotypes))
 * 		result = [Genotype(genotype.as_vector()) for genotype in genotypes[0]]             # <<<<<<<<<<<<<<
 * 		del genotypes
 * 		return result
 */
  { /* enter inner scope */
    __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 442, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_1 = &(__pyx_v_genotypes[0]);
    __pyx_t_3 = __pyx_t_1->begin();
    for (;;) {
      if (!(__pyx_t_3 != __pyx_t_1->end())) break;
      __pyx_t_4 = *__pyx_t_3;
      ++__pyx_t_3;
      __pyx_8genexpr5__pyx_v_genotype = __pyx_t_4;
      try {
        __pyx_t_5 = __pyx_8genexpr5__pyx_v_genotype.as_vector();
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 442, __pyx_L1_error)
      }
      __pyx_t_6 = __pyx_convert_vector_to_py_uint32_t(__pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_7 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_8whatshap_4core_Genotype), __pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) __PYX_ERR(1, 442, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    }
  } /* exit inner scope */
  __pyx_v_result = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":443
 * 		self.thisptr.get_genotypes(deref(genotypes))
 * 		result = [Genotype(genotype.as_vector()) for genotype in genotypes[0]]
 * 		del genotypes             # <<<<<<<<<<<<<<
 * 		return result
 * 
 */
  delete __pyx_v_genotypes;

  /* "whatshap/core.pyx":444
 * 		result = [Genotype(genotype.as_vector()) for genotype in genotypes[0]]
 * 		del genotypes
 * 		return result             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_result);
  __pyx_r = __pyx_v_result;
  goto __pyx_L0;

  /* "whatshap/core.pyx":439
 * 		return True
 * 
 * 	def genotypes(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.Genotype]* genotypes = new vector[cpp.Genotype]()
 * 		self.thisptr.get_genotypes(deref(genotypes))
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.genotypes", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_18__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_18__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_17__reduce_cython__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_17__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_20__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_20__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_19__setstate_cython__(((struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_24PhredGenotypeLikelihoods_19__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.PhredGenotypeLikelihoods.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":447
 * 
 * 
 * def binomial_coefficient(int n, int k):             # <<<<<<<<<<<<<<
 * 	return cpp.binomial_coefficient(n, k)
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_1binomial_coefficient(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyMethodDef __pyx_mdef_8whatshap_4core_1binomial_coefficient = {"binomial_coefficient", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_1binomial_coefficient, METH_VARARGS|METH_KEYWORDS, 0};
static PyObject *__pyx_pw_8whatshap_4core_1binomial_coefficient(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  int __pyx_v_n;
  int __pyx_v_k;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("binomial_coefficient (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_n,&__pyx_n_s_k,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_n)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_k)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("binomial_coefficient", 1, 2, 2, 1); __PYX_ERR(1, 447, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "binomial_coefficient") < 0)) __PYX_ERR(1, 447, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_n = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_n == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 447, __pyx_L3_error)
    __pyx_v_k = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_k == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 447, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("binomial_coefficient", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 447, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.binomial_coefficient", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_binomial_coefficient(__pyx_self, __pyx_v_n, __pyx_v_k);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_binomial_coefficient(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n, int __pyx_v_k) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("binomial_coefficient", 0);

  /* "whatshap/core.pyx":448
 * 
 * def binomial_coefficient(int n, int k):
 * 	return cpp.binomial_coefficient(n, k)             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = binomial_coefficient(__pyx_v_n, __pyx_v_k);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 448, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 448, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":447
 * 
 * 
 * def binomial_coefficient(int n, int k):             # <<<<<<<<<<<<<<
 * 	return cpp.binomial_coefficient(n, k)
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.binomial_coefficient", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":453
 * cdef class Genotype:
 * 
 * 	def __cinit__(self, vector[uint32_t] alleles):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_8Genotype_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_8Genotype_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  std::vector<uint32_t>  __pyx_v_alleles;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_alleles,0};
    PyObject* values[1] = {0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_alleles)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 453, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
    }
    __pyx_v_alleles = __pyx_convert_vector_from_py_uint32_t(values[0]); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 453, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 453, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.Genotype.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype___cinit__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), __pyx_v_alleles);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_8Genotype___cinit__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, std::vector<uint32_t>  __pyx_v_alleles) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  Genotype *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":454
 * 
 * 	def __cinit__(self, vector[uint32_t] alleles):
 * 		self.thisptr = new cpp.Genotype(alleles)             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  try {
    __pyx_t_1 = new Genotype(__pyx_v_alleles);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 454, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_1;

  /* "whatshap/core.pyx":453
 * cdef class Genotype:
 * 
 * 	def __cinit__(self, vector[uint32_t] alleles):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("whatshap.core.Genotype.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":456
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_8Genotype_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_8Genotype_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_8Genotype_2__dealloc__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_8Genotype_2__dealloc__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":457
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def __str__(self):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":456
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":459
 * 		del self.thisptr
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_5__str__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_5__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_4__str__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_4__str__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "whatshap/core.pyx":460
 * 
 * 	def __str__(self):
 * 		return self.thisptr.toString().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	def __repr__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->toString();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 460, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 460, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":459
 * 		del self.thisptr
 * 
 * 	def __str__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":462
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __repr__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_7__repr__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_7__repr__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__repr__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_6__repr__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_6__repr__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::string __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__repr__", 0);

  /* "whatshap/core.pyx":463
 * 
 * 	def __repr__(self):
 * 		return self.thisptr.toString().decode('utf-8')             # <<<<<<<<<<<<<<
 * 
 * 	def is_none(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->toString();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 463, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_decode_cpp_string(__pyx_t_1, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 463, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":462
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def __repr__(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__repr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":465
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def is_none(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_none()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_9is_none(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_9is_none(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("is_none (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_8is_none(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_8is_none(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("is_none", 0);

  /* "whatshap/core.pyx":466
 * 
 * 	def is_none(self):
 * 		return self.thisptr.is_none()             # <<<<<<<<<<<<<<
 * 
 * 	def get_index(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->is_none();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 466, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 466, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":465
 * 		return self.thisptr.toString().decode('utf-8')
 * 
 * 	def is_none(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_none()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.is_none", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":468
 * 		return self.thisptr.is_none()
 * 
 * 	def get_index(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_index()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_11get_index(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_11get_index(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_index (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_10get_index(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_10get_index(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  uint64_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_index", 0);

  /* "whatshap/core.pyx":469
 * 
 * 	def get_index(self):
 * 		return self.thisptr.get_index()             # <<<<<<<<<<<<<<
 * 
 * 	def as_vector(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_index();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 469, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint64_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 469, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":468
 * 		return self.thisptr.is_none()
 * 
 * 	def get_index(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_index()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.get_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":471
 * 		return self.thisptr.get_index()
 * 
 * 	def as_vector(self):             # <<<<<<<<<<<<<<
 * 		result = []
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_13as_vector(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_13as_vector(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("as_vector (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_12as_vector(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_12as_vector(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_v_result = NULL;
  std::vector<uint32_t>  __pyx_v_alleles;
  uint32_t __pyx_v_allele;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  std::vector<uint32_t>  __pyx_t_2;
  std::vector<uint32_t> ::iterator __pyx_t_3;
  uint32_t __pyx_t_4;
  int __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("as_vector", 0);

  /* "whatshap/core.pyx":472
 * 
 * 	def as_vector(self):
 * 		result = []             # <<<<<<<<<<<<<<
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 * 		for allele in alleles:
 */
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 472, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_result = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":473
 * 	def as_vector(self):
 * 		result = []
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()             # <<<<<<<<<<<<<<
 * 		for allele in alleles:
 * 			result.append(allele)
 */
  try {
    __pyx_t_2 = __pyx_v_self->thisptr->as_vector();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 473, __pyx_L1_error)
  }
  __pyx_v_alleles = __pyx_t_2;

  /* "whatshap/core.pyx":474
 * 		result = []
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 * 		for allele in alleles:             # <<<<<<<<<<<<<<
 * 			result.append(allele)
 * 		return alleles
 */
  __pyx_t_3 = __pyx_v_alleles.begin();
  for (;;) {
    if (!(__pyx_t_3 != __pyx_v_alleles.end())) break;
    __pyx_t_4 = *__pyx_t_3;
    ++__pyx_t_3;
    __pyx_v_allele = __pyx_t_4;

    /* "whatshap/core.pyx":475
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 * 		for allele in alleles:
 * 			result.append(allele)             # <<<<<<<<<<<<<<
 * 		return alleles
 * 
 */
    __pyx_t_1 = __Pyx_PyInt_From_uint32_t(__pyx_v_allele); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 475, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5 = __Pyx_PyList_Append(__pyx_v_result, __pyx_t_1); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(1, 475, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

    /* "whatshap/core.pyx":474
 * 		result = []
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 * 		for allele in alleles:             # <<<<<<<<<<<<<<
 * 			result.append(allele)
 * 		return alleles
 */
  }

  /* "whatshap/core.pyx":476
 * 		for allele in alleles:
 * 			result.append(allele)
 * 		return alleles             # <<<<<<<<<<<<<<
 * 
 * 	def is_homozygous(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __pyx_convert_vector_to_py_uint32_t(__pyx_v_alleles); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 476, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":471
 * 		return self.thisptr.get_index()
 * 
 * 	def as_vector(self):             # <<<<<<<<<<<<<<
 * 		result = []
 * 		cdef vector[uint32_t] alleles = self.thisptr.as_vector()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Genotype.as_vector", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":478
 * 		return alleles
 * 
 * 	def is_homozygous(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_homozygous()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_15is_homozygous(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_15is_homozygous(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("is_homozygous (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_14is_homozygous(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_14is_homozygous(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("is_homozygous", 0);

  /* "whatshap/core.pyx":479
 * 
 * 	def is_homozygous(self):
 * 		return self.thisptr.is_homozygous()             # <<<<<<<<<<<<<<
 * 
 * 	def is_diploid_and_biallelic(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->is_homozygous();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 479, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 479, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":478
 * 		return alleles
 * 
 * 	def is_homozygous(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_homozygous()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.is_homozygous", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":481
 * 		return self.thisptr.is_homozygous()
 * 
 * 	def is_diploid_and_biallelic(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_diploid_and_biallelic()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_17is_diploid_and_biallelic(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_17is_diploid_and_biallelic(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("is_diploid_and_biallelic (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_16is_diploid_and_biallelic(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_16is_diploid_and_biallelic(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("is_diploid_and_biallelic", 0);

  /* "whatshap/core.pyx":482
 * 
 * 	def is_diploid_and_biallelic(self):
 * 		return self.thisptr.is_diploid_and_biallelic()             # <<<<<<<<<<<<<<
 * 
 * 	def get_ploidy(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->is_diploid_and_biallelic();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 482, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 482, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":481
 * 		return self.thisptr.is_homozygous()
 * 
 * 	def is_diploid_and_biallelic(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.is_diploid_and_biallelic()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.is_diploid_and_biallelic", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":484
 * 		return self.thisptr.is_diploid_and_biallelic()
 * 
 * 	def get_ploidy(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_ploidy()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_19get_ploidy(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_19get_ploidy(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_ploidy (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_18get_ploidy(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_18get_ploidy(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  uint32_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_ploidy", 0);

  /* "whatshap/core.pyx":485
 * 
 * 	def get_ploidy(self):
 * 		return self.thisptr.get_ploidy()             # <<<<<<<<<<<<<<
 * 
 * 	def __eq__(self, Genotype g):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_ploidy();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 485, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 485, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":484
 * 		return self.thisptr.is_diploid_and_biallelic()
 * 
 * 	def get_ploidy(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_ploidy()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.get_ploidy", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":487
 * 		return self.thisptr.get_ploidy()
 * 
 * 	def __eq__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] == g.thisptr[0]
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_21__eq__(PyObject *__pyx_v_self, PyObject *__pyx_v_g); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_21__eq__(PyObject *__pyx_v_self, PyObject *__pyx_v_g) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__eq__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_g), __pyx_ptype_8whatshap_4core_Genotype, 1, "g", 0))) __PYX_ERR(1, 487, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_20__eq__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_g));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_20__eq__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__eq__", 0);

  /* "whatshap/core.pyx":488
 * 
 * 	def __eq__(self, Genotype g):
 * 		return self.thisptr[0] == g.thisptr[0]             # <<<<<<<<<<<<<<
 * 
 * 	def __ne__(self, Genotype g):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = ((__pyx_v_self->thisptr[0]) == (__pyx_v_g->thisptr[0]));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 488, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 488, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":487
 * 		return self.thisptr.get_ploidy()
 * 
 * 	def __eq__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] == g.thisptr[0]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__eq__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":490
 * 		return self.thisptr[0] == g.thisptr[0]
 * 
 * 	def __ne__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] != g.thisptr[0]
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_23__ne__(PyObject *__pyx_v_self, PyObject *__pyx_v_g); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_23__ne__(PyObject *__pyx_v_self, PyObject *__pyx_v_g) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__ne__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_g), __pyx_ptype_8whatshap_4core_Genotype, 1, "g", 0))) __PYX_ERR(1, 490, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_22__ne__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_g));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_22__ne__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__ne__", 0);

  /* "whatshap/core.pyx":491
 * 
 * 	def __ne__(self, Genotype g):
 * 		return self.thisptr[0] != g.thisptr[0]             # <<<<<<<<<<<<<<
 * 
 * 	def __lt__(self, Genotype g):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = ((__pyx_v_self->thisptr[0]) != (__pyx_v_g->thisptr[0]));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 491, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 491, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":490
 * 		return self.thisptr[0] == g.thisptr[0]
 * 
 * 	def __ne__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] != g.thisptr[0]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__ne__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":493
 * 		return self.thisptr[0] != g.thisptr[0]
 * 
 * 	def __lt__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] < g.thisptr[0]
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_25__lt__(PyObject *__pyx_v_self, PyObject *__pyx_v_g); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_25__lt__(PyObject *__pyx_v_self, PyObject *__pyx_v_g) {
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__lt__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_g), __pyx_ptype_8whatshap_4core_Genotype, 1, "g", 0))) __PYX_ERR(1, 493, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_24__lt__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_g));

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_24__lt__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_g) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  bool __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__lt__", 0);

  /* "whatshap/core.pyx":494
 * 
 * 	def __lt__(self, Genotype g):
 * 		return self.thisptr[0] < g.thisptr[0]             # <<<<<<<<<<<<<<
 * 
 * 	def __getstate__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = ((__pyx_v_self->thisptr[0]) < (__pyx_v_g->thisptr[0]));
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 494, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 494, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":493
 * 		return self.thisptr[0] != g.thisptr[0]
 * 
 * 	def __lt__(self, Genotype g):             # <<<<<<<<<<<<<<
 * 		return self.thisptr[0] < g.thisptr[0]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__lt__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":496
 * 		return self.thisptr[0] < g.thisptr[0]
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return (self.thisptr.get_index(), self.thisptr.get_ploidy())
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_27__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_27__getstate__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__getstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_26__getstate__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_26__getstate__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  uint64_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  uint32_t __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__getstate__", 0);

  /* "whatshap/core.pyx":497
 * 
 * 	def __getstate__(self):
 * 		return (self.thisptr.get_index(), self.thisptr.get_ploidy())             # <<<<<<<<<<<<<<
 * 
 * 	def __setstate__(self, state):
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_index();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 497, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint64_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 497, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  try {
    __pyx_t_3 = __pyx_v_self->thisptr->get_ploidy();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 497, __pyx_L1_error)
  }
  __pyx_t_4 = __Pyx_PyInt_From_uint32_t(__pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 497, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 497, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_GIVEREF(__pyx_t_2);
  PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
  __Pyx_GIVEREF(__pyx_t_4);
  PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_4);
  __pyx_t_2 = 0;
  __pyx_t_4 = 0;
  __pyx_r = __pyx_t_5;
  __pyx_t_5 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":496
 * 		return self.thisptr[0] < g.thisptr[0]
 * 
 * 	def __getstate__(self):             # <<<<<<<<<<<<<<
 * 		return (self.thisptr.get_index(), self.thisptr.get_ploidy())
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("whatshap.core.Genotype.__getstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":499
 * 		return (self.thisptr.get_index(), self.thisptr.get_ploidy())
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		index, ploidy = state
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_29__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_29__setstate__(PyObject *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_28__setstate__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((PyObject *)__pyx_v_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_28__setstate__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, PyObject *__pyx_v_state) {
  PyObject *__pyx_v_index = NULL;
  PyObject *__pyx_v_ploidy = NULL;
  std::vector<uint32_t>  __pyx_v_alleles;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *(*__pyx_t_4)(PyObject *);
  uint64_t __pyx_t_5;
  uint32_t __pyx_t_6;
  std::vector<uint32_t>  __pyx_t_7;
  int __pyx_t_8;
  Genotype *__pyx_t_9;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate__", 0);

  /* "whatshap/core.pyx":500
 * 
 * 	def __setstate__(self, state):
 * 		index, ploidy = state             # <<<<<<<<<<<<<<
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 * 		if self.thisptr != NULL:
 */
  if ((likely(PyTuple_CheckExact(__pyx_v_state))) || (PyList_CheckExact(__pyx_v_state))) {
    PyObject* sequence = __pyx_v_state;
    Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
    if (unlikely(size != 2)) {
      if (size > 2) __Pyx_RaiseTooManyValuesError(2);
      else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
      __PYX_ERR(1, 500, __pyx_L1_error)
    }
    #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    if (likely(PyTuple_CheckExact(sequence))) {
      __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); 
    } else {
      __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
      __pyx_t_2 = PyList_GET_ITEM(sequence, 1); 
    }
    __Pyx_INCREF(__pyx_t_1);
    __Pyx_INCREF(__pyx_t_2);
    #else
    __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 500, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 500, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    #endif
  } else {
    Py_ssize_t index = -1;
    __pyx_t_3 = PyObject_GetIter(__pyx_v_state); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 500, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
    index = 0; __pyx_t_1 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_1)) goto __pyx_L3_unpacking_failed;
    __Pyx_GOTREF(__pyx_t_1);
    index = 1; __pyx_t_2 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_2)) goto __pyx_L3_unpacking_failed;
    __Pyx_GOTREF(__pyx_t_2);
    if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) __PYX_ERR(1, 500, __pyx_L1_error)
    __pyx_t_4 = NULL;
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    goto __pyx_L4_unpacking_done;
    __pyx_L3_unpacking_failed:;
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_4 = NULL;
    if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
    __PYX_ERR(1, 500, __pyx_L1_error)
    __pyx_L4_unpacking_done:;
  }
  __pyx_v_index = __pyx_t_1;
  __pyx_t_1 = 0;
  __pyx_v_ploidy = __pyx_t_2;
  __pyx_t_2 = 0;

  /* "whatshap/core.pyx":501
 * 	def __setstate__(self, state):
 * 		index, ploidy = state
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)             # <<<<<<<<<<<<<<
 * 		if self.thisptr != NULL:
 * 			del self.thisptr
 */
  __pyx_t_5 = __Pyx_PyInt_As_uint64_t(__pyx_v_index); if (unlikely((__pyx_t_5 == ((uint64_t)-1)) && PyErr_Occurred())) __PYX_ERR(1, 501, __pyx_L1_error)
  __pyx_t_6 = __Pyx_PyInt_As_uint32_t(__pyx_v_ploidy); if (unlikely((__pyx_t_6 == ((uint32_t)-1)) && PyErr_Occurred())) __PYX_ERR(1, 501, __pyx_L1_error)
  try {
    __pyx_t_7 = convert_index_to_alleles(__pyx_t_5, __pyx_t_6);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 501, __pyx_L1_error)
  }
  __pyx_v_alleles = __pyx_t_7;

  /* "whatshap/core.pyx":502
 * 		index, ploidy = state
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 * 		if self.thisptr != NULL:             # <<<<<<<<<<<<<<
 * 			del self.thisptr
 * 		self.thisptr = new cpp.Genotype(alleles)
 */
  __pyx_t_8 = ((__pyx_v_self->thisptr != NULL) != 0);
  if (__pyx_t_8) {

    /* "whatshap/core.pyx":503
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 * 		if self.thisptr != NULL:
 * 			del self.thisptr             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 */
    delete __pyx_v_self->thisptr;

    /* "whatshap/core.pyx":502
 * 		index, ploidy = state
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 * 		if self.thisptr != NULL:             # <<<<<<<<<<<<<<
 * 			del self.thisptr
 * 		self.thisptr = new cpp.Genotype(alleles)
 */
  }

  /* "whatshap/core.pyx":504
 * 		if self.thisptr != NULL:
 * 			del self.thisptr
 * 		self.thisptr = new cpp.Genotype(alleles)             # <<<<<<<<<<<<<<
 * 
 * 	def __deepcopy__(self, memo):
 */
  try {
    __pyx_t_9 = new Genotype(__pyx_v_alleles);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 504, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_9;

  /* "whatshap/core.pyx":499
 * 		return (self.thisptr.get_index(), self.thisptr.get_ploidy())
 * 
 * 	def __setstate__(self, state):             # <<<<<<<<<<<<<<
 * 		index, ploidy = state
 * 		cdef vector[uint32_t] alleles = cpp.convert_index_to_alleles(index, ploidy)
 */

  /* function exit code */
  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("whatshap.core.Genotype.__setstate__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_index);
  __Pyx_XDECREF(__pyx_v_ploidy);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":506
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 * 	def __deepcopy__(self, memo):             # <<<<<<<<<<<<<<
 * 		return Genotype.__new__(Genotype, self.as_vector())
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_31__deepcopy__(PyObject *__pyx_v_self, PyObject *__pyx_v_memo); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_31__deepcopy__(PyObject *__pyx_v_self, PyObject *__pyx_v_memo) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__deepcopy__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_30__deepcopy__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((PyObject *)__pyx_v_memo));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_30__deepcopy__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_memo) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__deepcopy__", 0);

  /* "whatshap/core.pyx":507
 * 
 * 	def __deepcopy__(self, memo):
 * 		return Genotype.__new__(Genotype, self.as_vector())             # <<<<<<<<<<<<<<
 * 
 * 	def __hash__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_as_vector); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 507, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 507, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 507, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_GIVEREF(__pyx_t_1);
  PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
  __pyx_t_1 = 0;
  __pyx_t_1 = ((PyObject *)__pyx_tp_new_8whatshap_4core_Genotype(((PyTypeObject *)__pyx_ptype_8whatshap_4core_Genotype), __pyx_t_2, NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 507, __pyx_L1_error)
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_r = ((PyObject *)__pyx_t_1);
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":506
 * 		self.thisptr = new cpp.Genotype(alleles)
 * 
 * 	def __deepcopy__(self, memo):             # <<<<<<<<<<<<<<
 * 		return Genotype.__new__(Genotype, self.as_vector())
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("whatshap.core.Genotype.__deepcopy__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":509
 * 		return Genotype.__new__(Genotype, self.as_vector())
 * 
 * 	def __hash__(self):             # <<<<<<<<<<<<<<
 * 		return hash(self.thisptr.get_index())
 * 
 */

/* Python wrapper */
static Py_hash_t __pyx_pw_8whatshap_4core_8Genotype_33__hash__(PyObject *__pyx_v_self); /*proto*/
static Py_hash_t __pyx_pw_8whatshap_4core_8Genotype_33__hash__(PyObject *__pyx_v_self) {
  Py_hash_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_32__hash__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static Py_hash_t __pyx_pf_8whatshap_4core_8Genotype_32__hash__(struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  Py_hash_t __pyx_r;
  __Pyx_RefNannyDeclarations
  uint64_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  Py_hash_t __pyx_t_3;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__hash__", 0);

  /* "whatshap/core.pyx":510
 * 
 * 	def __hash__(self):
 * 		return hash(self.thisptr.get_index())             # <<<<<<<<<<<<<<
 * 
 * 
 */
  try {
    __pyx_t_1 = __pyx_v_self->thisptr->get_index();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 510, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint64_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 510, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = PyObject_Hash(__pyx_t_2); if (unlikely(__pyx_t_3 == ((Py_hash_t)-1))) __PYX_ERR(1, 510, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_r = __pyx_t_3;
  goto __pyx_L0;

  /* "whatshap/core.pyx":509
 * 		return Genotype.__new__(Genotype, self.as_vector())
 * 
 * 	def __hash__(self):             # <<<<<<<<<<<<<<
 * 		return hash(self.thisptr.get_index())
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.Genotype.__hash__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  if (unlikely(__pyx_r == -1) && !PyErr_Occurred()) __pyx_r = -2;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_35__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_35__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_34__reduce_cython__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_34__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Genotype.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_37__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_8Genotype_37__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_8Genotype_36__setstate_cython__(((struct __pyx_obj_8whatshap_4core_Genotype *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_8Genotype_36__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_Genotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.Genotype.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":513
 * 
 * 
 * def get_max_genotype_ploidy():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_ploidy()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_3get_max_genotype_ploidy(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyMethodDef __pyx_mdef_8whatshap_4core_3get_max_genotype_ploidy = {"get_max_genotype_ploidy", (PyCFunction)__pyx_pw_8whatshap_4core_3get_max_genotype_ploidy, METH_NOARGS, 0};
static PyObject *__pyx_pw_8whatshap_4core_3get_max_genotype_ploidy(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_max_genotype_ploidy (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_2get_max_genotype_ploidy(__pyx_self);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_2get_max_genotype_ploidy(CYTHON_UNUSED PyObject *__pyx_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  uint32_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_max_genotype_ploidy", 0);

  /* "whatshap/core.pyx":514
 * 
 * def get_max_genotype_ploidy():
 * 	return cpp.get_max_genotype_ploidy()             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = get_max_genotype_ploidy();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 514, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 514, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":513
 * 
 * 
 * def get_max_genotype_ploidy():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_ploidy()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.get_max_genotype_ploidy", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":517
 * 
 * 
 * def get_max_genotype_alleles():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_alleles()
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_5get_max_genotype_alleles(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyMethodDef __pyx_mdef_8whatshap_4core_5get_max_genotype_alleles = {"get_max_genotype_alleles", (PyCFunction)__pyx_pw_8whatshap_4core_5get_max_genotype_alleles, METH_NOARGS, 0};
static PyObject *__pyx_pw_8whatshap_4core_5get_max_genotype_alleles(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_max_genotype_alleles (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_4get_max_genotype_alleles(__pyx_self);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_4get_max_genotype_alleles(CYTHON_UNUSED PyObject *__pyx_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  uint32_t __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_max_genotype_alleles", 0);

  /* "whatshap/core.pyx":518
 * 
 * def get_max_genotype_alleles():
 * 	return cpp.get_max_genotype_alleles()             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  try {
    __pyx_t_1 = get_max_genotype_alleles();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 518, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyInt_From_uint32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 518, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_r = __pyx_t_2;
  __pyx_t_2 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":517
 * 
 * 
 * def get_max_genotype_alleles():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_alleles()
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("whatshap.core.get_max_genotype_alleles", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":522
 * 
 * cdef class GenotypeDPTable:
 * 	def __cinit__(self, numeric_sample_ids, ReadSet readset, recombcost, Pedigree pedigree, positions = None):             # <<<<<<<<<<<<<<
 * 		"""Build the DP table from the given read set which is assumed to be sorted;
 * 		that is, the variants in each read must be sorted by position and the reads
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_15GenotypeDPTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_15GenotypeDPTable_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_numeric_sample_ids = 0;
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset = 0;
  PyObject *__pyx_v_recombcost = 0;
  struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree = 0;
  PyObject *__pyx_v_positions = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_numeric_sample_ids,&__pyx_n_s_readset,&__pyx_n_s_recombcost,&__pyx_n_s_pedigree,&__pyx_n_s_positions,0};
    PyObject* values[5] = {0,0,0,0,0};
    values[4] = ((PyObject *)Py_None);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        CYTHON_FALLTHROUGH;
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        CYTHON_FALLTHROUGH;
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_numeric_sample_ids)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_readset)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); __PYX_ERR(1, 522, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_recombcost)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); __PYX_ERR(1, 522, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  3:
        if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pedigree)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); __PYX_ERR(1, 522, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  4:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_positions);
          if (value) { values[4] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 522, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
        CYTHON_FALLTHROUGH;
        case  4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
        values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_numeric_sample_ids = values[0];
    __pyx_v_readset = ((struct __pyx_obj_8whatshap_4core_ReadSet *)values[1]);
    __pyx_v_recombcost = values[2];
    __pyx_v_pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)values[3]);
    __pyx_v_positions = values[4];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 522, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_readset), __pyx_ptype_8whatshap_4core_ReadSet, 1, "readset", 0))) __PYX_ERR(1, 522, __pyx_L1_error)
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_pedigree), __pyx_ptype_8whatshap_4core_Pedigree, 1, "pedigree", 0))) __PYX_ERR(1, 522, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_15GenotypeDPTable___cinit__(((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)__pyx_v_self), __pyx_v_numeric_sample_ids, __pyx_v_readset, __pyx_v_recombcost, __pyx_v_pedigree, __pyx_v_positions);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_15GenotypeDPTable___cinit__(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, PyObject *__pyx_v_numeric_sample_ids, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_recombcost, struct __pyx_obj_8whatshap_4core_Pedigree *__pyx_v_pedigree, PyObject *__pyx_v_positions) {
  std::vector<unsigned int>  *__pyx_v_c_positions;
  PyObject *__pyx_v_pos = NULL;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  std::vector<unsigned int>  *__pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  Py_ssize_t __pyx_t_5;
  PyObject *(*__pyx_t_6)(PyObject *);
  PyObject *__pyx_t_7 = NULL;
  unsigned int __pyx_t_8;
  std::vector<unsigned int>  __pyx_t_9;
  GenotypeDPTable *__pyx_t_10;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":527
 * 		in the read set must also be sorted (by position of their left-most variant).
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL             # <<<<<<<<<<<<<<
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 */
  __pyx_v_c_positions = NULL;

  /* "whatshap/core.pyx":528
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:             # <<<<<<<<<<<<<<
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 */
  __pyx_t_1 = (__pyx_v_positions != Py_None);
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (__pyx_t_2) {

    /* "whatshap/core.pyx":529
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()             # <<<<<<<<<<<<<<
 * 			for pos in positions:
 * 				c_positions.push_back(pos)
 */
    try {
      __pyx_t_3 = new std::vector<unsigned int> ();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 529, __pyx_L1_error)
    }
    __pyx_v_c_positions = __pyx_t_3;

    /* "whatshap/core.pyx":530
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:             # <<<<<<<<<<<<<<
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)
 */
    if (likely(PyList_CheckExact(__pyx_v_positions)) || PyTuple_CheckExact(__pyx_v_positions)) {
      __pyx_t_4 = __pyx_v_positions; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
      __pyx_t_6 = NULL;
    } else {
      __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_positions); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 530, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext; if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 530, __pyx_L1_error)
    }
    for (;;) {
      if (likely(!__pyx_t_6)) {
        if (likely(PyList_CheckExact(__pyx_t_4))) {
          if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(1, 530, __pyx_L1_error)
          #else
          __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 530, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          #endif
        } else {
          if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(1, 530, __pyx_L1_error)
          #else
          __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 530, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          #endif
        }
      } else {
        __pyx_t_7 = __pyx_t_6(__pyx_t_4);
        if (unlikely(!__pyx_t_7)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 530, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_7);
      }
      __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_7);
      __pyx_t_7 = 0;

      /* "whatshap/core.pyx":531
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 * 				c_positions.push_back(pos)             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)
 * 		self.pedigree = pedigree
 */
      __pyx_t_8 = __Pyx_PyInt_As_unsigned_int(__pyx_v_pos); if (unlikely((__pyx_t_8 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 531, __pyx_L1_error)
      try {
        __pyx_v_c_positions->push_back(__pyx_t_8);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 531, __pyx_L1_error)
      }

      /* "whatshap/core.pyx":530
 * 		if positions is not None:
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:             # <<<<<<<<<<<<<<
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)
 */
    }
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

    /* "whatshap/core.pyx":528
 * 		"""
 * 		cdef vector[unsigned int]* c_positions = NULL
 * 		if positions is not None:             # <<<<<<<<<<<<<<
 * 			c_positions = new vector[unsigned int]()
 * 			for pos in positions:
 */
  }

  /* "whatshap/core.pyx":532
 * 			for pos in positions:
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)             # <<<<<<<<<<<<<<
 * 		self.pedigree = pedigree
 * 		self.numeric_sample_ids = numeric_sample_ids
 */
  __pyx_t_9 = __pyx_convert_vector_from_py_unsigned_int(__pyx_v_recombcost); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 532, __pyx_L1_error)
  try {
    __pyx_t_10 = new GenotypeDPTable(__pyx_v_readset->thisptr, __pyx_t_9, __pyx_v_pedigree->thisptr, __pyx_v_c_positions);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 532, __pyx_L1_error)
  }
  __pyx_v_self->thisptr = __pyx_t_10;

  /* "whatshap/core.pyx":533
 * 				c_positions.push_back(pos)
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)
 * 		self.pedigree = pedigree             # <<<<<<<<<<<<<<
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 */
  __Pyx_INCREF(((PyObject *)__pyx_v_pedigree));
  __Pyx_GIVEREF(((PyObject *)__pyx_v_pedigree));
  __Pyx_GOTREF(__pyx_v_self->pedigree);
  __Pyx_DECREF(((PyObject *)__pyx_v_self->pedigree));
  __pyx_v_self->pedigree = __pyx_v_pedigree;

  /* "whatshap/core.pyx":534
 * 		self.thisptr = new cpp.GenotypeDPTable(readset.thisptr, recombcost, pedigree.thisptr, c_positions)
 * 		self.pedigree = pedigree
 * 		self.numeric_sample_ids = numeric_sample_ids             # <<<<<<<<<<<<<<
 * 
 * 	def __dealloc__(self):
 */
  if (!(likely(((__pyx_v_numeric_sample_ids) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_numeric_sample_ids, __pyx_ptype_8whatshap_4core_NumericSampleIds))))) __PYX_ERR(1, 534, __pyx_L1_error)
  __pyx_t_4 = __pyx_v_numeric_sample_ids;
  __Pyx_INCREF(__pyx_t_4);
  __Pyx_GIVEREF(__pyx_t_4);
  __Pyx_GOTREF(__pyx_v_self->numeric_sample_ids);
  __Pyx_DECREF(((PyObject *)__pyx_v_self->numeric_sample_ids));
  __pyx_v_self->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)__pyx_t_4);
  __pyx_t_4 = 0;

  /* "whatshap/core.pyx":522
 * 
 * cdef class GenotypeDPTable:
 * 	def __cinit__(self, numeric_sample_ids, ReadSet readset, recombcost, Pedigree pedigree, positions = None):             # <<<<<<<<<<<<<<
 * 		"""Build the DP table from the given read set which is assumed to be sorted;
 * 		that is, the variants in each read must be sorted by position and the reads
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_pos);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":536
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_15GenotypeDPTable_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_15GenotypeDPTable_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_15GenotypeDPTable_2__dealloc__(((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_15GenotypeDPTable_2__dealloc__(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":537
 * 
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 
 * 	def get_genotype_likelihoods(self, sample_id, unsigned int pos):
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":536
 * 		self.numeric_sample_ids = numeric_sample_ids
 * 
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":539
 * 		del self.thisptr
 * 
 * 	def get_genotype_likelihoods(self, sample_id, unsigned int pos):             # <<<<<<<<<<<<<<
 * 		return PhredGenotypeLikelihoods(self.thisptr.get_genotype_likelihoods(self.numeric_sample_ids[sample_id],pos))
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_5get_genotype_likelihoods(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_5get_genotype_likelihoods(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_sample_id = 0;
  unsigned int __pyx_v_pos;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_genotype_likelihoods (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_sample_id,&__pyx_n_s_pos,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_sample_id)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pos)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("get_genotype_likelihoods", 1, 2, 2, 1); __PYX_ERR(1, 539, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_genotype_likelihoods") < 0)) __PYX_ERR(1, 539, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_sample_id = values[0];
    __pyx_v_pos = __Pyx_PyInt_As_unsigned_int(values[1]); if (unlikely((__pyx_v_pos == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 539, __pyx_L3_error)
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("get_genotype_likelihoods", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 539, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.get_genotype_likelihoods", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_8whatshap_4core_15GenotypeDPTable_4get_genotype_likelihoods(((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)__pyx_v_self), __pyx_v_sample_id, __pyx_v_pos);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_4get_genotype_likelihoods(struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, PyObject *__pyx_v_sample_id, unsigned int __pyx_v_pos) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  unsigned int __pyx_t_2;
  std::vector<long double>  __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_genotype_likelihoods", 0);

  /* "whatshap/core.pyx":540
 * 
 * 	def get_genotype_likelihoods(self, sample_id, unsigned int pos):
 * 		return PhredGenotypeLikelihoods(self.thisptr.get_genotype_likelihoods(self.numeric_sample_ids[sample_id],pos))             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_GetItem(((PyObject *)__pyx_v_self->numeric_sample_ids), __pyx_v_sample_id); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 540, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_unsigned_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 540, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  try {
    __pyx_t_3 = __pyx_v_self->thisptr->get_genotype_likelihoods(__pyx_t_2, __pyx_v_pos);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 540, __pyx_L1_error)
  }
  __pyx_t_1 = __pyx_convert_vector_to_py_long__double(__pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 540, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods), __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 540, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_r = __pyx_t_4;
  __pyx_t_4 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":539
 * 		del self.thisptr
 * 
 * 	def get_genotype_likelihoods(self, sample_id, unsigned int pos):             # <<<<<<<<<<<<<<
 * 		return PhredGenotypeLikelihoods(self.thisptr.get_genotype_likelihoods(self.numeric_sample_ids[sample_id],pos))
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.get_genotype_likelihoods", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15GenotypeDPTable_6__reduce_cython__(((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_9__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_15GenotypeDPTable_9__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_15GenotypeDPTable_8__setstate_cython__(((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_15GenotypeDPTable_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_GenotypeDPTable *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.GenotypeDPTable.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":543
 * 
 * 
 * def compute_genotypes(ReadSet readset, positions = None):             # <<<<<<<<<<<<<<
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_7compute_genotypes(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyMethodDef __pyx_mdef_8whatshap_4core_7compute_genotypes = {"compute_genotypes", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_7compute_genotypes, METH_VARARGS|METH_KEYWORDS, 0};
static PyObject *__pyx_pw_8whatshap_4core_7compute_genotypes(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset = 0;
  PyObject *__pyx_v_positions = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("compute_genotypes (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_readset,&__pyx_n_s_positions,0};
    PyObject* values[2] = {0,0};
    values[1] = ((PyObject *)Py_None);
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_readset)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_positions);
          if (value) { values[1] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compute_genotypes") < 0)) __PYX_ERR(1, 543, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_readset = ((struct __pyx_obj_8whatshap_4core_ReadSet *)values[0]);
    __pyx_v_positions = values[1];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("compute_genotypes", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 543, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.compute_genotypes", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_readset), __pyx_ptype_8whatshap_4core_ReadSet, 1, "readset", 0))) __PYX_ERR(1, 543, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_6compute_genotypes(__pyx_self, __pyx_v_readset, __pyx_v_positions);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_6compute_genotypes(CYTHON_UNUSED PyObject *__pyx_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset, PyObject *__pyx_v_positions) {
  std::vector<Genotype>  *__pyx_v_genotypes_vector;
  std::vector<GenotypeDistribution>  *__pyx_v_gl_vector;
  std::vector<unsigned int>  *__pyx_v_c_positions;
  PyObject *__pyx_v_pos = NULL;
  PyObject *__pyx_v_genotypes = NULL;
  PyObject *__pyx_v_gls = NULL;
  Genotype __pyx_8genexpr6__pyx_v_genotype;
  std::vector<GenotypeDistribution> ::size_type __pyx_8genexpr7__pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::vector<Genotype>  *__pyx_t_1;
  std::vector<GenotypeDistribution>  *__pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  std::vector<unsigned int>  *__pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  Py_ssize_t __pyx_t_7;
  PyObject *(*__pyx_t_8)(PyObject *);
  PyObject *__pyx_t_9 = NULL;
  unsigned int __pyx_t_10;
  std::vector<Genotype> ::iterator __pyx_t_11;
  Genotype __pyx_t_12;
  std::vector<uint32_t>  __pyx_t_13;
  PyObject *__pyx_t_14 = NULL;
  std::vector<GenotypeDistribution> ::size_type __pyx_t_15;
  std::vector<GenotypeDistribution> ::size_type __pyx_t_16;
  std::vector<GenotypeDistribution> ::size_type __pyx_t_17;
  double __pyx_t_18;
  PyObject *__pyx_t_19 = NULL;
  PyObject *__pyx_t_20 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("compute_genotypes", 0);

  /* "whatshap/core.pyx":544
 * 
 * def compute_genotypes(ReadSet readset, positions = None):
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()             # <<<<<<<<<<<<<<
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 * 	cdef vector[unsigned int]* c_positions = NULL
 */
  try {
    __pyx_t_1 = new std::vector<Genotype> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 544, __pyx_L1_error)
  }
  __pyx_v_genotypes_vector = __pyx_t_1;

  /* "whatshap/core.pyx":545
 * def compute_genotypes(ReadSet readset, positions = None):
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()             # <<<<<<<<<<<<<<
 * 	cdef vector[unsigned int]* c_positions = NULL
 * 	if positions is not None:
 */
  try {
    __pyx_t_2 = new std::vector<GenotypeDistribution> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 545, __pyx_L1_error)
  }
  __pyx_v_gl_vector = __pyx_t_2;

  /* "whatshap/core.pyx":546
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 * 	cdef vector[unsigned int]* c_positions = NULL             # <<<<<<<<<<<<<<
 * 	if positions is not None:
 * 		c_positions = new vector[unsigned int]()
 */
  __pyx_v_c_positions = NULL;

  /* "whatshap/core.pyx":547
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 * 	cdef vector[unsigned int]* c_positions = NULL
 * 	if positions is not None:             # <<<<<<<<<<<<<<
 * 		c_positions = new vector[unsigned int]()
 * 		for pos in positions:
 */
  __pyx_t_3 = (__pyx_v_positions != Py_None);
  __pyx_t_4 = (__pyx_t_3 != 0);
  if (__pyx_t_4) {

    /* "whatshap/core.pyx":548
 * 	cdef vector[unsigned int]* c_positions = NULL
 * 	if positions is not None:
 * 		c_positions = new vector[unsigned int]()             # <<<<<<<<<<<<<<
 * 		for pos in positions:
 * 			c_positions.push_back(pos)
 */
    try {
      __pyx_t_5 = new std::vector<unsigned int> ();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 548, __pyx_L1_error)
    }
    __pyx_v_c_positions = __pyx_t_5;

    /* "whatshap/core.pyx":549
 * 	if positions is not None:
 * 		c_positions = new vector[unsigned int]()
 * 		for pos in positions:             # <<<<<<<<<<<<<<
 * 			c_positions.push_back(pos)
 * 	cpp.compute_genotypes(readset.thisptr[0], genotypes_vector, gl_vector, c_positions)
 */
    if (likely(PyList_CheckExact(__pyx_v_positions)) || PyTuple_CheckExact(__pyx_v_positions)) {
      __pyx_t_6 = __pyx_v_positions; __Pyx_INCREF(__pyx_t_6); __pyx_t_7 = 0;
      __pyx_t_8 = NULL;
    } else {
      __pyx_t_7 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_v_positions); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 549, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_8 = Py_TYPE(__pyx_t_6)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 549, __pyx_L1_error)
    }
    for (;;) {
      if (likely(!__pyx_t_8)) {
        if (likely(PyList_CheckExact(__pyx_t_6))) {
          if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_6)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(1, 549, __pyx_L1_error)
          #else
          __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 549, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_9);
          #endif
        } else {
          if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(1, 549, __pyx_L1_error)
          #else
          __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 549, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_9);
          #endif
        }
      } else {
        __pyx_t_9 = __pyx_t_8(__pyx_t_6);
        if (unlikely(!__pyx_t_9)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(1, 549, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_9);
      }
      __Pyx_XDECREF_SET(__pyx_v_pos, __pyx_t_9);
      __pyx_t_9 = 0;

      /* "whatshap/core.pyx":550
 * 		c_positions = new vector[unsigned int]()
 * 		for pos in positions:
 * 			c_positions.push_back(pos)             # <<<<<<<<<<<<<<
 * 	cpp.compute_genotypes(readset.thisptr[0], genotypes_vector, gl_vector, c_positions)
 * 	# TODO: Inefficient
 */
      __pyx_t_10 = __Pyx_PyInt_As_unsigned_int(__pyx_v_pos); if (unlikely((__pyx_t_10 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(1, 550, __pyx_L1_error)
      try {
        __pyx_v_c_positions->push_back(__pyx_t_10);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 550, __pyx_L1_error)
      }

      /* "whatshap/core.pyx":549
 * 	if positions is not None:
 * 		c_positions = new vector[unsigned int]()
 * 		for pos in positions:             # <<<<<<<<<<<<<<
 * 			c_positions.push_back(pos)
 * 	cpp.compute_genotypes(readset.thisptr[0], genotypes_vector, gl_vector, c_positions)
 */
    }
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

    /* "whatshap/core.pyx":547
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 * 	cdef vector[unsigned int]* c_positions = NULL
 * 	if positions is not None:             # <<<<<<<<<<<<<<
 * 		c_positions = new vector[unsigned int]()
 * 		for pos in positions:
 */
  }

  /* "whatshap/core.pyx":551
 * 		for pos in positions:
 * 			c_positions.push_back(pos)
 * 	cpp.compute_genotypes(readset.thisptr[0], genotypes_vector, gl_vector, c_positions)             # <<<<<<<<<<<<<<
 * 	# TODO: Inefficient
 * 	genotypes = [Genotype(genotype.as_vector()) for genotype in genotypes_vector[0]]
 */
  try {
    compute_genotypes((__pyx_v_readset->thisptr[0]), __pyx_v_genotypes_vector, __pyx_v_gl_vector, __pyx_v_c_positions);
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 551, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":553
 * 	cpp.compute_genotypes(readset.thisptr[0], genotypes_vector, gl_vector, c_positions)
 * 	# TODO: Inefficient
 * 	genotypes = [Genotype(genotype.as_vector()) for genotype in genotypes_vector[0]]             # <<<<<<<<<<<<<<
 * 	#genotypes = list(genotypes_vector[0])
 * 	gls = [(gl_vector[0][i].probabilityOf(0), gl_vector[0][i].probabilityOf(1), gl_vector[0][i].probabilityOf(2)) for i in range(gl_vector[0].size())]
 */
  { /* enter inner scope */
    __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 553, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_1 = &(__pyx_v_genotypes_vector[0]);
    __pyx_t_11 = __pyx_t_1->begin();
    for (;;) {
      if (!(__pyx_t_11 != __pyx_t_1->end())) break;
      __pyx_t_12 = *__pyx_t_11;
      ++__pyx_t_11;
      __pyx_8genexpr6__pyx_v_genotype = __pyx_t_12;
      try {
        __pyx_t_13 = __pyx_8genexpr6__pyx_v_genotype.as_vector();
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 553, __pyx_L1_error)
      }
      __pyx_t_9 = __pyx_convert_vector_to_py_uint32_t(__pyx_t_13); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 553, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_9);
      __pyx_t_14 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_8whatshap_4core_Genotype), __pyx_t_9); if (unlikely(!__pyx_t_14)) __PYX_ERR(1, 553, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_14);
      __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_14))) __PYX_ERR(1, 553, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    }
  } /* exit inner scope */
  __pyx_v_genotypes = ((PyObject*)__pyx_t_6);
  __pyx_t_6 = 0;

  /* "whatshap/core.pyx":555
 * 	genotypes = [Genotype(genotype.as_vector()) for genotype in genotypes_vector[0]]
 * 	#genotypes = list(genotypes_vector[0])
 * 	gls = [(gl_vector[0][i].probabilityOf(0), gl_vector[0][i].probabilityOf(1), gl_vector[0][i].probabilityOf(2)) for i in range(gl_vector[0].size())]             # <<<<<<<<<<<<<<
 * 	del genotypes_vector
 * 	del gl_vector
 */
  { /* enter inner scope */
    __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 555, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_15 = (__pyx_v_gl_vector[0]).size();
    __pyx_t_16 = __pyx_t_15;
    for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) {
      __pyx_8genexpr7__pyx_v_i = __pyx_t_17;
      try {
        __pyx_t_18 = ((__pyx_v_gl_vector[0])[__pyx_8genexpr7__pyx_v_i]).probabilityOf(0);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 555, __pyx_L1_error)
      }
      __pyx_t_14 = PyFloat_FromDouble(__pyx_t_18); if (unlikely(!__pyx_t_14)) __PYX_ERR(1, 555, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_14);
      try {
        __pyx_t_18 = ((__pyx_v_gl_vector[0])[__pyx_8genexpr7__pyx_v_i]).probabilityOf(1);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 555, __pyx_L1_error)
      }
      __pyx_t_9 = PyFloat_FromDouble(__pyx_t_18); if (unlikely(!__pyx_t_9)) __PYX_ERR(1, 555, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_9);
      try {
        __pyx_t_18 = ((__pyx_v_gl_vector[0])[__pyx_8genexpr7__pyx_v_i]).probabilityOf(2);
      } catch(...) {
        __Pyx_CppExn2PyErr();
        __PYX_ERR(1, 555, __pyx_L1_error)
      }
      __pyx_t_19 = PyFloat_FromDouble(__pyx_t_18); if (unlikely(!__pyx_t_19)) __PYX_ERR(1, 555, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_20 = PyTuple_New(3); if (unlikely(!__pyx_t_20)) __PYX_ERR(1, 555, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_20);
      __Pyx_GIVEREF(__pyx_t_14);
      PyTuple_SET_ITEM(__pyx_t_20, 0, __pyx_t_14);
      __Pyx_GIVEREF(__pyx_t_9);
      PyTuple_SET_ITEM(__pyx_t_20, 1, __pyx_t_9);
      __Pyx_GIVEREF(__pyx_t_19);
      PyTuple_SET_ITEM(__pyx_t_20, 2, __pyx_t_19);
      __pyx_t_14 = 0;
      __pyx_t_9 = 0;
      __pyx_t_19 = 0;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_20))) __PYX_ERR(1, 555, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
    }
  } /* exit inner scope */
  __pyx_v_gls = ((PyObject*)__pyx_t_6);
  __pyx_t_6 = 0;

  /* "whatshap/core.pyx":556
 * 	#genotypes = list(genotypes_vector[0])
 * 	gls = [(gl_vector[0][i].probabilityOf(0), gl_vector[0][i].probabilityOf(1), gl_vector[0][i].probabilityOf(2)) for i in range(gl_vector[0].size())]
 * 	del genotypes_vector             # <<<<<<<<<<<<<<
 * 	del gl_vector
 * 	return genotypes, gls
 */
  delete __pyx_v_genotypes_vector;

  /* "whatshap/core.pyx":557
 * 	gls = [(gl_vector[0][i].probabilityOf(0), gl_vector[0][i].probabilityOf(1), gl_vector[0][i].probabilityOf(2)) for i in range(gl_vector[0].size())]
 * 	del genotypes_vector
 * 	del gl_vector             # <<<<<<<<<<<<<<
 * 	return genotypes, gls
 * 
 */
  delete __pyx_v_gl_vector;

  /* "whatshap/core.pyx":558
 * 	del genotypes_vector
 * 	del gl_vector
 * 	return genotypes, gls             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 558, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_INCREF(__pyx_v_genotypes);
  __Pyx_GIVEREF(__pyx_v_genotypes);
  PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_genotypes);
  __Pyx_INCREF(__pyx_v_gls);
  __Pyx_GIVEREF(__pyx_v_gls);
  PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_gls);
  __pyx_r = __pyx_t_6;
  __pyx_t_6 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":543
 * 
 * 
 * def compute_genotypes(ReadSet readset, positions = None):             # <<<<<<<<<<<<<<
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_14);
  __Pyx_XDECREF(__pyx_t_19);
  __Pyx_XDECREF(__pyx_t_20);
  __Pyx_AddTraceback("whatshap.core.compute_genotypes", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_pos);
  __Pyx_XDECREF(__pyx_v_genotypes);
  __Pyx_XDECREF(__pyx_v_gls);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":562
 * 
 * cdef class HapChatCore:
 * 	def __cinit__(self, ReadSet readset):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)
 * 	def __dealloc__(self):
 */

/* Python wrapper */
static int __pyx_pw_8whatshap_4core_11HapChatCore_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_8whatshap_4core_11HapChatCore_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_readset,0};
    PyObject* values[1] = {0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_readset)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(1, 562, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
    }
    __pyx_v_readset = ((struct __pyx_obj_8whatshap_4core_ReadSet *)values[0]);
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 562, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("whatshap.core.HapChatCore.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_readset), __pyx_ptype_8whatshap_4core_ReadSet, 1, "readset", 0))) __PYX_ERR(1, 562, __pyx_L1_error)
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore___cinit__(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self), __pyx_v_readset);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static int __pyx_pf_8whatshap_4core_11HapChatCore___cinit__(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self, struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_readset) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "whatshap/core.pyx":563
 * cdef class HapChatCore:
 * 	def __cinit__(self, ReadSet readset):
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)             # <<<<<<<<<<<<<<
 * 	def __dealloc__(self):
 * 		del self.thisptr
 */
  __pyx_v_self->thisptr = new HapChatCore(__pyx_v_readset->thisptr);

  /* "whatshap/core.pyx":562
 * 
 * cdef class HapChatCore:
 * 	def __cinit__(self, ReadSet readset):             # <<<<<<<<<<<<<<
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)
 * 	def __dealloc__(self):
 */

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":564
 * 	def __cinit__(self, ReadSet readset):
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 	def get_length(self):
 */

/* Python wrapper */
static void __pyx_pw_8whatshap_4core_11HapChatCore_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_8whatshap_4core_11HapChatCore_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_8whatshap_4core_11HapChatCore_2__dealloc__(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

static void __pyx_pf_8whatshap_4core_11HapChatCore_2__dealloc__(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "whatshap/core.pyx":565
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)
 * 	def __dealloc__(self):
 * 		del self.thisptr             # <<<<<<<<<<<<<<
 * 	def get_length(self):
 * 		return self.thisptr.get_length()
 */
  delete __pyx_v_self->thisptr;

  /* "whatshap/core.pyx":564
 * 	def __cinit__(self, ReadSet readset):
 * 		self.thisptr = new cpp.HapChatCore(readset.thisptr)
 * 	def __dealloc__(self):             # <<<<<<<<<<<<<<
 * 		del self.thisptr
 * 	def get_length(self):
 */

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

/* "whatshap/core.pyx":566
 * 	def __dealloc__(self):
 * 		del self.thisptr
 * 	def get_length(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_length()
 * 	def get_super_reads(self):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_5get_length(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_5get_length(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_length (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_4get_length(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_4get_length(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_length", 0);

  /* "whatshap/core.pyx":567
 * 		del self.thisptr
 * 	def get_length(self):
 * 		return self.thisptr.get_length()             # <<<<<<<<<<<<<<
 * 	def get_super_reads(self):
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->get_length()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 567, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":566
 * 	def __dealloc__(self):
 * 		del self.thisptr
 * 	def get_length(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_length()
 * 	def get_super_reads(self):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.get_length", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":568
 * 	def get_length(self):
 * 		return self.thisptr.get_length()
 * 	def get_super_reads(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 * 		leng=self.thisptr.get_length()
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_7get_super_reads(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_7get_super_reads(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_super_reads (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  std::vector<ReadSet *>  *__pyx_v_read_sets;
  int __pyx_v_leng;
  std::vector<ReadSet *> ::size_type __pyx_v_i;
  PyObject *__pyx_v_results = NULL;
  struct __pyx_obj_8whatshap_4core_ReadSet *__pyx_v_rs = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  std::vector<ReadSet *>  *__pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  std::vector<ReadSet *> ::size_type __pyx_t_4;
  ReadSet *__pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  std::vector<ReadSet *> ::size_type __pyx_t_7;
  std::vector<ReadSet *> ::size_type __pyx_t_8;
  int __pyx_t_9;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_super_reads", 0);

  /* "whatshap/core.pyx":569
 * 		return self.thisptr.get_length()
 * 	def get_super_reads(self):
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()             # <<<<<<<<<<<<<<
 * 		leng=self.thisptr.get_length()
 * 		for i in range(leng):
 */
  try {
    __pyx_t_1 = new std::vector<ReadSet *> ();
  } catch(...) {
    __Pyx_CppExn2PyErr();
    __PYX_ERR(1, 569, __pyx_L1_error)
  }
  __pyx_v_read_sets = __pyx_t_1;

  /* "whatshap/core.pyx":570
 * 	def get_super_reads(self):
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 * 		leng=self.thisptr.get_length()             # <<<<<<<<<<<<<<
 * 		for i in range(leng):
 * 			read_sets.push_back(new cpp.ReadSet())
 */
  __pyx_v_leng = __pyx_v_self->thisptr->get_length();

  /* "whatshap/core.pyx":571
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 * 		leng=self.thisptr.get_length()
 * 		for i in range(leng):             # <<<<<<<<<<<<<<
 * 			read_sets.push_back(new cpp.ReadSet())
 * 		self.thisptr.get_super_reads(read_sets)
 */
  __pyx_t_2 = __pyx_v_leng;
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "whatshap/core.pyx":572
 * 		leng=self.thisptr.get_length()
 * 		for i in range(leng):
 * 			read_sets.push_back(new cpp.ReadSet())             # <<<<<<<<<<<<<<
 * 		self.thisptr.get_super_reads(read_sets)
 * 
 */
    try {
      __pyx_t_5 = new ReadSet();
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 572, __pyx_L1_error)
    }
    try {
      __pyx_v_read_sets->push_back(__pyx_t_5);
    } catch(...) {
      __Pyx_CppExn2PyErr();
      __PYX_ERR(1, 572, __pyx_L1_error)
    }
  }

  /* "whatshap/core.pyx":573
 * 		for i in range(leng):
 * 			read_sets.push_back(new cpp.ReadSet())
 * 		self.thisptr.get_super_reads(read_sets)             # <<<<<<<<<<<<<<
 * 
 * 		results = []
 */
  __pyx_v_self->thisptr->get_super_reads(__pyx_v_read_sets);

  /* "whatshap/core.pyx":575
 * 		self.thisptr.get_super_reads(read_sets)
 * 
 * 		results = []             # <<<<<<<<<<<<<<
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()
 */
  __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 575, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_v_results = ((PyObject*)__pyx_t_6);
  __pyx_t_6 = 0;

  /* "whatshap/core.pyx":576
 * 
 * 		results = []
 * 		for i in range(read_sets.size()):             # <<<<<<<<<<<<<<
 * 			rs = ReadSet()
 * 			del rs.thisptr
 */
  __pyx_t_4 = __pyx_v_read_sets->size();
  __pyx_t_7 = __pyx_t_4;
  for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
    __pyx_v_i = __pyx_t_8;

    /* "whatshap/core.pyx":577
 * 		results = []
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()             # <<<<<<<<<<<<<<
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]
 */
    __pyx_t_6 = __Pyx_PyObject_CallNoArg(((PyObject *)__pyx_ptype_8whatshap_4core_ReadSet)); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 577, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_XDECREF_SET(__pyx_v_rs, ((struct __pyx_obj_8whatshap_4core_ReadSet *)__pyx_t_6));
    __pyx_t_6 = 0;

    /* "whatshap/core.pyx":578
 * 		for i in range(read_sets.size()):
 * 			rs = ReadSet()
 * 			del rs.thisptr             # <<<<<<<<<<<<<<
 * 			rs.thisptr = deref(read_sets)[i]
 * 			results.append(rs)
 */
    delete __pyx_v_rs->thisptr;

    /* "whatshap/core.pyx":579
 * 			rs = ReadSet()
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]             # <<<<<<<<<<<<<<
 * 			results.append(rs)
 * 
 */
    __pyx_v_rs->thisptr = ((*__pyx_v_read_sets)[__pyx_v_i]);

    /* "whatshap/core.pyx":580
 * 			del rs.thisptr
 * 			rs.thisptr = deref(read_sets)[i]
 * 			results.append(rs)             # <<<<<<<<<<<<<<
 * 
 * 		return results, None
 */
    __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_results, ((PyObject *)__pyx_v_rs)); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(1, 580, __pyx_L1_error)
  }

  /* "whatshap/core.pyx":582
 * 			results.append(rs)
 * 
 * 		return results, None             # <<<<<<<<<<<<<<
 * 	def get_optimal_cost(self):
 * 		return self.thisptr.get_optimal_cost()
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 582, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_INCREF(__pyx_v_results);
  __Pyx_GIVEREF(__pyx_v_results);
  PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_results);
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  PyTuple_SET_ITEM(__pyx_t_6, 1, Py_None);
  __pyx_r = __pyx_t_6;
  __pyx_t_6 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":568
 * 	def get_length(self):
 * 		return self.thisptr.get_length()
 * 	def get_super_reads(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[cpp.ReadSet*]* read_sets = new vector[cpp.ReadSet*]()
 * 		leng=self.thisptr.get_length()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.get_super_reads", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_results);
  __Pyx_XDECREF((PyObject *)__pyx_v_rs);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":583
 * 
 * 		return results, None
 * 	def get_optimal_cost(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_optimal_cost()
 * 	def get_optimal_partitioning(self):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_9get_optimal_cost(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_9get_optimal_cost(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_optimal_cost (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_8get_optimal_cost(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_8get_optimal_cost(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_optimal_cost", 0);

  /* "whatshap/core.pyx":584
 * 		return results, None
 * 	def get_optimal_cost(self):
 * 		return self.thisptr.get_optimal_cost()             # <<<<<<<<<<<<<<
 * 	def get_optimal_partitioning(self):
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->thisptr->get_optimal_cost()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 584, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "whatshap/core.pyx":583
 * 
 * 		return results, None
 * 	def get_optimal_cost(self):             # <<<<<<<<<<<<<<
 * 		return self.thisptr.get_optimal_cost()
 * 	def get_optimal_partitioning(self):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.get_optimal_cost", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "whatshap/core.pyx":585
 * 	def get_optimal_cost(self):
 * 		return self.thisptr.get_optimal_cost()
 * 	def get_optimal_partitioning(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = ['*' for x in p[0]]
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_11get_optimal_partitioning(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_11get_optimal_partitioning(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("get_optimal_partitioning (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_10get_optimal_partitioning(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_10get_optimal_partitioning(struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  std::vector<bool>  *__pyx_v_p;
  PyObject *__pyx_v_result = NULL;
  CYTHON_UNUSED bool __pyx_8genexpr8__pyx_v_x;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  std::vector<bool> ::iterator __pyx_t_2;
  std::vector<bool>  *__pyx_t_3;
  bool __pyx_t_4;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get_optimal_partitioning", 0);

  /* "whatshap/core.pyx":586
 * 		return self.thisptr.get_optimal_cost()
 * 	def get_optimal_partitioning(self):
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()             # <<<<<<<<<<<<<<
 * 		result = ['*' for x in p[0]]
 * 		del p
 */
  __pyx_v_p = __pyx_v_self->thisptr->get_optimal_partitioning();

  /* "whatshap/core.pyx":587
 * 	def get_optimal_partitioning(self):
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = ['*' for x in p[0]]             # <<<<<<<<<<<<<<
 * 		del p
 * 		return result
 */
  { /* enter inner scope */
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 587, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = &(__pyx_v_p[0]);
    __pyx_t_2 = __pyx_t_3->begin();
    for (;;) {
      if (!(__pyx_t_2 != __pyx_t_3->end())) break;
      __pyx_t_4 = *__pyx_t_2;
      ++__pyx_t_2;
      __pyx_8genexpr8__pyx_v_x = __pyx_t_4;
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_kp_u__22))) __PYX_ERR(1, 587, __pyx_L1_error)
    }
  } /* exit inner scope */
  __pyx_v_result = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "whatshap/core.pyx":588
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = ['*' for x in p[0]]
 * 		del p             # <<<<<<<<<<<<<<
 * 		return result
 */
  delete __pyx_v_p;

  /* "whatshap/core.pyx":589
 * 		result = ['*' for x in p[0]]
 * 		del p
 * 		return result             # <<<<<<<<<<<<<<
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_result);
  __pyx_r = __pyx_v_result;
  goto __pyx_L0;

  /* "whatshap/core.pyx":585
 * 	def get_optimal_cost(self):
 * 		return self.thisptr.get_optimal_cost()
 * 	def get_optimal_partitioning(self):             # <<<<<<<<<<<<<<
 * 		cdef vector[bool]* p = self.thisptr.get_optimal_partitioning()
 * 		result = ['*' for x in p[0]]
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.get_optimal_partitioning", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_13__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_13__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_12__reduce_cython__(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_15__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_8whatshap_4core_11HapChatCore_15__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_8whatshap_4core_11HapChatCore_14__setstate_cython__(((struct __pyx_obj_8whatshap_4core_HapChatCore *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_8whatshap_4core_11HapChatCore_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_8whatshap_4core_HapChatCore *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(0, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("whatshap.core.HapChatCore.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "vector.from_py":45
 * 
 * @cname("__pyx_convert_vector_from_py_double")
 * cdef vector[X] __pyx_convert_vector_from_py_double(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef vector[X] v
 *     for item in o:
 */

static std::vector<double>  __pyx_convert_vector_from_py_double(PyObject *__pyx_v_o) {
  std::vector<double>  __pyx_v_v;
  PyObject *__pyx_v_item = NULL;
  std::vector<double>  __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  PyObject *(*__pyx_t_3)(PyObject *);
  PyObject *__pyx_t_4 = NULL;
  double __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_from_py_double", 0);

  /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_double(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  if (likely(PyList_CheckExact(__pyx_v_o)) || PyTuple_CheckExact(__pyx_v_o)) {
    __pyx_t_1 = __pyx_v_o; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
    __pyx_t_3 = NULL;
  } else {
    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_o); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 47, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 47, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_3)) {
      if (likely(PyList_CheckExact(__pyx_t_1))) {
        if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      } else {
        if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      }
    } else {
      __pyx_t_4 = __pyx_t_3(__pyx_t_1);
      if (unlikely(!__pyx_t_4)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(0, 47, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_4);
    }
    __Pyx_XDECREF_SET(__pyx_v_item, __pyx_t_4);
    __pyx_t_4 = 0;

    /* "vector.from_py":48
 *     cdef vector[X] v
 *     for item in o:
 *         v.push_back(<X>item)             # <<<<<<<<<<<<<<
 *     return v
 * 
 */
    __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_v_item); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 48, __pyx_L1_error)
    __pyx_v_v.push_back(((double)__pyx_t_5));

    /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_double(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "vector.from_py":49
 *     for item in o:
 *         v.push_back(<X>item)
 *     return v             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_r = __pyx_v_v;
  goto __pyx_L0;

  /* "vector.from_py":45
 * 
 * @cname("__pyx_convert_vector_from_py_double")
 * cdef vector[X] __pyx_convert_vector_from_py_double(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef vector[X] v
 *     for item in o:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("vector.from_py.__pyx_convert_vector_from_py_double", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_pretend_to_initialize(&__pyx_r);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_item);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static std::vector<uint32_t>  __pyx_convert_vector_from_py_uint32_t(PyObject *__pyx_v_o) {
  std::vector<uint32_t>  __pyx_v_v;
  PyObject *__pyx_v_item = NULL;
  std::vector<uint32_t>  __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  PyObject *(*__pyx_t_3)(PyObject *);
  PyObject *__pyx_t_4 = NULL;
  uint32_t __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_from_py_uint32_t", 0);

  /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_uint32_t(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  if (likely(PyList_CheckExact(__pyx_v_o)) || PyTuple_CheckExact(__pyx_v_o)) {
    __pyx_t_1 = __pyx_v_o; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
    __pyx_t_3 = NULL;
  } else {
    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_o); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 47, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 47, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_3)) {
      if (likely(PyList_CheckExact(__pyx_t_1))) {
        if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      } else {
        if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      }
    } else {
      __pyx_t_4 = __pyx_t_3(__pyx_t_1);
      if (unlikely(!__pyx_t_4)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(0, 47, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_4);
    }
    __Pyx_XDECREF_SET(__pyx_v_item, __pyx_t_4);
    __pyx_t_4 = 0;

    /* "vector.from_py":48
 *     cdef vector[X] v
 *     for item in o:
 *         v.push_back(<X>item)             # <<<<<<<<<<<<<<
 *     return v
 * 
 */
    __pyx_t_5 = __Pyx_PyInt_As_uint32_t(__pyx_v_item); if (unlikely((__pyx_t_5 == ((uint32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 48, __pyx_L1_error)
    __pyx_v_v.push_back(((uint32_t)__pyx_t_5));

    /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_uint32_t(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "vector.from_py":49
 *     for item in o:
 *         v.push_back(<X>item)
 *     return v             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_r = __pyx_v_v;
  goto __pyx_L0;

  /* "vector.from_py":45
 * 
 * @cname("__pyx_convert_vector_from_py_uint32_t")
 * cdef vector[X] __pyx_convert_vector_from_py_uint32_t(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef vector[X] v
 *     for item in o:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("vector.from_py.__pyx_convert_vector_from_py_uint32_t", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_pretend_to_initialize(&__pyx_r);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_item);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.from_py":13
 * 
 * @cname("__pyx_convert_string_from_py_std__in_string")
 * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef Py_ssize_t length = 0
 *     cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length)
 */

static std::string __pyx_convert_string_from_py_std__in_string(PyObject *__pyx_v_o) {
  Py_ssize_t __pyx_v_length;
  char const *__pyx_v_data;
  std::string __pyx_r;
  __Pyx_RefNannyDeclarations
  char const *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_string_from_py_std__in_string", 0);

  /* "string.from_py":14
 * @cname("__pyx_convert_string_from_py_std__in_string")
 * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *:
 *     cdef Py_ssize_t length = 0             # <<<<<<<<<<<<<<
 *     cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length)
 *     return string(data, length)
 */
  __pyx_v_length = 0;

  /* "string.from_py":15
 * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *:
 *     cdef Py_ssize_t length = 0
 *     cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length)             # <<<<<<<<<<<<<<
 *     return string(data, length)
 * 
 */
  __pyx_t_1 = __Pyx_PyObject_AsStringAndSize(__pyx_v_o, (&__pyx_v_length)); if (unlikely(__pyx_t_1 == ((char const *)NULL))) __PYX_ERR(0, 15, __pyx_L1_error)
  __pyx_v_data = __pyx_t_1;

  /* "string.from_py":16
 *     cdef Py_ssize_t length = 0
 *     cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length)
 *     return string(data, length)             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_r = std::string(__pyx_v_data, __pyx_v_length);
  goto __pyx_L0;

  /* "string.from_py":13
 * 
 * @cname("__pyx_convert_string_from_py_std__in_string")
 * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef Py_ssize_t length = 0
 *     cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length)
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("string.from_py.__pyx_convert_string_from_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_pretend_to_initialize(&__pyx_r);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_int")
 * cdef object __pyx_convert_vector_to_py_int(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

static PyObject *__pyx_convert_vector_to_py_int(const std::vector<int>  &__pyx_v_v) {
  size_t __pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  size_t __pyx_t_2;
  size_t __pyx_t_3;
  size_t __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_to_py_int", 0);

  /* "vector.to_py":61
 * @cname("__pyx_convert_vector_to_py_int")
 * cdef object __pyx_convert_vector_to_py_int(vector[X]& v):
 *     return [v[i] for i in range(v.size())]             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __pyx_v_v.size();
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;
    __pyx_t_5 = __Pyx_PyInt_From_int((__pyx_v_v[__pyx_v_i])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_int")
 * cdef object __pyx_convert_vector_to_py_int(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("vector.to_py.__pyx_convert_vector_to_py_int", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.to_py":31
 * 
 * @cname("__pyx_convert_PyObject_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyObject_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

static CYTHON_INLINE PyObject *__pyx_convert_PyObject_string_to_py_std__in_string(std::string const &__pyx_v_s) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_PyObject_string_to_py_std__in_string", 0);

  /* "string.to_py":32
 * @cname("__pyx_convert_PyObject_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s):
 *     return __Pyx_PyObject_FromStringAndSize(s.data(), s.size())             # <<<<<<<<<<<<<<
 * cdef extern from *:
 *     cdef object __Pyx_PyUnicode_FromStringAndSize(const char*, size_t)
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyObject_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 32, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "string.to_py":31
 * 
 * @cname("__pyx_convert_PyObject_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyObject_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("string.to_py.__pyx_convert_PyObject_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.to_py":37
 * 
 * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

static CYTHON_INLINE PyObject *__pyx_convert_PyUnicode_string_to_py_std__in_string(std::string const &__pyx_v_s) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_PyUnicode_string_to_py_std__in_string", 0);

  /* "string.to_py":38
 * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s):
 *     return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size())             # <<<<<<<<<<<<<<
 * cdef extern from *:
 *     cdef object __Pyx_PyStr_FromStringAndSize(const char*, size_t)
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyUnicode_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 38, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "string.to_py":37
 * 
 * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("string.to_py.__pyx_convert_PyUnicode_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.to_py":43
 * 
 * @cname("__pyx_convert_PyStr_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyStr_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

static CYTHON_INLINE PyObject *__pyx_convert_PyStr_string_to_py_std__in_string(std::string const &__pyx_v_s) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_PyStr_string_to_py_std__in_string", 0);

  /* "string.to_py":44
 * @cname("__pyx_convert_PyStr_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s):
 *     return __Pyx_PyStr_FromStringAndSize(s.data(), s.size())             # <<<<<<<<<<<<<<
 * cdef extern from *:
 *     cdef object __Pyx_PyBytes_FromStringAndSize(const char*, size_t)
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyStr_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 44, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "string.to_py":43
 * 
 * @cname("__pyx_convert_PyStr_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyStr_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("string.to_py.__pyx_convert_PyStr_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.to_py":49
 * 
 * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

static CYTHON_INLINE PyObject *__pyx_convert_PyBytes_string_to_py_std__in_string(std::string const &__pyx_v_s) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_PyBytes_string_to_py_std__in_string", 0);

  /* "string.to_py":50
 * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s):
 *     return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size())             # <<<<<<<<<<<<<<
 * cdef extern from *:
 *     cdef object __Pyx_PyByteArray_FromStringAndSize(const char*, size_t)
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyBytes_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 50, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "string.to_py":49
 * 
 * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size())
 * cdef extern from *:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("string.to_py.__pyx_convert_PyBytes_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "string.to_py":55
 * 
 * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size())
 * 
 */

static CYTHON_INLINE PyObject *__pyx_convert_PyByteArray_string_to_py_std__in_string(std::string const &__pyx_v_s) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_PyByteArray_string_to_py_std__in_string", 0);

  /* "string.to_py":56
 * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s):
 *     return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size())             # <<<<<<<<<<<<<<
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyByteArray_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 56, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "string.to_py":55
 * 
 * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string")
 * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s):             # <<<<<<<<<<<<<<
 *     return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size())
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("string.to_py.__pyx_convert_PyByteArray_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_unsigned_int")
 * cdef object __pyx_convert_vector_to_py_unsigned_int(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

static PyObject *__pyx_convert_vector_to_py_unsigned_int(const std::vector<unsigned int>  &__pyx_v_v) {
  size_t __pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  size_t __pyx_t_2;
  size_t __pyx_t_3;
  size_t __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_to_py_unsigned_int", 0);

  /* "vector.to_py":61
 * @cname("__pyx_convert_vector_to_py_unsigned_int")
 * cdef object __pyx_convert_vector_to_py_unsigned_int(vector[X]& v):
 *     return [v[i] for i in range(v.size())]             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __pyx_v_v.size();
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;
    __pyx_t_5 = __Pyx_PyInt_From_unsigned_int((__pyx_v_v[__pyx_v_i])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_unsigned_int")
 * cdef object __pyx_convert_vector_to_py_unsigned_int(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("vector.to_py.__pyx_convert_vector_to_py_unsigned_int", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "vector.from_py":45
 * 
 * @cname("__pyx_convert_vector_from_py_unsigned_int")
 * cdef vector[X] __pyx_convert_vector_from_py_unsigned_int(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef vector[X] v
 *     for item in o:
 */

static std::vector<unsigned int>  __pyx_convert_vector_from_py_unsigned_int(PyObject *__pyx_v_o) {
  std::vector<unsigned int>  __pyx_v_v;
  PyObject *__pyx_v_item = NULL;
  std::vector<unsigned int>  __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  PyObject *(*__pyx_t_3)(PyObject *);
  PyObject *__pyx_t_4 = NULL;
  unsigned int __pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_from_py_unsigned_int", 0);

  /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_unsigned_int(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  if (likely(PyList_CheckExact(__pyx_v_o)) || PyTuple_CheckExact(__pyx_v_o)) {
    __pyx_t_1 = __pyx_v_o; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
    __pyx_t_3 = NULL;
  } else {
    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_o); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 47, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 47, __pyx_L1_error)
  }
  for (;;) {
    if (likely(!__pyx_t_3)) {
      if (likely(PyList_CheckExact(__pyx_t_1))) {
        if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      } else {
        if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 47, __pyx_L1_error)
        #else
        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 47, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        #endif
      }
    } else {
      __pyx_t_4 = __pyx_t_3(__pyx_t_1);
      if (unlikely(!__pyx_t_4)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(0, 47, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_4);
    }
    __Pyx_XDECREF_SET(__pyx_v_item, __pyx_t_4);
    __pyx_t_4 = 0;

    /* "vector.from_py":48
 *     cdef vector[X] v
 *     for item in o:
 *         v.push_back(<X>item)             # <<<<<<<<<<<<<<
 *     return v
 * 
 */
    __pyx_t_5 = __Pyx_PyInt_As_unsigned_int(__pyx_v_item); if (unlikely((__pyx_t_5 == (unsigned int)-1) && PyErr_Occurred())) __PYX_ERR(0, 48, __pyx_L1_error)
    __pyx_v_v.push_back(((unsigned int)__pyx_t_5));

    /* "vector.from_py":47
 * cdef vector[X] __pyx_convert_vector_from_py_unsigned_int(object o) except *:
 *     cdef vector[X] v
 *     for item in o:             # <<<<<<<<<<<<<<
 *         v.push_back(<X>item)
 *     return v
 */
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "vector.from_py":49
 *     for item in o:
 *         v.push_back(<X>item)
 *     return v             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_r = __pyx_v_v;
  goto __pyx_L0;

  /* "vector.from_py":45
 * 
 * @cname("__pyx_convert_vector_from_py_unsigned_int")
 * cdef vector[X] __pyx_convert_vector_from_py_unsigned_int(object o) except *:             # <<<<<<<<<<<<<<
 *     cdef vector[X] v
 *     for item in o:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("vector.from_py.__pyx_convert_vector_from_py_unsigned_int", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_pretend_to_initialize(&__pyx_r);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_item);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_uint32_t")
 * cdef object __pyx_convert_vector_to_py_uint32_t(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

static PyObject *__pyx_convert_vector_to_py_uint32_t(const std::vector<uint32_t>  &__pyx_v_v) {
  size_t __pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  size_t __pyx_t_2;
  size_t __pyx_t_3;
  size_t __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_to_py_uint32_t", 0);

  /* "vector.to_py":61
 * @cname("__pyx_convert_vector_to_py_uint32_t")
 * cdef object __pyx_convert_vector_to_py_uint32_t(vector[X]& v):
 *     return [v[i] for i in range(v.size())]             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __pyx_v_v.size();
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;
    __pyx_t_5 = __Pyx_PyInt_From_uint32_t((__pyx_v_v[__pyx_v_i])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_uint32_t")
 * cdef object __pyx_convert_vector_to_py_uint32_t(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("vector.to_py.__pyx_convert_vector_to_py_uint32_t", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_convert_vector_to_py_double(const std::vector<double>  &__pyx_v_v) {
  size_t __pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  size_t __pyx_t_2;
  size_t __pyx_t_3;
  size_t __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_to_py_double", 0);

  /* "vector.to_py":61
 * @cname("__pyx_convert_vector_to_py_double")
 * cdef object __pyx_convert_vector_to_py_double(vector[X]& v):
 *     return [v[i] for i in range(v.size())]             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __pyx_v_v.size();
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;
    __pyx_t_5 = PyFloat_FromDouble((__pyx_v_v[__pyx_v_i])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_double")
 * cdef object __pyx_convert_vector_to_py_double(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("vector.to_py.__pyx_convert_vector_to_py_double", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_convert_vector_to_py_long__double(const std::vector<long double>  &__pyx_v_v) {
  size_t __pyx_v_i;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  size_t __pyx_t_2;
  size_t __pyx_t_3;
  size_t __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__pyx_convert_vector_to_py_long__double", 0);

  /* "vector.to_py":61
 * @cname("__pyx_convert_vector_to_py_long__double")
 * cdef object __pyx_convert_vector_to_py_long__double(vector[X]& v):
 *     return [v[i] for i in range(v.size())]             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __pyx_v_v.size();
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;
    __pyx_t_5 = PyFloat_FromDouble((__pyx_v_v[__pyx_v_i])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 61, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_long__double")
 * cdef object __pyx_convert_vector_to_py_long__double(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("vector.to_py.__pyx_convert_vector_to_py_long__double", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_tp_new_8whatshap_4core_NumericSampleIds(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *p;
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)o);
  p->mapping = ((PyObject*)Py_None); Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_8whatshap_4core_16NumericSampleIds_1__cinit__(o, __pyx_empty_tuple, NULL) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_NumericSampleIds(PyObject *o) {
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *p = (struct __pyx_obj_8whatshap_4core_NumericSampleIds *)o;
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  Py_CLEAR(p->mapping);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_8whatshap_4core_NumericSampleIds(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *p = (struct __pyx_obj_8whatshap_4core_NumericSampleIds *)o;
  if (p->mapping) {
    e = (*v)(p->mapping, a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_8whatshap_4core_NumericSampleIds(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_8whatshap_4core_NumericSampleIds *p = (struct __pyx_obj_8whatshap_4core_NumericSampleIds *)o;
  tmp = ((PyObject*)p->mapping);
  p->mapping = ((PyObject*)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}
static PyObject *__pyx_sq_item_8whatshap_4core_NumericSampleIds(PyObject *o, Py_ssize_t i) {
  PyObject *r;
  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
  Py_DECREF(x);
  return r;
}

static PyMethodDef __pyx_methods_8whatshap_4core_NumericSampleIds[] = {
  {"freeze", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_9freeze, METH_NOARGS, __pyx_doc_8whatshap_4core_16NumericSampleIds_8freeze},
  {"inverse_mapping", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_11inverse_mapping, METH_NOARGS, __pyx_doc_8whatshap_4core_16NumericSampleIds_10inverse_mapping},
  {"__getstate__", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_13__getstate__, METH_NOARGS, 0},
  {"__setstate__", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_15__setstate__, METH_O, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_17__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_16NumericSampleIds_19__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PySequenceMethods __pyx_tp_as_sequence_NumericSampleIds = {
  __pyx_pw_8whatshap_4core_16NumericSampleIds_5__len__, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  __pyx_sq_item_8whatshap_4core_NumericSampleIds, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_NumericSampleIds = {
  __pyx_pw_8whatshap_4core_16NumericSampleIds_5__len__, /*mp_length*/
  __pyx_pw_8whatshap_4core_16NumericSampleIds_3__getitem__, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyTypeObject __pyx_type_8whatshap_4core_NumericSampleIds = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.NumericSampleIds", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_NumericSampleIds), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_NumericSampleIds, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  &__pyx_tp_as_sequence_NumericSampleIds, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_NumericSampleIds, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_8whatshap_4core_16NumericSampleIds_7__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  "\n\tMapping of sample names (strings) to numeric ids.\n\t", /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core_NumericSampleIds, /*tp_traverse*/
  __pyx_tp_clear_8whatshap_4core_NumericSampleIds, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_NumericSampleIds, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_NumericSampleIds, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_Read(PyTypeObject *t, PyObject *a, PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_8whatshap_4core_4Read_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_Read(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_4Read_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}
static PyObject *__pyx_sq_item_8whatshap_4core_Read(PyObject *o, Py_ssize_t i) {
  PyObject *r;
  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
  Py_DECREF(x);
  return r;
}

static int __pyx_mp_ass_subscript_8whatshap_4core_Read(PyObject *o, PyObject *i, PyObject *v) {
  if (v) {
    return __pyx_pw_8whatshap_4core_4Read_14__setitem__(o, i, v);
  }
  else {
    PyErr_Format(PyExc_NotImplementedError,
      "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name);
    return -1;
  }
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_mapqs(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_5mapqs_1__get__(o);
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_name(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_4name_1__get__(o);
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_source_id(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_9source_id_1__get__(o);
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_sample_id(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_9sample_id_1__get__(o);
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_reference_start(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_15reference_start_1__get__(o);
}

static PyObject *__pyx_getprop_8whatshap_4core_4Read_BX_tag(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_4Read_6BX_tag_1__get__(o);
}

static PyMethodDef __pyx_methods_8whatshap_4core_Read[] = {
  {"__getstate__", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_18__getstate__, METH_NOARGS, 0},
  {"__setstate__", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_20__setstate__, METH_O, 0},
  {"add_variant", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_4Read_22add_variant, METH_VARARGS|METH_KEYWORDS, 0},
  {"add_mapq", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_24add_mapq, METH_O, 0},
  {"sort", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_26sort, METH_NOARGS, 0},
  {"is_sorted", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_28is_sorted, METH_NOARGS, 0},
  {"has_BX_tag", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_30has_BX_tag, METH_NOARGS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_32__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_4Read_34__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_8whatshap_4core_Read[] = {
  {(char *)"mapqs", __pyx_getprop_8whatshap_4core_4Read_mapqs, 0, (char *)0, 0},
  {(char *)"name", __pyx_getprop_8whatshap_4core_4Read_name, 0, (char *)0, 0},
  {(char *)"source_id", __pyx_getprop_8whatshap_4core_4Read_source_id, 0, (char *)0, 0},
  {(char *)"sample_id", __pyx_getprop_8whatshap_4core_4Read_sample_id, 0, (char *)0, 0},
  {(char *)"reference_start", __pyx_getprop_8whatshap_4core_4Read_reference_start, 0, (char *)0, 0},
  {(char *)"BX_tag", __pyx_getprop_8whatshap_4core_4Read_BX_tag, 0, (char *)0, 0},
  {0, 0, 0, 0, 0}
};

static PySequenceMethods __pyx_tp_as_sequence_Read = {
  __pyx_pw_8whatshap_4core_4Read_10__len__, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  __pyx_sq_item_8whatshap_4core_Read, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  __pyx_pw_8whatshap_4core_4Read_16__contains__, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_Read = {
  __pyx_pw_8whatshap_4core_4Read_10__len__, /*mp_length*/
  __pyx_pw_8whatshap_4core_4Read_12__getitem__, /*mp_subscript*/
  __pyx_mp_ass_subscript_8whatshap_4core_Read, /*mp_ass_subscript*/
};

static PyTypeObject __pyx_type_8whatshap_4core_Read = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.Read", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_Read), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_Read, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  __pyx_pw_8whatshap_4core_4Read_5__repr__, /*tp_repr*/
  0, /*tp_as_number*/
  &__pyx_tp_as_sequence_Read, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_Read, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  0, /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pw_8whatshap_4core_4Read_7__iter__, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_Read, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_8whatshap_4core_Read, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_Read, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_ReadSet(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_8whatshap_4core_7ReadSet_1__cinit__(o, __pyx_empty_tuple, NULL) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_ReadSet(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_7ReadSet_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}
static PyObject *__pyx_sq_item_8whatshap_4core_ReadSet(PyObject *o, Py_ssize_t i) {
  PyObject *r;
  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
  Py_DECREF(x);
  return r;
}

static PyMethodDef __pyx_methods_8whatshap_4core_ReadSet[] = {
  {"add", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_5add, METH_O, __pyx_doc_8whatshap_4core_7ReadSet_4add},
  {"__getstate__", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_16__getstate__, METH_NOARGS, 0},
  {"__setstate__", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_18__setstate__, METH_O, 0},
  {"sort", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_20sort, METH_NOARGS, __pyx_doc_8whatshap_4core_7ReadSet_19sort},
  {"subset", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_22subset, METH_O, 0},
  {"get_positions", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_24get_positions, METH_NOARGS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_26__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_7ReadSet_28__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PySequenceMethods __pyx_tp_as_sequence_ReadSet = {
  __pyx_pw_8whatshap_4core_7ReadSet_12__len__, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  __pyx_sq_item_8whatshap_4core_ReadSet, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_ReadSet = {
  __pyx_pw_8whatshap_4core_7ReadSet_12__len__, /*mp_length*/
  __pyx_pw_8whatshap_4core_7ReadSet_14__getitem__, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyTypeObject __pyx_type_8whatshap_4core_ReadSet = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.ReadSet", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_ReadSet), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_ReadSet, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  &__pyx_tp_as_sequence_ReadSet, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_ReadSet, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_8whatshap_4core_7ReadSet_7__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  0, /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pw_8whatshap_4core_7ReadSet_9__iter__, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_ReadSet, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_ReadSet, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_Pedigree(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_8whatshap_4core_Pedigree *p;
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_8whatshap_4core_Pedigree *)o);
  p->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)Py_None); Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_8whatshap_4core_8Pedigree_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_Pedigree(PyObject *o) {
  struct __pyx_obj_8whatshap_4core_Pedigree *p = (struct __pyx_obj_8whatshap_4core_Pedigree *)o;
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_8Pedigree_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  Py_CLEAR(p->numeric_sample_ids);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_8whatshap_4core_Pedigree(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core_Pedigree *p = (struct __pyx_obj_8whatshap_4core_Pedigree *)o;
  if (p->numeric_sample_ids) {
    e = (*v)(((PyObject *)p->numeric_sample_ids), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_8whatshap_4core_Pedigree(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_8whatshap_4core_Pedigree *p = (struct __pyx_obj_8whatshap_4core_Pedigree *)o;
  tmp = ((PyObject*)p->numeric_sample_ids);
  p->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyObject *__pyx_getprop_8whatshap_4core_8Pedigree_variant_count(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_8whatshap_4core_8Pedigree_13variant_count_1__get__(o);
}

static PyMethodDef __pyx_methods_8whatshap_4core_Pedigree[] = {
  {"add_individual", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_8Pedigree_5add_individual, METH_VARARGS|METH_KEYWORDS, 0},
  {"add_relationship", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_8Pedigree_7add_relationship, METH_VARARGS|METH_KEYWORDS, 0},
  {"genotype", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_8Pedigree_9genotype, METH_VARARGS|METH_KEYWORDS, 0},
  {"genotype_likelihoods", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_8Pedigree_11genotype_likelihoods, METH_VARARGS|METH_KEYWORDS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_8Pedigree_17__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_8Pedigree_19__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_8whatshap_4core_Pedigree[] = {
  {(char *)"variant_count", __pyx_getprop_8whatshap_4core_8Pedigree_variant_count, 0, (char *)"Number of variants stored for each individual.", 0},
  {0, 0, 0, 0, 0}
};

static PySequenceMethods __pyx_tp_as_sequence_Pedigree = {
  __pyx_pw_8whatshap_4core_8Pedigree_13__len__, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_Pedigree = {
  __pyx_pw_8whatshap_4core_8Pedigree_13__len__, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyTypeObject __pyx_type_8whatshap_4core_Pedigree = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.Pedigree", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_Pedigree), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_Pedigree, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  &__pyx_tp_as_sequence_Pedigree, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_Pedigree, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_8whatshap_4core_8Pedigree_15__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core_Pedigree, /*tp_traverse*/
  __pyx_tp_clear_8whatshap_4core_Pedigree, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_Pedigree, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_8whatshap_4core_Pedigree, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_Pedigree, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_PedigreeDPTable(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_8whatshap_4core_PedigreeDPTable *p;
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)o);
  p->pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)Py_None); Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_8whatshap_4core_15PedigreeDPTable_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_PedigreeDPTable(PyObject *o) {
  struct __pyx_obj_8whatshap_4core_PedigreeDPTable *p = (struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)o;
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_15PedigreeDPTable_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  Py_CLEAR(p->pedigree);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_8whatshap_4core_PedigreeDPTable(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core_PedigreeDPTable *p = (struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)o;
  if (p->pedigree) {
    e = (*v)(((PyObject *)p->pedigree), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_8whatshap_4core_PedigreeDPTable(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_8whatshap_4core_PedigreeDPTable *p = (struct __pyx_obj_8whatshap_4core_PedigreeDPTable *)o;
  tmp = ((PyObject*)p->pedigree);
  p->pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyMethodDef __pyx_methods_8whatshap_4core_PedigreeDPTable[] = {
  {"get_super_reads", (PyCFunction)__pyx_pw_8whatshap_4core_15PedigreeDPTable_5get_super_reads, METH_NOARGS, __pyx_doc_8whatshap_4core_15PedigreeDPTable_4get_super_reads},
  {"get_optimal_cost", (PyCFunction)__pyx_pw_8whatshap_4core_15PedigreeDPTable_7get_optimal_cost, METH_NOARGS, __pyx_doc_8whatshap_4core_15PedigreeDPTable_6get_optimal_cost},
  {"get_optimal_partitioning", (PyCFunction)__pyx_pw_8whatshap_4core_15PedigreeDPTable_9get_optimal_partitioning, METH_NOARGS, __pyx_doc_8whatshap_4core_15PedigreeDPTable_8get_optimal_partitioning},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_15PedigreeDPTable_11__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_15PedigreeDPTable_13__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_8whatshap_4core_PedigreeDPTable = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.PedigreeDPTable", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_PedigreeDPTable), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_PedigreeDPTable, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core_PedigreeDPTable, /*tp_traverse*/
  __pyx_tp_clear_8whatshap_4core_PedigreeDPTable, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_PedigreeDPTable, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_PedigreeDPTable, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_PhredGenotypeLikelihoods(PyTypeObject *t, PyObject *a, PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_PhredGenotypeLikelihoods(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}
static PyObject *__pyx_sq_item_8whatshap_4core_PhredGenotypeLikelihoods(PyObject *o, Py_ssize_t i) {
  PyObject *r;
  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
  Py_DECREF(x);
  return r;
}

static PyObject *__pyx_tp_richcompare_8whatshap_4core_PhredGenotypeLikelihoods(PyObject *o1, PyObject *o2, int op) {
  switch (op) {
    case Py_EQ: {
      return __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_14__eq__(o1, o2);
    }
    case Py_NE: {
      PyObject *ret;
      ret = __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_14__eq__(o1, o2);
      if (likely(ret && ret != Py_NotImplemented)) {
        int b = __Pyx_PyObject_IsTrue(ret); Py_DECREF(ret);
        if (unlikely(b < 0)) return NULL;
        ret = (b) ? Py_False : Py_True;
        Py_INCREF(ret);
      }
      return ret;
    }
    default: {
      return __Pyx_NewRef(Py_NotImplemented);
    }
  }
}

static PyMethodDef __pyx_methods_8whatshap_4core_PhredGenotypeLikelihoods[] = {
  {"genotypes", (PyCFunction)__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_16genotypes, METH_NOARGS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_18__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_20__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PySequenceMethods __pyx_tp_as_sequence_PhredGenotypeLikelihoods = {
  __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_9__len__, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  __pyx_sq_item_8whatshap_4core_PhredGenotypeLikelihoods, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_PhredGenotypeLikelihoods = {
  __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_9__len__, /*mp_length*/
  __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_7__getitem__, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyTypeObject __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.PhredGenotypeLikelihoods", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_PhredGenotypeLikelihoods), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_PhredGenotypeLikelihoods, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  &__pyx_tp_as_sequence_PhredGenotypeLikelihoods, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_PhredGenotypeLikelihoods, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_5__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  0, /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  __pyx_tp_richcompare_8whatshap_4core_PhredGenotypeLikelihoods, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pw_8whatshap_4core_24PhredGenotypeLikelihoods_11__iter__, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_PhredGenotypeLikelihoods, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_PhredGenotypeLikelihoods, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_Genotype(PyTypeObject *t, PyObject *a, PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_8whatshap_4core_8Genotype_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_Genotype(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_8Genotype_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyObject *__pyx_tp_richcompare_8whatshap_4core_Genotype(PyObject *o1, PyObject *o2, int op) {
  switch (op) {
    case Py_EQ: {
      return __pyx_pw_8whatshap_4core_8Genotype_21__eq__(o1, o2);
    }
    case Py_NE: {
      return __pyx_pw_8whatshap_4core_8Genotype_23__ne__(o1, o2);
    }
    case Py_LT: {
      return __pyx_pw_8whatshap_4core_8Genotype_25__lt__(o1, o2);
    }
    default: {
      return __Pyx_NewRef(Py_NotImplemented);
    }
  }
}

static PyMethodDef __pyx_methods_8whatshap_4core_Genotype[] = {
  {"is_none", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_9is_none, METH_NOARGS, 0},
  {"get_index", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_11get_index, METH_NOARGS, 0},
  {"as_vector", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_13as_vector, METH_NOARGS, 0},
  {"is_homozygous", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_15is_homozygous, METH_NOARGS, 0},
  {"is_diploid_and_biallelic", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_17is_diploid_and_biallelic, METH_NOARGS, 0},
  {"get_ploidy", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_19get_ploidy, METH_NOARGS, 0},
  {"__getstate__", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_27__getstate__, METH_NOARGS, 0},
  {"__setstate__", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_29__setstate__, METH_O, 0},
  {"__deepcopy__", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_31__deepcopy__, METH_O, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_35__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_8Genotype_37__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_8whatshap_4core_Genotype = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.Genotype", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_Genotype), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_Genotype, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  __pyx_pw_8whatshap_4core_8Genotype_7__repr__, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  __pyx_pw_8whatshap_4core_8Genotype_33__hash__, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_8whatshap_4core_8Genotype_5__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  0, /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  __pyx_tp_richcompare_8whatshap_4core_Genotype, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_Genotype, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_Genotype, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_GenotypeDPTable(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_8whatshap_4core_GenotypeDPTable *p;
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)o);
  p->pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)Py_None); Py_INCREF(Py_None);
  p->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)Py_None); Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_8whatshap_4core_15GenotypeDPTable_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_GenotypeDPTable(PyObject *o) {
  struct __pyx_obj_8whatshap_4core_GenotypeDPTable *p = (struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)o;
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_15GenotypeDPTable_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  Py_CLEAR(p->pedigree);
  Py_CLEAR(p->numeric_sample_ids);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_8whatshap_4core_GenotypeDPTable(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core_GenotypeDPTable *p = (struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)o;
  if (p->pedigree) {
    e = (*v)(((PyObject *)p->pedigree), a); if (e) return e;
  }
  if (p->numeric_sample_ids) {
    e = (*v)(((PyObject *)p->numeric_sample_ids), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_8whatshap_4core_GenotypeDPTable(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_8whatshap_4core_GenotypeDPTable *p = (struct __pyx_obj_8whatshap_4core_GenotypeDPTable *)o;
  tmp = ((PyObject*)p->pedigree);
  p->pedigree = ((struct __pyx_obj_8whatshap_4core_Pedigree *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->numeric_sample_ids);
  p->numeric_sample_ids = ((struct __pyx_obj_8whatshap_4core_NumericSampleIds *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyMethodDef __pyx_methods_8whatshap_4core_GenotypeDPTable[] = {
  {"get_genotype_likelihoods", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_8whatshap_4core_15GenotypeDPTable_5get_genotype_likelihoods, METH_VARARGS|METH_KEYWORDS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_15GenotypeDPTable_7__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_15GenotypeDPTable_9__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_8whatshap_4core_GenotypeDPTable = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.GenotypeDPTable", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_GenotypeDPTable), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_GenotypeDPTable, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core_GenotypeDPTable, /*tp_traverse*/
  __pyx_tp_clear_8whatshap_4core_GenotypeDPTable, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_GenotypeDPTable, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_GenotypeDPTable, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyObject *__pyx_tp_new_8whatshap_4core_HapChatCore(PyTypeObject *t, PyObject *a, PyObject *k) {
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  if (unlikely(__pyx_pw_8whatshap_4core_11HapChatCore_1__cinit__(o, a, k) < 0)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_8whatshap_4core_HapChatCore(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
    __pyx_pw_8whatshap_4core_11HapChatCore_3__dealloc__(o);
    __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_8whatshap_4core_HapChatCore[] = {
  {"get_length", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_5get_length, METH_NOARGS, 0},
  {"get_super_reads", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_7get_super_reads, METH_NOARGS, 0},
  {"get_optimal_cost", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_9get_optimal_cost, METH_NOARGS, 0},
  {"get_optimal_partitioning", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_11get_optimal_partitioning, METH_NOARGS, 0},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_13__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_8whatshap_4core_11HapChatCore_15__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_8whatshap_4core_HapChatCore = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.HapChatCore", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core_HapChatCore), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core_HapChatCore, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  0, /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_8whatshap_4core_HapChatCore, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core_HapChatCore, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *__pyx_freelist_8whatshap_4core___pyx_scope_struct____iter__[8];
static int __pyx_freecount_8whatshap_4core___pyx_scope_struct____iter__ = 0;

static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct____iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_8whatshap_4core___pyx_scope_struct____iter__ > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__)))) {
    o = (PyObject*)__pyx_freelist_8whatshap_4core___pyx_scope_struct____iter__[--__pyx_freecount_8whatshap_4core___pyx_scope_struct____iter__];
    memset(o, 0, sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__));
    (void) PyObject_INIT(o, t);
    PyObject_GC_Track(o);
  } else {
    o = (*t->tp_alloc)(t, 0);
    if (unlikely(!o)) return 0;
  }
  return o;
}

static void __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct____iter__(PyObject *o) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)o;
  PyObject_GC_UnTrack(o);
  Py_CLEAR(p->__pyx_v_self);
  if (CYTHON_COMPILING_IN_CPYTHON && ((__pyx_freecount_8whatshap_4core___pyx_scope_struct____iter__ < 8) & (Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__)))) {
    __pyx_freelist_8whatshap_4core___pyx_scope_struct____iter__[__pyx_freecount_8whatshap_4core___pyx_scope_struct____iter__++] = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)o);
  } else {
    (*Py_TYPE(o)->tp_free)(o);
  }
}

static int __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct____iter__(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__ *)o;
  if (p->__pyx_v_self) {
    e = (*v)(((PyObject *)p->__pyx_v_self), a); if (e) return e;
  }
  return 0;
}

static PyTypeObject __pyx_type_8whatshap_4core___pyx_scope_struct____iter__ = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.__pyx_scope_struct____iter__", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct____iter__), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct____iter__, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct____iter__, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  0, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core___pyx_scope_struct____iter__, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *__pyx_freelist_8whatshap_4core___pyx_scope_struct_1___iter__[8];
static int __pyx_freecount_8whatshap_4core___pyx_scope_struct_1___iter__ = 0;

static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct_1___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_8whatshap_4core___pyx_scope_struct_1___iter__ > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__)))) {
    o = (PyObject*)__pyx_freelist_8whatshap_4core___pyx_scope_struct_1___iter__[--__pyx_freecount_8whatshap_4core___pyx_scope_struct_1___iter__];
    memset(o, 0, sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__));
    (void) PyObject_INIT(o, t);
    PyObject_GC_Track(o);
  } else {
    o = (*t->tp_alloc)(t, 0);
    if (unlikely(!o)) return 0;
  }
  return o;
}

static void __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct_1___iter__(PyObject *o) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)o;
  PyObject_GC_UnTrack(o);
  Py_CLEAR(p->__pyx_v_self);
  if (CYTHON_COMPILING_IN_CPYTHON && ((__pyx_freecount_8whatshap_4core___pyx_scope_struct_1___iter__ < 8) & (Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__)))) {
    __pyx_freelist_8whatshap_4core___pyx_scope_struct_1___iter__[__pyx_freecount_8whatshap_4core___pyx_scope_struct_1___iter__++] = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)o);
  } else {
    (*Py_TYPE(o)->tp_free)(o);
  }
}

static int __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct_1___iter__(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__ *)o;
  if (p->__pyx_v_self) {
    e = (*v)(((PyObject *)p->__pyx_v_self), a); if (e) return e;
  }
  return 0;
}

static PyTypeObject __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__ = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.__pyx_scope_struct_1___iter__", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_1___iter__), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct_1___iter__, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct_1___iter__, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  0, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core___pyx_scope_struct_1___iter__, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *__pyx_freelist_8whatshap_4core___pyx_scope_struct_2___iter__[8];
static int __pyx_freecount_8whatshap_4core___pyx_scope_struct_2___iter__ = 0;

static PyObject *__pyx_tp_new_8whatshap_4core___pyx_scope_struct_2___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  PyObject *o;
  if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_8whatshap_4core___pyx_scope_struct_2___iter__ > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__)))) {
    o = (PyObject*)__pyx_freelist_8whatshap_4core___pyx_scope_struct_2___iter__[--__pyx_freecount_8whatshap_4core___pyx_scope_struct_2___iter__];
    memset(o, 0, sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__));
    (void) PyObject_INIT(o, t);
    PyObject_GC_Track(o);
  } else {
    o = (*t->tp_alloc)(t, 0);
    if (unlikely(!o)) return 0;
  }
  return o;
}

static void __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct_2___iter__(PyObject *o) {
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)o;
  PyObject_GC_UnTrack(o);
  Py_CLEAR(p->__pyx_v_genotype);
  Py_CLEAR(p->__pyx_v_self);
  Py_CLEAR(p->__pyx_t_0);
  if (CYTHON_COMPILING_IN_CPYTHON && ((__pyx_freecount_8whatshap_4core___pyx_scope_struct_2___iter__ < 8) & (Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__)))) {
    __pyx_freelist_8whatshap_4core___pyx_scope_struct_2___iter__[__pyx_freecount_8whatshap_4core___pyx_scope_struct_2___iter__++] = ((struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)o);
  } else {
    (*Py_TYPE(o)->tp_free)(o);
  }
}

static int __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct_2___iter__(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *p = (struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__ *)o;
  if (p->__pyx_v_genotype) {
    e = (*v)(p->__pyx_v_genotype, a); if (e) return e;
  }
  if (p->__pyx_v_self) {
    e = (*v)(((PyObject *)p->__pyx_v_self), a); if (e) return e;
  }
  if (p->__pyx_t_0) {
    e = (*v)(p->__pyx_t_0, a); if (e) return e;
  }
  return 0;
}

static PyTypeObject __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__ = {
  PyVarObject_HEAD_INIT(0, 0)
  "whatshap.core.__pyx_scope_struct_2___iter__", /*tp_name*/
  sizeof(struct __pyx_obj_8whatshap_4core___pyx_scope_struct_2___iter__), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_8whatshap_4core___pyx_scope_struct_2___iter__, /*tp_dealloc*/
  #if PY_VERSION_HEX < 0x030800b4
  0, /*tp_print*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4
  0, /*tp_vectorcall_offset*/
  #endif
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  0, /*tp_doc*/
  __pyx_tp_traverse_8whatshap_4core___pyx_scope_struct_2___iter__, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  0, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_8whatshap_4core___pyx_scope_struct_2___iter__, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
  0, /*tp_vectorcall*/
  #endif
  #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
  0, /*tp_print*/
  #endif
  #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
  0, /*tp_pypy_flags*/
  #endif
};

static PyMethodDef __pyx_methods[] = {
  {0, 0, 0, 0}
};

#if PY_MAJOR_VERSION >= 3
#if CYTHON_PEP489_MULTI_PHASE_INIT
static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
static int __pyx_pymod_exec_core(PyObject* module); /*proto*/
static PyModuleDef_Slot __pyx_moduledef_slots[] = {
  {Py_mod_create, (void*)__pyx_pymod_create},
  {Py_mod_exec, (void*)__pyx_pymod_exec_core},
  {0, NULL}
};
#endif

static struct PyModuleDef __pyx_moduledef = {
    PyModuleDef_HEAD_INIT,
    "core",
    __pyx_k_Wrappers_for_core_C_classes, /* m_doc */
  #if CYTHON_PEP489_MULTI_PHASE_INIT
    0, /* m_size */
  #else
    -1, /* m_size */
  #endif
    __pyx_methods /* m_methods */,
  #if CYTHON_PEP489_MULTI_PHASE_INIT
    __pyx_moduledef_slots, /* m_slots */
  #else
    NULL, /* m_reload */
  #endif
    NULL, /* m_traverse */
    NULL, /* m_clear */
    NULL /* m_free */
};
#endif
#ifndef CYTHON_SMALL_CODE
#if defined(__clang__)
    #define CYTHON_SMALL_CODE
#elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))
    #define CYTHON_SMALL_CODE __attribute__((cold))
#else
    #define CYTHON_SMALL_CODE
#endif
#endif

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_n_s_BX_tag, __pyx_k_BX_tag, sizeof(__pyx_k_BX_tag), 0, 0, 1, 1},
  {&__pyx_kp_u_Expected_instance_of_Variant_but, __pyx_k_Expected_instance_of_Variant_but, sizeof(__pyx_k_Expected_instance_of_Variant_but), 0, 1, 0, 0},
  {&__pyx_n_s_Genotype, __pyx_k_Genotype, sizeof(__pyx_k_Genotype), 0, 0, 1, 1},
  {&__pyx_n_s_GenotypeDPTable, __pyx_k_GenotypeDPTable, sizeof(__pyx_k_GenotypeDPTable), 0, 0, 1, 1},
  {&__pyx_n_s_HapChatCore, __pyx_k_HapChatCore, sizeof(__pyx_k_HapChatCore), 0, 0, 1, 1},
  {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1},
  {&__pyx_kp_u_Index_out_of_bounds, __pyx_k_Index_out_of_bounds, sizeof(__pyx_k_Index_out_of_bounds), 0, 1, 0, 0},
  {&__pyx_kp_u_Invalid_key, __pyx_k_Invalid_key, sizeof(__pyx_k_Invalid_key), 0, 1, 0, 0},
  {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1},
  {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1},
  {&__pyx_n_s_NumericSampleIds, __pyx_k_NumericSampleIds, sizeof(__pyx_k_NumericSampleIds), 0, 0, 1, 1},
  {&__pyx_n_s_Pedigree, __pyx_k_Pedigree, sizeof(__pyx_k_Pedigree), 0, 0, 1, 1},
  {&__pyx_n_s_PedigreeDPTable, __pyx_k_PedigreeDPTable, sizeof(__pyx_k_PedigreeDPTable), 0, 0, 1, 1},
  {&__pyx_n_s_PhredGenotypeLikelihoods, __pyx_k_PhredGenotypeLikelihoods, sizeof(__pyx_k_PhredGenotypeLikelihoods), 0, 0, 1, 1},
  {&__pyx_n_s_PhredGenotypeLikelihoods___iter, __pyx_k_PhredGenotypeLikelihoods___iter, sizeof(__pyx_k_PhredGenotypeLikelihoods___iter), 0, 0, 1, 1},
  {&__pyx_kp_u_Querying_a_ReadSet_by_read_name, __pyx_k_Querying_a_ReadSet_by_read_name, sizeof(__pyx_k_Querying_a_ReadSet_by_read_name), 0, 1, 0, 0},
  {&__pyx_n_s_Read, __pyx_k_Read, sizeof(__pyx_k_Read), 0, 0, 1, 1},
  {&__pyx_n_s_ReadSet, __pyx_k_ReadSet, sizeof(__pyx_k_ReadSet), 0, 0, 1, 1},
  {&__pyx_n_s_ReadSet___iter, __pyx_k_ReadSet___iter, sizeof(__pyx_k_ReadSet___iter), 0, 0, 1, 1},
  {&__pyx_kp_u_ReadSet_does_not_support_slices, __pyx_k_ReadSet_does_not_support_slices, sizeof(__pyx_k_ReadSet_does_not_support_slices), 0, 1, 0, 0},
  {&__pyx_n_s_Read___iter, __pyx_k_Read___iter, sizeof(__pyx_k_Read___iter), 0, 0, 1, 1},
  {&__pyx_kp_u_Read_does_not_support_slices, __pyx_k_Read_does_not_support_slices, sizeof(__pyx_k_Read_does_not_support_slices), 0, 1, 0, 0},
  {&__pyx_kp_u_Read_name_r_mapq_source_id_sampl, __pyx_k_Read_name_r_mapq_source_id_sampl, sizeof(__pyx_k_Read_name_r_mapq_source_id_sampl), 0, 1, 0, 0},
  {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
  {&__pyx_kp_u_UTF_8, __pyx_k_UTF_8, sizeof(__pyx_k_UTF_8), 0, 1, 0, 0},
  {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
  {&__pyx_n_s_Variant, __pyx_k_Variant, sizeof(__pyx_k_Variant), 0, 0, 1, 1},
  {&__pyx_kp_u__22, __pyx_k__22, sizeof(__pyx_k__22), 0, 1, 0, 0},
  {&__pyx_kp_b__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 0, 0, 0},
  {&__pyx_kp_u__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 1, 0, 0},
  {&__pyx_n_s_add, __pyx_k_add, sizeof(__pyx_k_add), 0, 0, 1, 1},
  {&__pyx_n_s_add_mapq, __pyx_k_add_mapq, sizeof(__pyx_k_add_mapq), 0, 0, 1, 1},
  {&__pyx_n_s_add_variant, __pyx_k_add_variant, sizeof(__pyx_k_add_variant), 0, 0, 1, 1},
  {&__pyx_n_s_allele, __pyx_k_allele, sizeof(__pyx_k_allele), 0, 0, 1, 1},
  {&__pyx_n_s_alleles, __pyx_k_alleles, sizeof(__pyx_k_alleles), 0, 0, 1, 1},
  {&__pyx_n_s_args, __pyx_k_args, sizeof(__pyx_k_args), 0, 0, 1, 1},
  {&__pyx_n_s_as_vector, __pyx_k_as_vector, sizeof(__pyx_k_as_vector), 0, 0, 1, 1},
  {&__pyx_n_s_binomial_coefficient, __pyx_k_binomial_coefficient, sizeof(__pyx_k_binomial_coefficient), 0, 0, 1, 1},
  {&__pyx_n_s_c_positions, __pyx_k_c_positions, sizeof(__pyx_k_c_positions), 0, 0, 1, 1},
  {&__pyx_n_s_child_id, __pyx_k_child_id, sizeof(__pyx_k_child_id), 0, 0, 1, 1},
  {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1},
  {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
  {&__pyx_n_s_collections, __pyx_k_collections, sizeof(__pyx_k_collections), 0, 0, 1, 1},
  {&__pyx_n_s_compute_genotypes, __pyx_k_compute_genotypes, sizeof(__pyx_k_compute_genotypes), 0, 0, 1, 1},
  {&__pyx_n_s_distrust_genotypes, __pyx_k_distrust_genotypes, sizeof(__pyx_k_distrust_genotypes), 0, 0, 1, 1},
  {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1},
  {&__pyx_n_s_father_id, __pyx_k_father_id, sizeof(__pyx_k_father_id), 0, 0, 1, 1},
  {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1},
  {&__pyx_n_s_genotype, __pyx_k_genotype, sizeof(__pyx_k_genotype), 0, 0, 1, 1},
  {&__pyx_n_s_genotype_likelihoods, __pyx_k_genotype_likelihoods, sizeof(__pyx_k_genotype_likelihoods), 0, 0, 1, 1},
  {&__pyx_n_s_genotypes, __pyx_k_genotypes, sizeof(__pyx_k_genotypes), 0, 0, 1, 1},
  {&__pyx_n_s_genotypes_vector, __pyx_k_genotypes_vector, sizeof(__pyx_k_genotypes_vector), 0, 0, 1, 1},
  {&__pyx_n_s_get_max_genotype_alleles, __pyx_k_get_max_genotype_alleles, sizeof(__pyx_k_get_max_genotype_alleles), 0, 0, 1, 1},
  {&__pyx_n_s_get_max_genotype_ploidy, __pyx_k_get_max_genotype_ploidy, sizeof(__pyx_k_get_max_genotype_ploidy), 0, 0, 1, 1},
  {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1},
  {&__pyx_n_s_gl, __pyx_k_gl, sizeof(__pyx_k_gl), 0, 0, 1, 1},
  {&__pyx_n_s_gl_vector, __pyx_k_gl_vector, sizeof(__pyx_k_gl_vector), 0, 0, 1, 1},
  {&__pyx_n_s_gls, __pyx_k_gls, sizeof(__pyx_k_gls), 0, 0, 1, 1},
  {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1},
  {&__pyx_n_s_id, __pyx_k_id, sizeof(__pyx_k_id), 0, 0, 1, 1},
  {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
  {&__pyx_n_s_is_diploid_and_biallelic, __pyx_k_is_diploid_and_biallelic, sizeof(__pyx_k_is_diploid_and_biallelic), 0, 0, 1, 1},
  {&__pyx_n_s_items, __pyx_k_items, sizeof(__pyx_k_items), 0, 0, 1, 1},
  {&__pyx_n_s_iter, __pyx_k_iter, sizeof(__pyx_k_iter), 0, 0, 1, 1},
  {&__pyx_n_s_k, __pyx_k_k, sizeof(__pyx_k_k), 0, 0, 1, 1},
  {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_mapq, __pyx_k_mapq, sizeof(__pyx_k_mapq), 0, 0, 1, 1},
  {&__pyx_n_s_mapqs, __pyx_k_mapqs, sizeof(__pyx_k_mapqs), 0, 0, 1, 1},
  {&__pyx_n_s_mother_id, __pyx_k_mother_id, sizeof(__pyx_k_mother_id), 0, 0, 1, 1},
  {&__pyx_n_s_n, __pyx_k_n, sizeof(__pyx_k_n), 0, 0, 1, 1},
  {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
  {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1},
  {&__pyx_n_s_namedtuple, __pyx_k_namedtuple, sizeof(__pyx_k_namedtuple), 0, 0, 1, 1},
  {&__pyx_kp_s_no_default___reduce___due_to_non, __pyx_k_no_default___reduce___due_to_non, sizeof(__pyx_k_no_default___reduce___due_to_non), 0, 0, 1, 0},
  {&__pyx_n_s_nr_alleles, __pyx_k_nr_alleles, sizeof(__pyx_k_nr_alleles), 0, 0, 1, 1},
  {&__pyx_n_s_numeric_sample_ids, __pyx_k_numeric_sample_ids, sizeof(__pyx_k_numeric_sample_ids), 0, 0, 1, 1},
  {&__pyx_n_s_pedigree, __pyx_k_pedigree, sizeof(__pyx_k_pedigree), 0, 0, 1, 1},
  {&__pyx_n_s_ploidy, __pyx_k_ploidy, sizeof(__pyx_k_ploidy), 0, 0, 1, 1},
  {&__pyx_n_s_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 0, 1, 1},
  {&__pyx_n_s_position, __pyx_k_position, sizeof(__pyx_k_position), 0, 0, 1, 1},
  {&__pyx_n_s_positions, __pyx_k_positions, sizeof(__pyx_k_positions), 0, 0, 1, 1},
  {&__pyx_n_s_quality, __pyx_k_quality, sizeof(__pyx_k_quality), 0, 0, 1, 1},
  {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
  {&__pyx_n_s_readset, __pyx_k_readset, sizeof(__pyx_k_readset), 0, 0, 1, 1},
  {&__pyx_n_s_recombcost, __pyx_k_recombcost, sizeof(__pyx_k_recombcost), 0, 0, 1, 1},
  {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1},
  {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1},
  {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1},
  {&__pyx_n_s_reference_start, __pyx_k_reference_start, sizeof(__pyx_k_reference_start), 0, 0, 1, 1},
  {&__pyx_n_s_sample_id, __pyx_k_sample_id, sizeof(__pyx_k_sample_id), 0, 0, 1, 1},
  {&__pyx_n_s_send, __pyx_k_send, sizeof(__pyx_k_send), 0, 0, 1, 1},
  {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
  {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1},
  {&__pyx_n_s_source_id, __pyx_k_source_id, sizeof(__pyx_k_source_id), 0, 0, 1, 1},
  {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 0, 0, 1, 1},
  {&__pyx_n_s_variant, __pyx_k_variant, sizeof(__pyx_k_variant), 0, 0, 1, 1},
  {&__pyx_n_s_variant_index, __pyx_k_variant_index, sizeof(__pyx_k_variant_index), 0, 0, 1, 1},
  {&__pyx_n_s_whatshap_core, __pyx_k_whatshap_core, sizeof(__pyx_k_whatshap_core), 0, 0, 1, 1},
  {&__pyx_kp_s_whatshap_core_pyx, __pyx_k_whatshap_core_pyx, sizeof(__pyx_k_whatshap_core_pyx), 0, 0, 1, 0},
  {0, 0, 0, 0, 0, 0, 0}
};
static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(0, 2, __pyx_L1_error)
  __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(1, 118, __pyx_L1_error)
  __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(1, 130, __pyx_L1_error)
  __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) __PYX_ERR(1, 134, __pyx_L1_error)
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(1, 151, __pyx_L1_error)
  __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(1, 254, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple_)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple_);
  __Pyx_GIVEREF(__pyx_tuple_);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__2);
  __Pyx_GIVEREF(__pyx_tuple__2);

  /* "whatshap/core.pyx":130
 * 		assert self.thisptr != NULL
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError("Read does not support slices")             # <<<<<<<<<<<<<<
 * 		assert isinstance(key, int)
 * 		cdef int n = self.thisptr.getVariantCount()
 */
  __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Read_does_not_support_slices); if (unlikely(!__pyx_tuple__4)) __PYX_ERR(1, 130, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__4);
  __Pyx_GIVEREF(__pyx_tuple__4);

  /* "whatshap/core.pyx":189
 * 			self.ownsptr = True
 * 
 * 		for mapq in mapqs[1:]:             # <<<<<<<<<<<<<<
 * 			self.add_mapq(mapq)
 * 		for (pos, allele, quality) in variants:
 */
  __pyx_slice__5 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_slice__5)) __PYX_ERR(1, 189, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_slice__5);
  __Pyx_GIVEREF(__pyx_slice__5);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__6);
  __Pyx_GIVEREF(__pyx_tuple__6);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__7)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__7);
  __Pyx_GIVEREF(__pyx_tuple__7);

  /* "whatshap/core.pyx":241
 * 	def __getitem__(self, key):
 * 		if isinstance(key, slice):
 * 			raise NotImplementedError('ReadSet does not support slices')             # <<<<<<<<<<<<<<
 * 		cdef string name = b''
 * 		cdef cpp.Read* cread = NULL
 */
  __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_u_ReadSet_does_not_support_slices); if (unlikely(!__pyx_tuple__8)) __PYX_ERR(1, 241, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__8);
  __Pyx_GIVEREF(__pyx_tuple__8);

  /* "whatshap/core.pyx":248
 * 			read.thisptr = self.thisptr.get(key)
 * 		elif isinstance(key, str):
 * 			raise NotImplementedError('Querying a ReadSet by read name is deprecated, please query by (source_id, name) instead')             # <<<<<<<<<<<<<<
 * 		elif isinstance(key, tuple) and (len(key) == 2) and (isinstance(key[0],int) and isinstance(key[1],str)):
 * 			source_id = key[0]
 */
  __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_u_Querying_a_ReadSet_by_read_name); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(1, 248, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__9);
  __Pyx_GIVEREF(__pyx_tuple__9);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__10)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__10);
  __Pyx_GIVEREF(__pyx_tuple__10);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__11)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__11);
  __Pyx_GIVEREF(__pyx_tuple__11);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__12);
  __Pyx_GIVEREF(__pyx_tuple__12);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__13)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__13);
  __Pyx_GIVEREF(__pyx_tuple__13);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__14)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__14);
  __Pyx_GIVEREF(__pyx_tuple__14);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__15)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__15);
  __Pyx_GIVEREF(__pyx_tuple__15);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__16);
  __Pyx_GIVEREF(__pyx_tuple__16);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__17)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__17);
  __Pyx_GIVEREF(__pyx_tuple__17);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__18)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__18);
  __Pyx_GIVEREF(__pyx_tuple__18);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__19)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__19);
  __Pyx_GIVEREF(__pyx_tuple__19);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__20)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__20);
  __Pyx_GIVEREF(__pyx_tuple__20);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__21)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__21);
  __Pyx_GIVEREF(__pyx_tuple__21);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__23)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__23);
  __Pyx_GIVEREF(__pyx_tuple__23);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__24)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__24);
  __Pyx_GIVEREF(__pyx_tuple__24);

  /* "whatshap/core.pyx":447
 * 
 * 
 * def binomial_coefficient(int n, int k):             # <<<<<<<<<<<<<<
 * 	return cpp.binomial_coefficient(n, k)
 * 
 */
  __pyx_tuple__25 = PyTuple_Pack(2, __pyx_n_s_n, __pyx_n_s_k); if (unlikely(!__pyx_tuple__25)) __PYX_ERR(1, 447, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__25);
  __Pyx_GIVEREF(__pyx_tuple__25);
  __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__25, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_whatshap_core_pyx, __pyx_n_s_binomial_coefficient, 447, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) __PYX_ERR(1, 447, __pyx_L1_error)

  /* "whatshap/core.pyx":513
 * 
 * 
 * def get_max_genotype_ploidy():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_ploidy()
 * 
 */
  __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_whatshap_core_pyx, __pyx_n_s_get_max_genotype_ploidy, 513, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) __PYX_ERR(1, 513, __pyx_L1_error)

  /* "whatshap/core.pyx":517
 * 
 * 
 * def get_max_genotype_alleles():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_alleles()
 * 
 */
  __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_whatshap_core_pyx, __pyx_n_s_get_max_genotype_alleles, 517, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) __PYX_ERR(1, 517, __pyx_L1_error)

  /* "whatshap/core.pyx":543
 * 
 * 
 * def compute_genotypes(ReadSet readset, positions = None):             # <<<<<<<<<<<<<<
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 */
  __pyx_tuple__29 = PyTuple_Pack(10, __pyx_n_s_readset, __pyx_n_s_positions, __pyx_n_s_genotypes_vector, __pyx_n_s_gl_vector, __pyx_n_s_c_positions, __pyx_n_s_pos, __pyx_n_s_genotypes, __pyx_n_s_gls, __pyx_n_s_genotype, __pyx_n_s_i); if (unlikely(!__pyx_tuple__29)) __PYX_ERR(1, 543, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__29);
  __Pyx_GIVEREF(__pyx_tuple__29);
  __pyx_codeobj__30 = (PyObject*)__Pyx_PyCode_New(2, 0, 10, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__29, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_whatshap_core_pyx, __pyx_n_s_compute_genotypes, 543, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__30)) __PYX_ERR(1, 543, __pyx_L1_error)
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) {
  if (__Pyx_InitStrings(__pyx_string_tab) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(1, 1, __pyx_L1_error)
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(1, 1, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/

static int __Pyx_modinit_global_init_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0);
  /*--- Global init code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_variable_export_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0);
  /*--- Variable export code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_function_export_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0);
  /*--- Function export code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_type_init_code(void) {
  __Pyx_RefNannyDeclarations
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
  /*--- Type init code ---*/
  if (PyType_Ready(&__pyx_type_8whatshap_4core_NumericSampleIds) < 0) __PYX_ERR(1, 22, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_NumericSampleIds.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_NumericSampleIds.tp_dictoffset && __pyx_type_8whatshap_4core_NumericSampleIds.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_NumericSampleIds.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_NumericSampleIds, (PyObject *)&__pyx_type_8whatshap_4core_NumericSampleIds) < 0) __PYX_ERR(1, 22, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_NumericSampleIds) < 0) __PYX_ERR(1, 22, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_NumericSampleIds = &__pyx_type_8whatshap_4core_NumericSampleIds;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_Read) < 0) __PYX_ERR(1, 60, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_Read.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_Read.tp_dictoffset && __pyx_type_8whatshap_4core_Read.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_Read.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  #if CYTHON_UPDATE_DESCRIPTOR_DOC
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_8whatshap_4core_Read, "__iter__"); if (unlikely(!wrapper)) __PYX_ERR(1, 60, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_8whatshap_4core_4Read_6__iter__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_8whatshap_4core_4Read_6__iter__.doc = __pyx_doc_8whatshap_4core_4Read_6__iter__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_8whatshap_4core_4Read_6__iter__;
    }
  }
  #endif
  #if CYTHON_UPDATE_DESCRIPTOR_DOC
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_8whatshap_4core_Read, "__len__"); if (unlikely(!wrapper)) __PYX_ERR(1, 60, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_8whatshap_4core_4Read_9__len__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_8whatshap_4core_4Read_9__len__.doc = __pyx_doc_8whatshap_4core_4Read_9__len__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_8whatshap_4core_4Read_9__len__;
    }
  }
  #endif
  #if CYTHON_UPDATE_DESCRIPTOR_DOC
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_8whatshap_4core_Read, "__getitem__"); if (unlikely(!wrapper)) __PYX_ERR(1, 60, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_8whatshap_4core_4Read_11__getitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_8whatshap_4core_4Read_11__getitem__.doc = __pyx_doc_8whatshap_4core_4Read_11__getitem__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_8whatshap_4core_4Read_11__getitem__;
    }
  }
  #endif
  #if CYTHON_UPDATE_DESCRIPTOR_DOC
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_8whatshap_4core_Read, "__contains__"); if (unlikely(!wrapper)) __PYX_ERR(1, 60, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_8whatshap_4core_4Read_15__contains__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_8whatshap_4core_4Read_15__contains__.doc = __pyx_doc_8whatshap_4core_4Read_15__contains__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_8whatshap_4core_4Read_15__contains__;
    }
  }
  #endif
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Read, (PyObject *)&__pyx_type_8whatshap_4core_Read) < 0) __PYX_ERR(1, 60, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_Read) < 0) __PYX_ERR(1, 60, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_Read = &__pyx_type_8whatshap_4core_Read;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_ReadSet) < 0) __PYX_ERR(1, 215, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_ReadSet.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_ReadSet.tp_dictoffset && __pyx_type_8whatshap_4core_ReadSet.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_ReadSet.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_ReadSet, (PyObject *)&__pyx_type_8whatshap_4core_ReadSet) < 0) __PYX_ERR(1, 215, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_ReadSet) < 0) __PYX_ERR(1, 215, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_ReadSet = &__pyx_type_8whatshap_4core_ReadSet;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_Pedigree) < 0) __PYX_ERR(1, 359, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_Pedigree.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_Pedigree.tp_dictoffset && __pyx_type_8whatshap_4core_Pedigree.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_Pedigree.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Pedigree, (PyObject *)&__pyx_type_8whatshap_4core_Pedigree) < 0) __PYX_ERR(1, 359, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_Pedigree) < 0) __PYX_ERR(1, 359, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_Pedigree = &__pyx_type_8whatshap_4core_Pedigree;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_PedigreeDPTable) < 0) __PYX_ERR(1, 304, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_PedigreeDPTable.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_PedigreeDPTable.tp_dictoffset && __pyx_type_8whatshap_4core_PedigreeDPTable.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_PedigreeDPTable.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_PedigreeDPTable, (PyObject *)&__pyx_type_8whatshap_4core_PedigreeDPTable) < 0) __PYX_ERR(1, 304, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_PedigreeDPTable) < 0) __PYX_ERR(1, 304, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_PedigreeDPTable = &__pyx_type_8whatshap_4core_PedigreeDPTable;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_PhredGenotypeLikelihoods) < 0) __PYX_ERR(1, 409, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_dictoffset && __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_PhredGenotypeLikelihoods, (PyObject *)&__pyx_type_8whatshap_4core_PhredGenotypeLikelihoods) < 0) __PYX_ERR(1, 409, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_PhredGenotypeLikelihoods) < 0) __PYX_ERR(1, 409, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_PhredGenotypeLikelihoods = &__pyx_type_8whatshap_4core_PhredGenotypeLikelihoods;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_Genotype) < 0) __PYX_ERR(1, 451, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_Genotype.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_Genotype.tp_dictoffset && __pyx_type_8whatshap_4core_Genotype.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_Genotype.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Genotype, (PyObject *)&__pyx_type_8whatshap_4core_Genotype) < 0) __PYX_ERR(1, 451, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_Genotype) < 0) __PYX_ERR(1, 451, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_Genotype = &__pyx_type_8whatshap_4core_Genotype;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_GenotypeDPTable) < 0) __PYX_ERR(1, 521, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_GenotypeDPTable.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_GenotypeDPTable.tp_dictoffset && __pyx_type_8whatshap_4core_GenotypeDPTable.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_GenotypeDPTable.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GenotypeDPTable, (PyObject *)&__pyx_type_8whatshap_4core_GenotypeDPTable) < 0) __PYX_ERR(1, 521, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_GenotypeDPTable) < 0) __PYX_ERR(1, 521, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_GenotypeDPTable = &__pyx_type_8whatshap_4core_GenotypeDPTable;
  if (PyType_Ready(&__pyx_type_8whatshap_4core_HapChatCore) < 0) __PYX_ERR(1, 561, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core_HapChatCore.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core_HapChatCore.tp_dictoffset && __pyx_type_8whatshap_4core_HapChatCore.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core_HapChatCore.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_HapChatCore, (PyObject *)&__pyx_type_8whatshap_4core_HapChatCore) < 0) __PYX_ERR(1, 561, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_8whatshap_4core_HapChatCore) < 0) __PYX_ERR(1, 561, __pyx_L1_error)
  __pyx_ptype_8whatshap_4core_HapChatCore = &__pyx_type_8whatshap_4core_HapChatCore;
  if (PyType_Ready(&__pyx_type_8whatshap_4core___pyx_scope_struct____iter__) < 0) __PYX_ERR(1, 115, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_dictoffset && __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
  }
  __pyx_ptype_8whatshap_4core___pyx_scope_struct____iter__ = &__pyx_type_8whatshap_4core___pyx_scope_struct____iter__;
  if (PyType_Ready(&__pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__) < 0) __PYX_ERR(1, 232, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_dictoffset && __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
  }
  __pyx_ptype_8whatshap_4core___pyx_scope_struct_1___iter__ = &__pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__;
  if (PyType_Ready(&__pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__) < 0) __PYX_ERR(1, 427, __pyx_L1_error)
  #if PY_VERSION_HEX < 0x030800B1
  __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_print = 0;
  #endif
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_dictoffset && __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
  }
  __pyx_ptype_8whatshap_4core___pyx_scope_struct_2___iter__ = &__pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_type_import_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
  /*--- Type import code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_variable_import_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0);
  /*--- Variable import code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_function_import_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0);
  /*--- Function import code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}


#ifndef CYTHON_NO_PYINIT_EXPORT
#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
#elif PY_MAJOR_VERSION < 3
#ifdef __cplusplus
#define __Pyx_PyMODINIT_FUNC extern "C" void
#else
#define __Pyx_PyMODINIT_FUNC void
#endif
#else
#ifdef __cplusplus
#define __Pyx_PyMODINIT_FUNC extern "C" PyObject *
#else
#define __Pyx_PyMODINIT_FUNC PyObject *
#endif
#endif


#if PY_MAJOR_VERSION < 3
__Pyx_PyMODINIT_FUNC initcore(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC initcore(void)
#else
__Pyx_PyMODINIT_FUNC PyInit_core(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC PyInit_core(void)
#if CYTHON_PEP489_MULTI_PHASE_INIT
{
  return PyModuleDef_Init(&__pyx_moduledef);
}
static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) {
    #if PY_VERSION_HEX >= 0x030700A1
    static PY_INT64_T main_interpreter_id = -1;
    PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp);
    if (main_interpreter_id == -1) {
        main_interpreter_id = current_id;
        return (unlikely(current_id == -1)) ? -1 : 0;
    } else if (unlikely(main_interpreter_id != current_id))
    #else
    static PyInterpreterState *main_interpreter = NULL;
    PyInterpreterState *current_interpreter = PyThreadState_Get()->interp;
    if (!main_interpreter) {
        main_interpreter = current_interpreter;
    } else if (unlikely(main_interpreter != current_interpreter))
    #endif
    {
        PyErr_SetString(
            PyExc_ImportError,
            "Interpreter change detected - this module can only be loaded into one interpreter per process.");
        return -1;
    }
    return 0;
}
static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *moddict, const char* from_name, const char* to_name, int allow_none) {
    PyObject *value = PyObject_GetAttrString(spec, from_name);
    int result = 0;
    if (likely(value)) {
        if (allow_none || value != Py_None) {
            result = PyDict_SetItemString(moddict, to_name, value);
        }
        Py_DECREF(value);
    } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) {
        PyErr_Clear();
    } else {
        result = -1;
    }
    return result;
}
static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, CYTHON_UNUSED PyModuleDef *def) {
    PyObject *module = NULL, *moddict, *modname;
    if (__Pyx_check_single_interpreter())
        return NULL;
    if (__pyx_m)
        return __Pyx_NewRef(__pyx_m);
    modname = PyObject_GetAttrString(spec, "name");
    if (unlikely(!modname)) goto bad;
    module = PyModule_NewObject(modname);
    Py_DECREF(modname);
    if (unlikely(!module)) goto bad;
    moddict = PyModule_GetDict(module);
    if (unlikely(!moddict)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad;
    return module;
bad:
    Py_XDECREF(module);
    return NULL;
}


static CYTHON_SMALL_CODE int __pyx_pymod_exec_core(PyObject *__pyx_pyinit_module)
#endif
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  if (__pyx_m) {
    if (__pyx_m == __pyx_pyinit_module) return 0;
    PyErr_SetString(PyExc_RuntimeError, "Module 'core' has already been imported. Re-initialisation is not supported.");
    return -1;
  }
  #elif PY_MAJOR_VERSION >= 3
  if (__pyx_m) return __Pyx_NewRef(__pyx_m);
  #endif
  #if CYTHON_REFNANNY
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
if (!__Pyx_RefNanny) {
  PyErr_Clear();
  __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
  if (!__Pyx_RefNanny)
      Py_FatalError("failed to import 'refnanny' module");
}
#endif
  __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_core(void)", 0);
  if (__Pyx_check_binary_version() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #ifdef __Pxy_PyFrame_Initialize_Offsets
  __Pxy_PyFrame_Initialize_Offsets();
  #endif
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(1, 1, __pyx_L1_error)
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(1, 1, __pyx_L1_error)
  __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(1, 1, __pyx_L1_error)
  #ifdef __Pyx_CyFunction_USED
  if (__pyx_CyFunction_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Coroutine_USED
  if (__pyx_Coroutine_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_AsyncGen_USED
  if (__pyx_AsyncGen_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_StopAsyncIteration_USED
  if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  PyEval_InitThreads();
  #endif
  /*--- Module creation code ---*/
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  __pyx_m = __pyx_pyinit_module;
  Py_INCREF(__pyx_m);
  #else
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4("core", __pyx_methods, __pyx_k_Wrappers_for_core_C_classes, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(1, 1, __pyx_L1_error)
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(1, 1, __pyx_L1_error)
  Py_INCREF(__pyx_b);
  __pyx_cython_runtime = PyImport_AddModule((char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(1, 1, __pyx_L1_error)
  Py_INCREF(__pyx_cython_runtime);
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  /*--- Initialize various global constants etc. ---*/
  if (__Pyx_InitGlobals() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
  if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif
  if (__pyx_module_is_main_whatshap__core) {
    if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(1, 1, __pyx_L1_error)
    if (!PyDict_GetItemString(modules, "whatshap.core")) {
      if (unlikely(PyDict_SetItemString(modules, "whatshap.core", __pyx_m) < 0)) __PYX_ERR(1, 1, __pyx_L1_error)
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  /*--- Constants init code ---*/
  if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  /*--- Global type/function init code ---*/
  (void)__Pyx_modinit_global_init_code();
  (void)__Pyx_modinit_variable_export_code();
  (void)__Pyx_modinit_function_export_code();
  if (unlikely(__Pyx_modinit_type_init_code() < 0)) __PYX_ERR(1, 1, __pyx_L1_error)
  (void)__Pyx_modinit_type_import_code();
  (void)__Pyx_modinit_variable_import_code();
  (void)__Pyx_modinit_function_import_code();
  /*--- Execution code ---*/
  #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
  if (__Pyx_patch_abc() < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  #endif

  /* "whatshap/core.pyx":17
 * from . cimport cpp
 * 
 * from .variant import Variant             # <<<<<<<<<<<<<<
 * from collections import namedtuple
 * from cython.operator cimport dereference as deref
 */
  __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_INCREF(__pyx_n_s_Variant);
  __Pyx_GIVEREF(__pyx_n_s_Variant);
  PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_Variant);
  __pyx_t_2 = __Pyx_Import(__pyx_n_s_variant, __pyx_t_1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 17, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_Variant); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_Variant, __pyx_t_1) < 0) __PYX_ERR(1, 17, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "whatshap/core.pyx":18
 * 
 * from .variant import Variant
 * from collections import namedtuple             # <<<<<<<<<<<<<<
 * from cython.operator cimport dereference as deref
 * 
 */
  __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 18, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_INCREF(__pyx_n_s_namedtuple);
  __Pyx_GIVEREF(__pyx_n_s_namedtuple);
  PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_namedtuple);
  __pyx_t_1 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_2, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 18, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_1, __pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 18, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_namedtuple, __pyx_t_2) < 0) __PYX_ERR(1, 18, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":447
 * 
 * 
 * def binomial_coefficient(int n, int k):             # <<<<<<<<<<<<<<
 * 	return cpp.binomial_coefficient(n, k)
 * 
 */
  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_8whatshap_4core_1binomial_coefficient, NULL, __pyx_n_s_whatshap_core); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 447, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_binomial_coefficient, __pyx_t_1) < 0) __PYX_ERR(1, 447, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":513
 * 
 * 
 * def get_max_genotype_ploidy():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_ploidy()
 * 
 */
  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_8whatshap_4core_3get_max_genotype_ploidy, NULL, __pyx_n_s_whatshap_core); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 513, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_get_max_genotype_ploidy, __pyx_t_1) < 0) __PYX_ERR(1, 513, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":517
 * 
 * 
 * def get_max_genotype_alleles():             # <<<<<<<<<<<<<<
 * 	return cpp.get_max_genotype_alleles()
 * 
 */
  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_8whatshap_4core_5get_max_genotype_alleles, NULL, __pyx_n_s_whatshap_core); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 517, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_get_max_genotype_alleles, __pyx_t_1) < 0) __PYX_ERR(1, 517, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":543
 * 
 * 
 * def compute_genotypes(ReadSet readset, positions = None):             # <<<<<<<<<<<<<<
 * 	cdef vector[cpp.Genotype]* genotypes_vector = new vector[cpp.Genotype]()
 * 	cdef vector[cpp.GenotypeDistribution]* gl_vector = new vector[cpp.GenotypeDistribution]()
 */
  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_8whatshap_4core_7compute_genotypes, NULL, __pyx_n_s_whatshap_core); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 543, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_compute_genotypes, __pyx_t_1) < 0) __PYX_ERR(1, 543, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "whatshap/core.pyx":1
 * # cython: language_level=3             # <<<<<<<<<<<<<<
 * 
 * """
 */
  __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "vector.to_py":60
 * 
 * @cname("__pyx_convert_vector_to_py_long__double")
 * cdef object __pyx_convert_vector_to_py_long__double(vector[X]& v):             # <<<<<<<<<<<<<<
 *     return [v[i] for i in range(v.size())]
 * 
 */

  /*--- Wrapped vars code ---*/

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init whatshap.core", __pyx_clineno, __pyx_lineno, __pyx_filename);
    }
    Py_CLEAR(__pyx_m);
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init whatshap.core");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  return (__pyx_m != NULL) ? 0 : -1;
  #elif PY_MAJOR_VERSION >= 3
  return __pyx_m;
  #else
  return;
  #endif
}

/* --- Runtime support code --- */
/* Refnanny */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
    PyObject *m = NULL, *p = NULL;
    void *r = NULL;
    m = PyImport_ImportModule(modname);
    if (!m) goto end;
    p = PyObject_GetAttrString(m, "RefNannyAPI");
    if (!p) goto end;
    r = PyLong_AsVoidPtr(p);
end:
    Py_XDECREF(p);
    Py_XDECREF(m);
    return (__Pyx_RefNannyAPIStruct *)r;
}
#endif

/* PyObjectGetAttrStr */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
    PyTypeObject* tp = Py_TYPE(obj);
    if (likely(tp->tp_getattro))
        return tp->tp_getattro(obj, attr_name);
#if PY_MAJOR_VERSION < 3
    if (likely(tp->tp_getattr))
        return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
#endif
    return PyObject_GetAttr(obj, attr_name);
}
#endif

/* GetBuiltinName */
static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
    PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
    if (unlikely(!result)) {
        PyErr_Format(PyExc_NameError,
#if PY_MAJOR_VERSION >= 3
            "name '%U' is not defined", name);
#else
            "name '%.200s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

/* RaiseArgTupleInvalid */
static void __Pyx_RaiseArgtupleInvalid(
    const char* func_name,
    int exact,
    Py_ssize_t num_min,
    Py_ssize_t num_max,
    Py_ssize_t num_found)
{
    Py_ssize_t num_expected;
    const char *more_or_less;
    if (num_found < num_min) {
        num_expected = num_min;
        more_or_less = "at least";
    } else {
        num_expected = num_max;
        more_or_less = "at most";
    }
    if (exact) {
        more_or_less = "exactly";
    }
    PyErr_Format(PyExc_TypeError,
                 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                 func_name, more_or_less, num_expected,
                 (num_expected == 1) ? "" : "s", num_found);
}

/* KeywordStringCheck */
static int __Pyx_CheckKeywordStrings(
    PyObject *kwdict,
    const char* function_name,
    int kw_allowed)
{
    PyObject* key = 0;
    Py_ssize_t pos = 0;
#if CYTHON_COMPILING_IN_PYPY
    if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
        goto invalid_keyword;
    return 1;
#else
    while (PyDict_Next(kwdict, &pos, &key, 0)) {
        #if PY_MAJOR_VERSION < 3
        if (unlikely(!PyString_Check(key)))
        #endif
            if (unlikely(!PyUnicode_Check(key)))
                goto invalid_keyword_type;
    }
    if ((!kw_allowed) && unlikely(key))
        goto invalid_keyword;
    return 1;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%.200s() keywords must be strings", function_name);
    return 0;
#endif
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
    return 0;
}

/* DictGetItem */
#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
    PyObject *value;
    value = PyDict_GetItemWithError(d, key);
    if (unlikely(!value)) {
        if (!PyErr_Occurred()) {
            if (unlikely(PyTuple_Check(key))) {
                PyObject* args = PyTuple_Pack(1, key);
                if (likely(args)) {
                    PyErr_SetObject(PyExc_KeyError, args);
                    Py_DECREF(args);
                }
            } else {
                PyErr_SetObject(PyExc_KeyError, key);
            }
        }
        return NULL;
    }
    Py_INCREF(value);
    return value;
}
#endif

/* PyCFunctionFastCall */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) {
    PyCFunctionObject *func = (PyCFunctionObject*)func_obj;
    PyCFunction meth = PyCFunction_GET_FUNCTION(func);
    PyObject *self = PyCFunction_GET_SELF(func);
    int flags = PyCFunction_GET_FLAGS(func);
    assert(PyCFunction_Check(func));
    assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS)));
    assert(nargs >= 0);
    assert(nargs == 0 || args != NULL);
    /* _PyCFunction_FastCallDict() must not be called with an exception set,
       because it may clear it (directly or indirectly) and so the
       caller loses its exception */
    assert(!PyErr_Occurred());
    if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) {
        return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL);
    } else {
        return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs);
    }
}
#endif

/* PyFunctionFastCall */
#if CYTHON_FAST_PYCALL
static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
                                               PyObject *globals) {
    PyFrameObject *f;
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    PyObject **fastlocals;
    Py_ssize_t i;
    PyObject *result;
    assert(globals != NULL);
    /* XXX Perhaps we should create a specialized
       PyFrame_New() that doesn't take locals, but does
       take builtins without sanity checking them.
       */
    assert(tstate != NULL);
    f = PyFrame_New(tstate, co, globals, NULL);
    if (f == NULL) {
        return NULL;
    }
    fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
    for (i = 0; i < na; i++) {
        Py_INCREF(*args);
        fastlocals[i] = *args++;
    }
    result = PyEval_EvalFrameEx(f,0);
    ++tstate->recursion_depth;
    Py_DECREF(f);
    --tstate->recursion_depth;
    return result;
}
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) {
    PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
    PyObject *globals = PyFunction_GET_GLOBALS(func);
    PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
    PyObject *closure;
#if PY_MAJOR_VERSION >= 3
    PyObject *kwdefs;
#endif
    PyObject *kwtuple, **k;
    PyObject **d;
    Py_ssize_t nd;
    Py_ssize_t nk;
    PyObject *result;
    assert(kwargs == NULL || PyDict_Check(kwargs));
    nk = kwargs ? PyDict_Size(kwargs) : 0;
    if (Py_EnterRecursiveCall((char*)" while calling a Python object")) {
        return NULL;
    }
    if (
#if PY_MAJOR_VERSION >= 3
            co->co_kwonlyargcount == 0 &&
#endif
            likely(kwargs == NULL || nk == 0) &&
            co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
        if (argdefs == NULL && co->co_argcount == nargs) {
            result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
            goto done;
        }
        else if (nargs == 0 && argdefs != NULL
                 && co->co_argcount == Py_SIZE(argdefs)) {
            /* function called with no arguments, but all parameters have
               a default value: use default values as arguments .*/
            args = &PyTuple_GET_ITEM(argdefs, 0);
            result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
            goto done;
        }
    }
    if (kwargs != NULL) {
        Py_ssize_t pos, i;
        kwtuple = PyTuple_New(2 * nk);
        if (kwtuple == NULL) {
            result = NULL;
            goto done;
        }
        k = &PyTuple_GET_ITEM(kwtuple, 0);
        pos = i = 0;
        while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
            Py_INCREF(k[i]);
            Py_INCREF(k[i+1]);
            i += 2;
        }
        nk = i / 2;
    }
    else {
        kwtuple = NULL;
        k = NULL;
    }
    closure = PyFunction_GET_CLOSURE(func);
#if PY_MAJOR_VERSION >= 3
    kwdefs = PyFunction_GET_KW_DEFAULTS(func);
#endif
    if (argdefs != NULL) {
        d = &PyTuple_GET_ITEM(argdefs, 0);
        nd = Py_SIZE(argdefs);
    }
    else {
        d = NULL;
        nd = 0;
    }
#if PY_MAJOR_VERSION >= 3
    result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
                               args, (int)nargs,
                               k, (int)nk,
                               d, (int)nd, kwdefs, closure);
#else
    result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
                               args, (int)nargs,
                               k, (int)nk,
                               d, (int)nd, closure);
#endif
    Py_XDECREF(kwtuple);
done:
    Py_LeaveRecursiveCall();
    return result;
}
#endif
#endif

/* PyObjectCall */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
    PyObject *result;
    ternaryfunc call = Py_TYPE(func)->tp_call;
    if (unlikely(!call))
        return PyObject_Call(func, arg, kw);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = (*call)(func, arg, kw);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCallMethO */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
    PyObject *self, *result;
    PyCFunction cfunc;
    cfunc = PyCFunction_GET_FUNCTION(func);
    self = PyCFunction_GET_SELF(func);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = cfunc(self, arg);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCallOneArg */
#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_New(1);
    if (unlikely(!args)) return NULL;
    Py_INCREF(arg);
    PyTuple_SET_ITEM(args, 0, arg);
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
#if CYTHON_FAST_PYCALL
    if (PyFunction_Check(func)) {
        return __Pyx_PyFunction_FastCall(func, &arg, 1);
    }
#endif
    if (likely(PyCFunction_Check(func))) {
        if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
            return __Pyx_PyObject_CallMethO(func, arg);
#if CYTHON_FAST_PYCCALL
        } else if (__Pyx_PyFastCFunction_Check(func)) {
            return __Pyx_PyCFunction_FastCall(func, &arg, 1);
#endif
        }
    }
    return __Pyx__PyObject_CallOneArg(func, arg);
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_Pack(1, arg);
    if (unlikely(!args)) return NULL;
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
#endif

/* IterFinish */
static CYTHON_INLINE int __Pyx_IterFinish(void) {
#if CYTHON_FAST_THREAD_STATE
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    PyObject* exc_type = tstate->curexc_type;
    if (unlikely(exc_type)) {
        if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) {
            PyObject *exc_value, *exc_tb;
            exc_value = tstate->curexc_value;
            exc_tb = tstate->curexc_traceback;
            tstate->curexc_type = 0;
            tstate->curexc_value = 0;
            tstate->curexc_traceback = 0;
            Py_DECREF(exc_type);
            Py_XDECREF(exc_value);
            Py_XDECREF(exc_tb);
            return 0;
        } else {
            return -1;
        }
    }
    return 0;
#else
    if (unlikely(PyErr_Occurred())) {
        if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
            PyErr_Clear();
            return 0;
        } else {
            return -1;
        }
    }
    return 0;
#endif
}

/* PyObjectCallNoArg */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
#if CYTHON_FAST_PYCALL
    if (PyFunction_Check(func)) {
        return __Pyx_PyFunction_FastCall(func, NULL, 0);
    }
#endif
#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG)
    if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func)))
#else
    if (likely(PyCFunction_Check(func)))
#endif
    {
        if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) {
            return __Pyx_PyObject_CallMethO(func, NULL);
        }
    }
    return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL);
}
#endif

/* PyObjectGetMethod */
static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) {
    PyObject *attr;
#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP
    PyTypeObject *tp = Py_TYPE(obj);
    PyObject *descr;
    descrgetfunc f = NULL;
    PyObject **dictptr, *dict;
    int meth_found = 0;
    assert (*method == NULL);
    if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) {
        attr = __Pyx_PyObject_GetAttrStr(obj, name);
        goto try_unpack;
    }
    if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) {
        return 0;
    }
    descr = _PyType_Lookup(tp, name);
    if (likely(descr != NULL)) {
        Py_INCREF(descr);
#if PY_MAJOR_VERSION >= 3
        #ifdef __Pyx_CyFunction_USED
        if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr)))
        #else
        if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type)))
        #endif
#else
        #ifdef __Pyx_CyFunction_USED
        if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr)))
        #else
        if (likely(PyFunction_Check(descr)))
        #endif
#endif
        {
            meth_found = 1;
        } else {
            f = Py_TYPE(descr)->tp_descr_get;
            if (f != NULL && PyDescr_IsData(descr)) {
                attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
                Py_DECREF(descr);
                goto try_unpack;
            }
        }
    }
    dictptr = _PyObject_GetDictPtr(obj);
    if (dictptr != NULL && (dict = *dictptr) != NULL) {
        Py_INCREF(dict);
        attr = __Pyx_PyDict_GetItemStr(dict, name);
        if (attr != NULL) {
            Py_INCREF(attr);
            Py_DECREF(dict);
            Py_XDECREF(descr);
            goto try_unpack;
        }
        Py_DECREF(dict);
    }
    if (meth_found) {
        *method = descr;
        return 1;
    }
    if (f != NULL) {
        attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
        Py_DECREF(descr);
        goto try_unpack;
    }
    if (descr != NULL) {
        *method = descr;
        return 0;
    }
    PyErr_Format(PyExc_AttributeError,
#if PY_MAJOR_VERSION >= 3
                 "'%.50s' object has no attribute '%U'",
                 tp->tp_name, name);
#else
                 "'%.50s' object has no attribute '%.400s'",
                 tp->tp_name, PyString_AS_STRING(name));
#endif
    return 0;
#else
    attr = __Pyx_PyObject_GetAttrStr(obj, name);
    goto try_unpack;
#endif
try_unpack:
#if CYTHON_UNPACK_METHODS
    if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) {
        PyObject *function = PyMethod_GET_FUNCTION(attr);
        Py_INCREF(function);
        Py_DECREF(attr);
        *method = function;
        return 1;
    }
#endif
    *method = attr;
    return 0;
}

/* PyObjectCallMethod0 */
static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) {
    PyObject *method = NULL, *result = NULL;
    int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
    if (likely(is_method)) {
        result = __Pyx_PyObject_CallOneArg(method, obj);
        Py_DECREF(method);
        return result;
    }
    if (unlikely(!method)) goto bad;
    result = __Pyx_PyObject_CallNoArg(method);
    Py_DECREF(method);
bad:
    return result;
}

/* RaiseNeedMoreValuesToUnpack */
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
    PyErr_Format(PyExc_ValueError,
                 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
                 index, (index == 1) ? "" : "s");
}

/* RaiseTooManyValuesToUnpack */
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
    PyErr_Format(PyExc_ValueError,
                 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}

/* UnpackItemEndCheck */
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
    if (unlikely(retval)) {
        Py_DECREF(retval);
        __Pyx_RaiseTooManyValuesError(expected);
        return -1;
    }
    return __Pyx_IterFinish();
}

/* RaiseNoneIterError */
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
}

/* UnpackTupleError */
static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
    if (t == Py_None) {
      __Pyx_RaiseNoneNotIterableError();
    } else if (PyTuple_GET_SIZE(t) < index) {
      __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
    } else {
      __Pyx_RaiseTooManyValuesError(index);
    }
}

/* UnpackTuple2 */
static CYTHON_INLINE int __Pyx_unpack_tuple2_exact(
        PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) {
    PyObject *value1 = NULL, *value2 = NULL;
#if CYTHON_COMPILING_IN_PYPY
    value1 = PySequence_ITEM(tuple, 0);  if (unlikely(!value1)) goto bad;
    value2 = PySequence_ITEM(tuple, 1);  if (unlikely(!value2)) goto bad;
#else
    value1 = PyTuple_GET_ITEM(tuple, 0);  Py_INCREF(value1);
    value2 = PyTuple_GET_ITEM(tuple, 1);  Py_INCREF(value2);
#endif
    if (decref_tuple) {
        Py_DECREF(tuple);
    }
    *pvalue1 = value1;
    *pvalue2 = value2;
    return 0;
#if CYTHON_COMPILING_IN_PYPY
bad:
    Py_XDECREF(value1);
    Py_XDECREF(value2);
    if (decref_tuple) { Py_XDECREF(tuple); }
    return -1;
#endif
}
static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
                                       int has_known_size, int decref_tuple) {
    Py_ssize_t index;
    PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
    iternextfunc iternext;
    iter = PyObject_GetIter(tuple);
    if (unlikely(!iter)) goto bad;
    if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
    iternext = Py_TYPE(iter)->tp_iternext;
    value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
    value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
    if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
    Py_DECREF(iter);
    *pvalue1 = value1;
    *pvalue2 = value2;
    return 0;
unpacking_failed:
    if (!has_known_size && __Pyx_IterFinish() == 0)
        __Pyx_RaiseNeedMoreValuesError(index);
bad:
    Py_XDECREF(iter);
    Py_XDECREF(value1);
    Py_XDECREF(value2);
    if (decref_tuple) { Py_XDECREF(tuple); }
    return -1;
}

/* dict_iter */
static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
                                                   Py_ssize_t* p_orig_length, int* p_source_is_dict) {
    is_dict = is_dict || likely(PyDict_CheckExact(iterable));
    *p_source_is_dict = is_dict;
    if (is_dict) {
#if !CYTHON_COMPILING_IN_PYPY
        *p_orig_length = PyDict_Size(iterable);
        Py_INCREF(iterable);
        return iterable;
#elif PY_MAJOR_VERSION >= 3
        static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL;
        PyObject **pp = NULL;
        if (method_name) {
            const char *name = PyUnicode_AsUTF8(method_name);
            if (strcmp(name, "iteritems") == 0) pp = &py_items;
            else if (strcmp(name, "iterkeys") == 0) pp = &py_keys;
            else if (strcmp(name, "itervalues") == 0) pp = &py_values;
            if (pp) {
                if (!*pp) {
                    *pp = PyUnicode_FromString(name + 4);
                    if (!*pp)
                        return NULL;
                }
                method_name = *pp;
            }
        }
#endif
    }
    *p_orig_length = 0;
    if (method_name) {
        PyObject* iter;
        iterable = __Pyx_PyObject_CallMethod0(iterable, method_name);
        if (!iterable)
            return NULL;
#if !CYTHON_COMPILING_IN_PYPY
        if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
            return iterable;
#endif
        iter = PyObject_GetIter(iterable);
        Py_DECREF(iterable);
        return iter;
    }
    return PyObject_GetIter(iterable);
}
static CYTHON_INLINE int __Pyx_dict_iter_next(
        PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos,
        PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
    PyObject* next_item;
#if !CYTHON_COMPILING_IN_PYPY
    if (source_is_dict) {
        PyObject *key, *value;
        if (unlikely(orig_length != PyDict_Size(iter_obj))) {
            PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
            return -1;
        }
        if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
            return 0;
        }
        if (pitem) {
            PyObject* tuple = PyTuple_New(2);
            if (unlikely(!tuple)) {
                return -1;
            }
            Py_INCREF(key);
            Py_INCREF(value);
            PyTuple_SET_ITEM(tuple, 0, key);
            PyTuple_SET_ITEM(tuple, 1, value);
            *pitem = tuple;
        } else {
            if (pkey) {
                Py_INCREF(key);
                *pkey = key;
            }
            if (pvalue) {
                Py_INCREF(value);
                *pvalue = value;
            }
        }
        return 1;
    } else if (PyTuple_CheckExact(iter_obj)) {
        Py_ssize_t pos = *ppos;
        if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
        *ppos = pos + 1;
        next_item = PyTuple_GET_ITEM(iter_obj, pos);
        Py_INCREF(next_item);
    } else if (PyList_CheckExact(iter_obj)) {
        Py_ssize_t pos = *ppos;
        if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
        *ppos = pos + 1;
        next_item = PyList_GET_ITEM(iter_obj, pos);
        Py_INCREF(next_item);
    } else
#endif
    {
        next_item = PyIter_Next(iter_obj);
        if (unlikely(!next_item)) {
            return __Pyx_IterFinish();
        }
    }
    if (pitem) {
        *pitem = next_item;
    } else if (pkey && pvalue) {
        if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
            return -1;
    } else if (pkey) {
        *pkey = next_item;
    } else {
        *pvalue = next_item;
    }
    return 1;
}

/* PyErrFetchRestore */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    tmp_type = tstate->curexc_type;
    tmp_value = tstate->curexc_value;
    tmp_tb = tstate->curexc_traceback;
    tstate->curexc_type = type;
    tstate->curexc_value = value;
    tstate->curexc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
}
static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
    *type = tstate->curexc_type;
    *value = tstate->curexc_value;
    *tb = tstate->curexc_traceback;
    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
}
#endif

/* RaiseException */
#if PY_MAJOR_VERSION < 3
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                        CYTHON_UNUSED PyObject *cause) {
    __Pyx_PyThreadState_declare
    Py_XINCREF(type);
    if (!value || value == Py_None)
        value = NULL;
    else
        Py_INCREF(value);
    if (!tb || tb == Py_None)
        tb = NULL;
    else {
        Py_INCREF(tb);
        if (!PyTraceBack_Check(tb)) {
            PyErr_SetString(PyExc_TypeError,
                "raise: arg 3 must be a traceback or None");
            goto raise_error;
        }
    }
    if (PyType_Check(type)) {
#if CYTHON_COMPILING_IN_PYPY
        if (!value) {
            Py_INCREF(Py_None);
            value = Py_None;
        }
#endif
        PyErr_NormalizeException(&type, &value, &tb);
    } else {
        if (value) {
            PyErr_SetString(PyExc_TypeError,
                "instance exception may not have a separate value");
            goto raise_error;
        }
        value = type;
        type = (PyObject*) Py_TYPE(type);
        Py_INCREF(type);
        if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
            PyErr_SetString(PyExc_TypeError,
                "raise: exception class must be a subclass of BaseException");
            goto raise_error;
        }
    }
    __Pyx_PyThreadState_assign
    __Pyx_ErrRestore(type, value, tb);
    return;
raise_error:
    Py_XDECREF(value);
    Py_XDECREF(type);
    Py_XDECREF(tb);
    return;
}
#else
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
    PyObject* owned_instance = NULL;
    if (tb == Py_None) {
        tb = 0;
    } else if (tb && !PyTraceBack_Check(tb)) {
        PyErr_SetString(PyExc_TypeError,
            "raise: arg 3 must be a traceback or None");
        goto bad;
    }
    if (value == Py_None)
        value = 0;
    if (PyExceptionInstance_Check(type)) {
        if (value) {
            PyErr_SetString(PyExc_TypeError,
                "instance exception may not have a separate value");
            goto bad;
        }
        value = type;
        type = (PyObject*) Py_TYPE(value);
    } else if (PyExceptionClass_Check(type)) {
        PyObject *instance_class = NULL;
        if (value && PyExceptionInstance_Check(value)) {
            instance_class = (PyObject*) Py_TYPE(value);
            if (instance_class != type) {
                int is_subclass = PyObject_IsSubclass(instance_class, type);
                if (!is_subclass) {
                    instance_class = NULL;
                } else if (unlikely(is_subclass == -1)) {
                    goto bad;
                } else {
                    type = instance_class;
                }
            }
        }
        if (!instance_class) {
            PyObject *args;
            if (!value)
                args = PyTuple_New(0);
            else if (PyTuple_Check(value)) {
                Py_INCREF(value);
                args = value;
            } else
                args = PyTuple_Pack(1, value);
            if (!args)
                goto bad;
            owned_instance = PyObject_Call(type, args, NULL);
            Py_DECREF(args);
            if (!owned_instance)
                goto bad;
            value = owned_instance;
            if (!PyExceptionInstance_Check(value)) {
                PyErr_Format(PyExc_TypeError,
                             "calling %R should have returned an instance of "
                             "BaseException, not %R",
                             type, Py_TYPE(value));
                goto bad;
            }
        }
    } else {
        PyErr_SetString(PyExc_TypeError,
            "raise: exception class must be a subclass of BaseException");
        goto bad;
    }
    if (cause) {
        PyObject *fixed_cause;
        if (cause == Py_None) {
            fixed_cause = NULL;
        } else if (PyExceptionClass_Check(cause)) {
            fixed_cause = PyObject_CallObject(cause, NULL);
            if (fixed_cause == NULL)
                goto bad;
        } else if (PyExceptionInstance_Check(cause)) {
            fixed_cause = cause;
            Py_INCREF(fixed_cause);
        } else {
            PyErr_SetString(PyExc_TypeError,
                            "exception causes must derive from "
                            "BaseException");
            goto bad;
        }
        PyException_SetCause(value, fixed_cause);
    }
    PyErr_SetObject(type, value);
    if (tb) {
#if CYTHON_FAST_THREAD_STATE
        PyThreadState *tstate = __Pyx_PyThreadState_Current;
        PyObject* tmp_tb = tstate->curexc_traceback;
        if (tb != tmp_tb) {
            Py_INCREF(tb);
            tstate->curexc_traceback = tb;
            Py_XDECREF(tmp_tb);
        }
#else
        PyObject *tmp_type, *tmp_value, *tmp_tb;
        PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
        Py_INCREF(tb);
        PyErr_Restore(tmp_type, tmp_value, tb);
        Py_XDECREF(tmp_tb);
#endif
    }
bad:
    Py_XDECREF(owned_instance);
    return;
}
#endif

/* RaiseDoubleKeywords */
static void __Pyx_RaiseDoubleKeywordsError(
    const char* func_name,
    PyObject* kw_name)
{
    PyErr_Format(PyExc_TypeError,
        #if PY_MAJOR_VERSION >= 3
        "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
        #else
        "%s() got multiple values for keyword argument '%s'", func_name,
        PyString_AsString(kw_name));
        #endif
}

/* ParseKeywords */
static int __Pyx_ParseOptionalKeywords(
    PyObject *kwds,
    PyObject **argnames[],
    PyObject *kwds2,
    PyObject *values[],
    Py_ssize_t num_pos_args,
    const char* function_name)
{
    PyObject *key = 0, *value = 0;
    Py_ssize_t pos = 0;
    PyObject*** name;
    PyObject*** first_kw_arg = argnames + num_pos_args;
    while (PyDict_Next(kwds, &pos, &key, &value)) {
        name = first_kw_arg;
        while (*name && (**name != key)) name++;
        if (*name) {
            values[name-argnames] = value;
            continue;
        }
        name = first_kw_arg;
        #if PY_MAJOR_VERSION < 3
        if (likely(PyString_Check(key))) {
            while (*name) {
                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
                        && _PyString_Eq(**name, key)) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    if ((**argname == key) || (
                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
                             && _PyString_Eq(**argname, key))) {
                        goto arg_passed_twice;
                    }
                    argname++;
                }
            }
        } else
        #endif
        if (likely(PyUnicode_Check(key))) {
            while (*name) {
                int cmp = (**name == key) ? 0 :
                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                    (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
                #endif
                    PyUnicode_Compare(**name, key);
                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                if (cmp == 0) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    int cmp = (**argname == key) ? 0 :
                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                        (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
                    #endif
                        PyUnicode_Compare(**argname, key);
                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                    if (cmp == 0) goto arg_passed_twice;
                    argname++;
                }
            }
        } else
            goto invalid_keyword_type;
        if (kwds2) {
            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
        } else {
            goto invalid_keyword;
        }
    }
    return 0;
arg_passed_twice:
    __Pyx_RaiseDoubleKeywordsError(function_name, key);
    goto bad;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%.200s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

/* ArgTypeTest */
static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact)
{
    if (unlikely(!type)) {
        PyErr_SetString(PyExc_SystemError, "Missing type object");
        return 0;
    }
    else if (exact) {
        #if PY_MAJOR_VERSION == 2
        if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
        #endif
    }
    else {
        if (likely(__Pyx_TypeCheck(obj, type))) return 1;
    }
    PyErr_Format(PyExc_TypeError,
        "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)",
        name, type->tp_name, Py_TYPE(obj)->tp_name);
    return 0;
}

/* WriteUnraisableException */
static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
                                  int full_traceback, CYTHON_UNUSED int nogil) {
    PyObject *old_exc, *old_val, *old_tb;
    PyObject *ctx;
    __Pyx_PyThreadState_declare
#ifdef WITH_THREAD
    PyGILState_STATE state;
    if (nogil)
        state = PyGILState_Ensure();
    else state = (PyGILState_STATE)0;
#endif
    __Pyx_PyThreadState_assign
    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
    if (full_traceback) {
        Py_XINCREF(old_exc);
        Py_XINCREF(old_val);
        Py_XINCREF(old_tb);
        __Pyx_ErrRestore(old_exc, old_val, old_tb);
        PyErr_PrintEx(1);
    }
    #if PY_MAJOR_VERSION < 3
    ctx = PyString_FromString(name);
    #else
    ctx = PyUnicode_FromString(name);
    #endif
    __Pyx_ErrRestore(old_exc, old_val, old_tb);
    if (!ctx) {
        PyErr_WriteUnraisable(Py_None);
    } else {
        PyErr_WriteUnraisable(ctx);
        Py_DECREF(ctx);
    }
#ifdef WITH_THREAD
    if (nogil)
        PyGILState_Release(state);
#endif
}

/* decode_c_bytes */
static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes(
         const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop,
         const char* encoding, const char* errors,
         PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
    if (unlikely((start < 0) | (stop < 0))) {
        if (start < 0) {
            start += length;
            if (start < 0)
                start = 0;
        }
        if (stop < 0)
            stop += length;
    }
    if (stop > length)
        stop = length;
    if (unlikely(stop <= start))
        return __Pyx_NewRef(__pyx_empty_unicode);
    length = stop - start;
    cstring += start;
    if (decode_func) {
        return decode_func(cstring, length, errors);
    } else {
        return PyUnicode_Decode(cstring, length, encoding, errors);
    }
}

/* GetItemInt */
static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
    PyObject *r;
    if (!j) return NULL;
    r = PyObject_GetItem(o, j);
    Py_DECREF(j);
    return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    Py_ssize_t wrapped_i = i;
    if (wraparound & unlikely(i < 0)) {
        wrapped_i += PyList_GET_SIZE(o);
    }
    if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
        PyObject *r = PyList_GET_ITEM(o, wrapped_i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    Py_ssize_t wrapped_i = i;
    if (wraparound & unlikely(i < 0)) {
        wrapped_i += PyTuple_GET_SIZE(o);
    }
    if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
        PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
                                                     CYTHON_NCP_UNUSED int wraparound,
                                                     CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
    if (is_list || PyList_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
        if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) {
            PyObject *r = PyList_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    }
    else if (PyTuple_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
        if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) {
            PyObject *r = PyTuple_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    } else {
        PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
        if (likely(m && m->sq_item)) {
            if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
                Py_ssize_t l = m->sq_length(o);
                if (likely(l >= 0)) {
                    i += l;
                } else {
                    if (!PyErr_ExceptionMatches(PyExc_OverflowError))
                        return NULL;
                    PyErr_Clear();
                }
            }
            return m->sq_item(o, i);
        }
    }
#else
    if (is_list || PySequence_Check(o)) {
        return PySequence_GetItem(o, i);
    }
#endif
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}

/* PyObjectCall2Args */
static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) {
    PyObject *args, *result = NULL;
    #if CYTHON_FAST_PYCALL
    if (PyFunction_Check(function)) {
        PyObject *args[2] = {arg1, arg2};
        return __Pyx_PyFunction_FastCall(function, args, 2);
    }
    #endif
    #if CYTHON_FAST_PYCCALL
    if (__Pyx_PyFastCFunction_Check(function)) {
        PyObject *args[2] = {arg1, arg2};
        return __Pyx_PyCFunction_FastCall(function, args, 2);
    }
    #endif
    args = PyTuple_New(2);
    if (unlikely(!args)) goto done;
    Py_INCREF(arg1);
    PyTuple_SET_ITEM(args, 0, arg1);
    Py_INCREF(arg2);
    PyTuple_SET_ITEM(args, 1, arg2);
    Py_INCREF(function);
    result = __Pyx_PyObject_Call(function, args, NULL);
    Py_DECREF(args);
    Py_DECREF(function);
done:
    return result;
}

/* PyDictVersioning */
#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) {
    PyObject *dict = Py_TYPE(obj)->tp_dict;
    return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
}
static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) {
    PyObject **dictptr = NULL;
    Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset;
    if (offset) {
#if CYTHON_COMPILING_IN_CPYTHON
        dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj);
#else
        dictptr = _PyObject_GetDictPtr(obj);
#endif
    }
    return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
}
static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) {
    PyObject *dict = Py_TYPE(obj)->tp_dict;
    if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
        return 0;
    return obj_dict_version == __Pyx_get_object_dict_version(obj);
}
#endif

/* GetModuleGlobalName */
#if CYTHON_USE_DICT_VERSIONS
static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
#else
static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
#endif
{
    PyObject *result;
#if !CYTHON_AVOID_BORROWED_REFS
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1
    result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    } else if (unlikely(PyErr_Occurred())) {
        return NULL;
    }
#else
    result = PyDict_GetItem(__pyx_d, name);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    }
#endif
#else
    result = PyObject_GetItem(__pyx_d, name);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    }
    PyErr_Clear();
#endif
    return __Pyx_GetBuiltinName(name);
}

/* SliceObject */
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj,
        Py_ssize_t cstart, Py_ssize_t cstop,
        PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
        int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
#if CYTHON_USE_TYPE_SLOTS
    PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
    PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
    if (likely(ms && ms->sq_slice)) {
        if (!has_cstart) {
            if (_py_start && (*_py_start != Py_None)) {
                cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
                if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
            } else
                cstart = 0;
        }
        if (!has_cstop) {
            if (_py_stop && (*_py_stop != Py_None)) {
                cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
                if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
            } else
                cstop = PY_SSIZE_T_MAX;
        }
        if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
            Py_ssize_t l = ms->sq_length(obj);
            if (likely(l >= 0)) {
                if (cstop < 0) {
                    cstop += l;
                    if (cstop < 0) cstop = 0;
                }
                if (cstart < 0) {
                    cstart += l;
                    if (cstart < 0) cstart = 0;
                }
            } else {
                if (!PyErr_ExceptionMatches(PyExc_OverflowError))
                    goto bad;
                PyErr_Clear();
            }
        }
        return ms->sq_slice(obj, cstart, cstop);
    }
#endif
    mp = Py_TYPE(obj)->tp_as_mapping;
    if (likely(mp && mp->mp_subscript))
#endif
    {
        PyObject* result;
        PyObject *py_slice, *py_start, *py_stop;
        if (_py_slice) {
            py_slice = *_py_slice;
        } else {
            PyObject* owned_start = NULL;
            PyObject* owned_stop = NULL;
            if (_py_start) {
                py_start = *_py_start;
            } else {
                if (has_cstart) {
                    owned_start = py_start = PyInt_FromSsize_t(cstart);
                    if (unlikely(!py_start)) goto bad;
                } else
                    py_start = Py_None;
            }
            if (_py_stop) {
                py_stop = *_py_stop;
            } else {
                if (has_cstop) {
                    owned_stop = py_stop = PyInt_FromSsize_t(cstop);
                    if (unlikely(!py_stop)) {
                        Py_XDECREF(owned_start);
                        goto bad;
                    }
                } else
                    py_stop = Py_None;
            }
            py_slice = PySlice_New(py_start, py_stop, Py_None);
            Py_XDECREF(owned_start);
            Py_XDECREF(owned_stop);
            if (unlikely(!py_slice)) goto bad;
        }
#if CYTHON_USE_TYPE_SLOTS
        result = mp->mp_subscript(obj, py_slice);
#else
        result = PyObject_GetItem(obj, py_slice);
#endif
        if (!_py_slice) {
            Py_DECREF(py_slice);
        }
        return result;
    }
    PyErr_Format(PyExc_TypeError,
        "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
bad:
    return NULL;
}

/* ExtTypeTest */
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
    if (unlikely(!type)) {
        PyErr_SetString(PyExc_SystemError, "Missing type object");
        return 0;
    }
    if (likely(__Pyx_TypeCheck(obj, type)))
        return 1;
    PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
                 Py_TYPE(obj)->tp_name, type->tp_name);
    return 0;
}

/* ObjectGetItem */
#if CYTHON_USE_TYPE_SLOTS
static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) {
    PyObject *runerr = NULL;
    Py_ssize_t key_value;
    PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence;
    if (unlikely(!(m && m->sq_item))) {
        PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name);
        return NULL;
    }
    key_value = __Pyx_PyIndex_AsSsize_t(index);
    if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) {
        return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1);
    }
    if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) {
        PyErr_Clear();
        PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name);
    }
    return NULL;
}
static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) {
    PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping;
    if (likely(m && m->mp_subscript)) {
        return m->mp_subscript(obj, key);
    }
    return __Pyx_PyObject_GetIndex(obj, key);
}
#endif

/* PyObject_GenericGetAttrNoDict */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) {
    PyErr_Format(PyExc_AttributeError,
#if PY_MAJOR_VERSION >= 3
                 "'%.50s' object has no attribute '%U'",
                 tp->tp_name, attr_name);
#else
                 "'%.50s' object has no attribute '%.400s'",
                 tp->tp_name, PyString_AS_STRING(attr_name));
#endif
    return NULL;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) {
    PyObject *descr;
    PyTypeObject *tp = Py_TYPE(obj);
    if (unlikely(!PyString_Check(attr_name))) {
        return PyObject_GenericGetAttr(obj, attr_name);
    }
    assert(!tp->tp_dictoffset);
    descr = _PyType_Lookup(tp, attr_name);
    if (unlikely(!descr)) {
        return __Pyx_RaiseGenericGetAttributeError(tp, attr_name);
    }
    Py_INCREF(descr);
    #if PY_MAJOR_VERSION < 3
    if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS)))
    #endif
    {
        descrgetfunc f = Py_TYPE(descr)->tp_descr_get;
        if (unlikely(f)) {
            PyObject *res = f(descr, obj, (PyObject *)tp);
            Py_DECREF(descr);
            return res;
        }
    }
    return descr;
}
#endif

/* PyObject_GenericGetAttr */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) {
    if (unlikely(Py_TYPE(obj)->tp_dictoffset)) {
        return PyObject_GenericGetAttr(obj, attr_name);
    }
    return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name);
}
#endif

/* PyErrExceptionMatches */
#if CYTHON_FAST_THREAD_STATE
static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
    Py_ssize_t i, n;
    n = PyTuple_GET_SIZE(tuple);
#if PY_MAJOR_VERSION >= 3
    for (i=0; i<n; i++) {
        if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
    }
#endif
    for (i=0; i<n; i++) {
        if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1;
    }
    return 0;
}
static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
    PyObject *exc_type = tstate->curexc_type;
    if (exc_type == err) return 1;
    if (unlikely(!exc_type)) return 0;
    if (unlikely(PyTuple_Check(err)))
        return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err);
    return __Pyx_PyErr_GivenExceptionMatches(exc_type, err);
}
#endif

/* PyObjectGetAttrStrNoError */
static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) {
    __Pyx_PyThreadState_declare
    __Pyx_PyThreadState_assign
    if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
        __Pyx_PyErr_Clear();
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) {
    PyObject *result;
#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1
    PyTypeObject* tp = Py_TYPE(obj);
    if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) {
        return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1);
    }
#endif
    result = __Pyx_PyObject_GetAttrStr(obj, attr_name);
    if (unlikely(!result)) {
        __Pyx_PyObject_GetAttrStr_ClearAttributeError();
    }
    return result;
}

/* SetupReduce */
static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
  int ret;
  PyObject *name_attr;
  name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name_2);
  if (likely(name_attr)) {
      ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
  } else {
      ret = -1;
  }
  if (unlikely(ret < 0)) {
      PyErr_Clear();
      ret = 0;
  }
  Py_XDECREF(name_attr);
  return ret;
}
static int __Pyx_setup_reduce(PyObject* type_obj) {
    int ret = 0;
    PyObject *object_reduce = NULL;
    PyObject *object_getstate = NULL;
    PyObject *object_reduce_ex = NULL;
    PyObject *reduce = NULL;
    PyObject *reduce_ex = NULL;
    PyObject *reduce_cython = NULL;
    PyObject *setstate = NULL;
    PyObject *setstate_cython = NULL;
    PyObject *getstate = NULL;
#if CYTHON_USE_PYTYPE_LOOKUP
    getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate);
#else
    getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate);
    if (!getstate && PyErr_Occurred()) {
        goto __PYX_BAD;
    }
#endif
    if (getstate) {
#if CYTHON_USE_PYTYPE_LOOKUP
        object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate);
#else
        object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate);
        if (!object_getstate && PyErr_Occurred()) {
            goto __PYX_BAD;
        }
#endif
        if (object_getstate != getstate) {
            goto __PYX_GOOD;
        }
    }
#if CYTHON_USE_PYTYPE_LOOKUP
    object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
#else
    object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
#endif
    reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD;
    if (reduce_ex == object_reduce_ex) {
#if CYTHON_USE_PYTYPE_LOOKUP
        object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
#else
        object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
#endif
        reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD;
        if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
            reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython);
            if (likely(reduce_cython)) {
                ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
                ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
            } else if (reduce == object_reduce || PyErr_Occurred()) {
                goto __PYX_BAD;
            }
            setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate);
            if (!setstate) PyErr_Clear();
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
                setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython);
                if (likely(setstate_cython)) {
                    ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
                    ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
                } else if (!setstate || PyErr_Occurred()) {
                    goto __PYX_BAD;
                }
            }
            PyType_Modified((PyTypeObject*)type_obj);
        }
    }
    goto __PYX_GOOD;
__PYX_BAD:
    if (!PyErr_Occurred())
        PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name);
    ret = -1;
__PYX_GOOD:
#if !CYTHON_USE_PYTYPE_LOOKUP
    Py_XDECREF(object_reduce);
    Py_XDECREF(object_reduce_ex);
    Py_XDECREF(object_getstate);
    Py_XDECREF(getstate);
#endif
    Py_XDECREF(reduce);
    Py_XDECREF(reduce_ex);
    Py_XDECREF(reduce_cython);
    Py_XDECREF(setstate);
    Py_XDECREF(setstate_cython);
    return ret;
}

/* Import */
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
    PyObject *empty_list = 0;
    PyObject *module = 0;
    PyObject *global_dict = 0;
    PyObject *empty_dict = 0;
    PyObject *list;
    #if PY_MAJOR_VERSION < 3
    PyObject *py_import;
    py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
    if (!py_import)
        goto bad;
    #endif
    if (from_list)
        list = from_list;
    else {
        empty_list = PyList_New(0);
        if (!empty_list)
            goto bad;
        list = empty_list;
    }
    global_dict = PyModule_GetDict(__pyx_m);
    if (!global_dict)
        goto bad;
    empty_dict = PyDict_New();
    if (!empty_dict)
        goto bad;
    {
        #if PY_MAJOR_VERSION >= 3
        if (level == -1) {
            if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) {
                module = PyImport_ImportModuleLevelObject(
                    name, global_dict, empty_dict, list, 1);
                if (!module) {
                    if (!PyErr_ExceptionMatches(PyExc_ImportError))
                        goto bad;
                    PyErr_Clear();
                }
            }
            level = 0;
        }
        #endif
        if (!module) {
            #if PY_MAJOR_VERSION < 3
            PyObject *py_level = PyInt_FromLong(level);
            if (!py_level)
                goto bad;
            module = PyObject_CallFunctionObjArgs(py_import,
                name, global_dict, empty_dict, list, py_level, (PyObject *)NULL);
            Py_DECREF(py_level);
            #else
            module = PyImport_ImportModuleLevelObject(
                name, global_dict, empty_dict, list, level);
            #endif
        }
    }
bad:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(py_import);
    #endif
    Py_XDECREF(empty_list);
    Py_XDECREF(empty_dict);
    return module;
}

/* ImportFrom */
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
    PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
    if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
        PyErr_Format(PyExc_ImportError,
        #if PY_MAJOR_VERSION < 3
            "cannot import name %.230s", PyString_AS_STRING(name));
        #else
            "cannot import name %S", name);
        #endif
    }
    return value;
}

/* CLineInTraceback */
#ifndef CYTHON_CLINE_IN_TRACEBACK
static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) {
    PyObject *use_cline;
    PyObject *ptype, *pvalue, *ptraceback;
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject **cython_runtime_dict;
#endif
    if (unlikely(!__pyx_cython_runtime)) {
        return c_line;
    }
    __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
#if CYTHON_COMPILING_IN_CPYTHON
    cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
    if (likely(cython_runtime_dict)) {
        __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            use_cline, *cython_runtime_dict,
            __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
    } else
#endif
    {
      PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
      if (use_cline_obj) {
        use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
        Py_DECREF(use_cline_obj);
      } else {
        PyErr_Clear();
        use_cline = NULL;
      }
    }
    if (!use_cline) {
        c_line = 0;
        (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
    }
    else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
        c_line = 0;
    }
    __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
    return c_line;
}
#endif

/* CodeObjectCache */
static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
    int start = 0, mid = 0, end = count - 1;
    if (end >= 0 && code_line > entries[end].code_line) {
        return count;
    }
    while (start < end) {
        mid = start + (end - start) / 2;
        if (code_line < entries[mid].code_line) {
            end = mid;
        } else if (code_line > entries[mid].code_line) {
             start = mid + 1;
        } else {
            return mid;
        }
    }
    if (code_line <= entries[mid].code_line) {
        return mid;
    } else {
        return mid + 1;
    }
}
static PyCodeObject *__pyx_find_code_object(int code_line) {
    PyCodeObject* code_object;
    int pos;
    if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
        return NULL;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
        return NULL;
    }
    code_object = __pyx_code_cache.entries[pos].code_object;
    Py_INCREF(code_object);
    return code_object;
}
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
    int pos, i;
    __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
    if (unlikely(!code_line)) {
        return;
    }
    if (unlikely(!entries)) {
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
        if (likely(entries)) {
            __pyx_code_cache.entries = entries;
            __pyx_code_cache.max_count = 64;
            __pyx_code_cache.count = 1;
            entries[0].code_line = code_line;
            entries[0].code_object = code_object;
            Py_INCREF(code_object);
        }
        return;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
        PyCodeObject* tmp = entries[pos].code_object;
        entries[pos].code_object = code_object;
        Py_DECREF(tmp);
        return;
    }
    if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
        int new_max = __pyx_code_cache.max_count + 64;
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
            __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry));
        if (unlikely(!entries)) {
            return;
        }
        __pyx_code_cache.entries = entries;
        __pyx_code_cache.max_count = new_max;
    }
    for (i=__pyx_code_cache.count; i>pos; i--) {
        entries[i] = entries[i-1];
    }
    entries[pos].code_line = code_line;
    entries[pos].code_object = code_object;
    __pyx_code_cache.count++;
    Py_INCREF(code_object);
}

/* AddTraceback */
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
#if PY_VERSION_HEX >= 0x030b00a6
  #ifndef Py_BUILD_CORE
    #define Py_BUILD_CORE 1
  #endif
  #include "internal/pycore_frame.h"
#endif
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
            const char *funcname, int c_line,
            int py_line, const char *filename) {
    PyCodeObject *py_code = NULL;
    PyObject *py_funcname = NULL;
    #if PY_MAJOR_VERSION < 3
    PyObject *py_srcfile = NULL;
    py_srcfile = PyString_FromString(filename);
    if (!py_srcfile) goto bad;
    #endif
    if (c_line) {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        if (!py_funcname) goto bad;
        #else
        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        if (!py_funcname) goto bad;
        funcname = PyUnicode_AsUTF8(py_funcname);
        if (!funcname) goto bad;
        #endif
    }
    else {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromString(funcname);
        if (!py_funcname) goto bad;
        #endif
    }
    #if PY_MAJOR_VERSION < 3
    py_code = __Pyx_PyCode_New(
        0,
        0,
        0,
        0,
        0,
        __pyx_empty_bytes, /*PyObject *code,*/
        __pyx_empty_tuple, /*PyObject *consts,*/
        __pyx_empty_tuple, /*PyObject *names,*/
        __pyx_empty_tuple, /*PyObject *varnames,*/
        __pyx_empty_tuple, /*PyObject *freevars,*/
        __pyx_empty_tuple, /*PyObject *cellvars,*/
        py_srcfile,   /*PyObject *filename,*/
        py_funcname,  /*PyObject *name,*/
        py_line,
        __pyx_empty_bytes  /*PyObject *lnotab*/
    );
    Py_DECREF(py_srcfile);
    #else
    py_code = PyCode_NewEmpty(filename, funcname, py_line);
    #endif
    Py_XDECREF(py_funcname);  // XDECREF since it's only set on Py3 if cline
    return py_code;
bad:
    Py_XDECREF(py_funcname);
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(py_srcfile);
    #endif
    return NULL;
}
static void __Pyx_AddTraceback(const char *funcname, int c_line,
                               int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyFrameObject *py_frame = 0;
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    PyObject *ptype, *pvalue, *ptraceback;
    if (c_line) {
        c_line = __Pyx_CLineForTraceback(tstate, c_line);
    }
    py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
    if (!py_code) {
        __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
        py_code = __Pyx_CreateCodeObjectForTraceback(
            funcname, c_line, py_line, filename);
        if (!py_code) {
            /* If the code object creation fails, then we should clear the
               fetched exception references and propagate the new exception */
            Py_XDECREF(ptype);
            Py_XDECREF(pvalue);
            Py_XDECREF(ptraceback);
            goto bad;
        }
        __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
        __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
    }
    py_frame = PyFrame_New(
        tstate,            /*PyThreadState *tstate,*/
        py_code,           /*PyCodeObject *code,*/
        __pyx_d,    /*PyObject *globals,*/
        0                  /*PyObject *locals*/
    );
    if (!py_frame) goto bad;
    __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
    PyTraceBack_Here(py_frame);
bad:
    Py_XDECREF(py_code);
    Py_XDECREF(py_frame);
}

/* CIntFromPyVerify */
#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
    {\
        func_type value = func_value;\
        if (sizeof(target_type) < sizeof(func_type)) {\
            if (unlikely(value != (func_type) (target_type) value)) {\
                func_type zero = 0;\
                if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
                    return (target_type) -1;\
                if (is_unsigned && unlikely(value < zero))\
                    goto raise_neg_overflow;\
                else\
                    goto raise_overflow;\
            }\
        }\
        return (target_type) value;\
    }

/* CIntFromPy */
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const int neg_one = (int) -1, const_zero = (int) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(int) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (int) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case  1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0])
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) {
                            return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) {
                            return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) {
                            return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (int) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(int) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(int,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(int) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            int val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (int) -1;
        }
    } else {
        int val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (int) -1;
        val = __Pyx_PyInt_As_int(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to int");
    return (int) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to int");
    return (int) -1;
}

/* CIntFromPy */
static CYTHON_INLINE unsigned int __Pyx_PyInt_As_unsigned_int(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const unsigned int neg_one = (unsigned int) -1, const_zero = (unsigned int) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(unsigned int) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(unsigned int, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (unsigned int) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (unsigned int) 0;
                case  1: __PYX_VERIFY_RETURN_INT(unsigned int, digit, digits[0])
                case 2:
                    if (8 * sizeof(unsigned int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) >= 2 * PyLong_SHIFT) {
                            return (unsigned int) (((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(unsigned int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) >= 3 * PyLong_SHIFT) {
                            return (unsigned int) (((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(unsigned int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) >= 4 * PyLong_SHIFT) {
                            return (unsigned int) (((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (unsigned int) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(unsigned int) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(unsigned int, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(unsigned int) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(unsigned int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (unsigned int) 0;
                case -1: __PYX_VERIFY_RETURN_INT(unsigned int, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(unsigned int,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(unsigned int) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) {
                            return (unsigned int) (((unsigned int)-1)*(((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(unsigned int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) {
                            return (unsigned int) ((((((unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(unsigned int) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) {
                            return (unsigned int) (((unsigned int)-1)*(((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(unsigned int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) {
                            return (unsigned int) ((((((((unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(unsigned int) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 4 * PyLong_SHIFT) {
                            return (unsigned int) (((unsigned int)-1)*(((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(unsigned int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(unsigned int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(unsigned int) - 1 > 4 * PyLong_SHIFT) {
                            return (unsigned int) ((((((((((unsigned int)digits[3]) << PyLong_SHIFT) | (unsigned int)digits[2]) << PyLong_SHIFT) | (unsigned int)digits[1]) << PyLong_SHIFT) | (unsigned int)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(unsigned int) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(unsigned int, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(unsigned int) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(unsigned int, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            unsigned int val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (unsigned int) -1;
        }
    } else {
        unsigned int val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (unsigned int) -1;
        val = __Pyx_PyInt_As_unsigned_int(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to unsigned int");
    return (unsigned int) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to unsigned int");
    return (unsigned int) -1;
}

/* CIntFromPy */
static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_t) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(uint32_t) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(uint32_t, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (uint32_t) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (uint32_t) 0;
                case  1: __PYX_VERIFY_RETURN_INT(uint32_t, digit, digits[0])
                case 2:
                    if (8 * sizeof(uint32_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) >= 2 * PyLong_SHIFT) {
                            return (uint32_t) (((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(uint32_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) >= 3 * PyLong_SHIFT) {
                            return (uint32_t) (((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(uint32_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) >= 4 * PyLong_SHIFT) {
                            return (uint32_t) (((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (uint32_t) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(uint32_t) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint32_t, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (uint32_t) 0;
                case -1: __PYX_VERIFY_RETURN_INT(uint32_t, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(uint32_t,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(uint32_t) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT) {
                            return (uint32_t) (((uint32_t)-1)*(((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(uint32_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT) {
                            return (uint32_t) ((((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT) {
                            return (uint32_t) (((uint32_t)-1)*(((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(uint32_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT) {
                            return (uint32_t) ((((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 4 * PyLong_SHIFT) {
                            return (uint32_t) (((uint32_t)-1)*(((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(uint32_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint32_t) - 1 > 4 * PyLong_SHIFT) {
                            return (uint32_t) ((((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(uint32_t) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint32_t, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint32_t, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            uint32_t val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (uint32_t) -1;
        }
    } else {
        uint32_t val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (uint32_t) -1;
        val = __Pyx_PyInt_As_uint32_t(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to uint32_t");
    return (uint32_t) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to uint32_t");
    return (uint32_t) -1;
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const int neg_one = (int) -1, const_zero = (int) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(int) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(int) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(int) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(int),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const long neg_one = (long) -1, const_zero = (long) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(long) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(long) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(long) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(long),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_int(unsigned int value) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const unsigned int neg_one = (unsigned int) -1, const_zero = (unsigned int) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(unsigned int) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(unsigned int) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(unsigned int) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(unsigned int) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(unsigned int) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(unsigned int),
                                     little, !is_unsigned);
    }
}

/* CIntFromPy */
static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const size_t neg_one = (size_t) -1, const_zero = (size_t) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(size_t) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (size_t) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (size_t) 0;
                case  1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0])
                case 2:
                    if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) {
                            return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) {
                            return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) >= 4 * PyLong_SHIFT) {
                            return (size_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (size_t) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(size_t) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (size_t) 0;
                case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(size_t,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) {
                            return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) {
                            return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) {
                            return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) {
                            return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) {
                            return (size_t) (((size_t)-1)*(((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(size_t) - 1 > 4 * PyLong_SHIFT) {
                            return (size_t) ((((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(size_t) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            size_t val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (size_t) -1;
        }
    } else {
        size_t val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (size_t) -1;
        val = __Pyx_PyInt_As_size_t(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to size_t");
    return (size_t) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to size_t");
    return (size_t) -1;
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_t) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(uint32_t) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(uint32_t) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(uint64_t) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(uint64_t) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(uint64_t) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(uint64_t),
                                     little, !is_unsigned);
    }
}

/* CIntFromPy */
static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(uint64_t) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(uint64_t, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (uint64_t) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (uint64_t) 0;
                case  1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, digits[0])
                case 2:
                    if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) >= 2 * PyLong_SHIFT) {
                            return (uint64_t) (((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) >= 3 * PyLong_SHIFT) {
                            return (uint64_t) (((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) >= 4 * PyLong_SHIFT) {
                            return (uint64_t) (((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (uint64_t) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(uint64_t) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (uint64_t) 0;
                case -1: __PYX_VERIFY_RETURN_INT(uint64_t, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(uint64_t,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(uint64_t) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
                            return (uint64_t) (((uint64_t)-1)*(((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
                            return (uint64_t) ((((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
                            return (uint64_t) (((uint64_t)-1)*(((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
                            return (uint64_t) ((((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT) {
                            return (uint64_t) (((uint64_t)-1)*(((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT) {
                            return (uint64_t) ((((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(uint64_t) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            uint64_t val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (uint64_t) -1;
        }
    } else {
        uint64_t val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (uint64_t) -1;
        val = __Pyx_PyInt_As_uint64_t(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to uint64_t");
    return (uint64_t) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to uint64_t");
    return (uint64_t) -1;
}

/* CIntFromPy */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wconversion"
#endif
    const long neg_one = (long) -1, const_zero = (long) 0;
#ifdef __Pyx_HAS_GCC_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(long) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (long) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case  1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0])
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) {
                            return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) {
                            return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) {
                            return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (long) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(long) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(long,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(long) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            long val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (long) -1;
        }
    } else {
        long val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (long) -1;
        val = __Pyx_PyInt_As_long(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to long");
    return (long) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to long");
    return (long) -1;
}

/* FastTypeChecks */
#if CYTHON_COMPILING_IN_CPYTHON
static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
    while (a) {
        a = a->tp_base;
        if (a == b)
            return 1;
    }
    return b == &PyBaseObject_Type;
}
static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
    PyObject *mro;
    if (a == b) return 1;
    mro = a->tp_mro;
    if (likely(mro)) {
        Py_ssize_t i, n;
        n = PyTuple_GET_SIZE(mro);
        for (i = 0; i < n; i++) {
            if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
                return 1;
        }
        return 0;
    }
    return __Pyx_InBases(a, b);
}
#if PY_MAJOR_VERSION == 2
static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
    PyObject *exception, *value, *tb;
    int res;
    __Pyx_PyThreadState_declare
    __Pyx_PyThreadState_assign
    __Pyx_ErrFetch(&exception, &value, &tb);
    res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
    if (unlikely(res == -1)) {
        PyErr_WriteUnraisable(err);
        res = 0;
    }
    if (!res) {
        res = PyObject_IsSubclass(err, exc_type2);
        if (unlikely(res == -1)) {
            PyErr_WriteUnraisable(err);
            res = 0;
        }
    }
    __Pyx_ErrRestore(exception, value, tb);
    return res;
}
#else
static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
    int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0;
    if (!res) {
        res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
    }
    return res;
}
#endif
static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
    Py_ssize_t i, n;
    assert(PyExceptionClass_Check(exc_type));
    n = PyTuple_GET_SIZE(tuple);
#if PY_MAJOR_VERSION >= 3
    for (i=0; i<n; i++) {
        if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
    }
#endif
    for (i=0; i<n; i++) {
        PyObject *t = PyTuple_GET_ITEM(tuple, i);
        #if PY_MAJOR_VERSION < 3
        if (likely(exc_type == t)) return 1;
        #endif
        if (likely(PyExceptionClass_Check(t))) {
            if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
        } else {
        }
    }
    return 0;
}
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
    if (likely(err == exc_type)) return 1;
    if (likely(PyExceptionClass_Check(err))) {
        if (likely(PyExceptionClass_Check(exc_type))) {
            return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
        } else if (likely(PyTuple_Check(exc_type))) {
            return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
        } else {
        }
    }
    return PyErr_GivenExceptionMatches(err, exc_type);
}
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
    assert(PyExceptionClass_Check(exc_type1));
    assert(PyExceptionClass_Check(exc_type2));
    if (likely(err == exc_type1 || err == exc_type2)) return 1;
    if (likely(PyExceptionClass_Check(err))) {
        return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
    }
    return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
}
#endif

/* FetchCommonType */
static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
    PyObject* fake_module;
    PyTypeObject* cached_type = NULL;
    fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
    if (!fake_module) return NULL;
    Py_INCREF(fake_module);
    cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
    if (cached_type) {
        if (!PyType_Check((PyObject*)cached_type)) {
            PyErr_Format(PyExc_TypeError,
                "Shared Cython type %.200s is not a type object",
                type->tp_name);
            goto bad;
        }
        if (cached_type->tp_basicsize != type->tp_basicsize) {
            PyErr_Format(PyExc_TypeError,
                "Shared Cython type %.200s has the wrong size, try recompiling",
                type->tp_name);
            goto bad;
        }
    } else {
        if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
        PyErr_Clear();
        if (PyType_Ready(type) < 0) goto bad;
        if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
            goto bad;
        Py_INCREF(type);
        cached_type = type;
    }
done:
    Py_DECREF(fake_module);
    return cached_type;
bad:
    Py_XDECREF(cached_type);
    cached_type = NULL;
    goto done;
}

/* GetTopmostException */
#if CYTHON_USE_EXC_INFO_STACK
static _PyErr_StackItem *
__Pyx_PyErr_GetTopmostException(PyThreadState *tstate)
{
    _PyErr_StackItem *exc_info = tstate->exc_info;
    while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
           exc_info->previous_item != NULL)
    {
        exc_info = exc_info->previous_item;
    }
    return exc_info;
}
#endif

/* SaveResetException */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
    #if CYTHON_USE_EXC_INFO_STACK
    _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
    *type = exc_info->exc_type;
    *value = exc_info->exc_value;
    *tb = exc_info->exc_traceback;
    #else
    *type = tstate->exc_type;
    *value = tstate->exc_value;
    *tb = tstate->exc_traceback;
    #endif
    Py_XINCREF(*type);
    Py_XINCREF(*value);
    Py_XINCREF(*tb);
}
static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    #if CYTHON_USE_EXC_INFO_STACK
    _PyErr_StackItem *exc_info = tstate->exc_info;
    tmp_type = exc_info->exc_type;
    tmp_value = exc_info->exc_value;
    tmp_tb = exc_info->exc_traceback;
    exc_info->exc_type = type;
    exc_info->exc_value = value;
    exc_info->exc_traceback = tb;
    #else
    tmp_type = tstate->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = type;
    tstate->exc_value = value;
    tstate->exc_traceback = tb;
    #endif
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
}
#endif

/* SwapException */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    #if CYTHON_USE_EXC_INFO_STACK
    _PyErr_StackItem *exc_info = tstate->exc_info;
    tmp_type = exc_info->exc_type;
    tmp_value = exc_info->exc_value;
    tmp_tb = exc_info->exc_traceback;
    exc_info->exc_type = *type;
    exc_info->exc_value = *value;
    exc_info->exc_traceback = *tb;
    #else
    tmp_type = tstate->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = *type;
    tstate->exc_value = *value;
    tstate->exc_traceback = *tb;
    #endif
    *type = tmp_type;
    *value = tmp_value;
    *tb = tmp_tb;
}
#else
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
    PyErr_SetExcInfo(*type, *value, *tb);
    *type = tmp_type;
    *value = tmp_value;
    *tb = tmp_tb;
}
#endif

/* PyObjectCallMethod1 */
static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) {
    PyObject *result = __Pyx_PyObject_CallOneArg(method, arg);
    Py_DECREF(method);
    return result;
}
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
    PyObject *method = NULL, *result;
    int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
    if (likely(is_method)) {
        result = __Pyx_PyObject_Call2Args(method, obj, arg);
        Py_DECREF(method);
        return result;
    }
    if (unlikely(!method)) return NULL;
    return __Pyx__PyObject_CallMethod1(method, arg);
}

/* CoroutineBase */
#include <structmember.h>
#include <frameobject.h>
#if PY_VERSION_HEX >= 0x030b00a6
  #ifndef Py_BUILD_CORE
    #define Py_BUILD_CORE 1
  #endif
  #include "internal/pycore_frame.h"
#endif
#define __Pyx_Coroutine_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
static int __Pyx_PyGen__FetchStopIterationValue(CYTHON_UNUSED PyThreadState *__pyx_tstate, PyObject **pvalue) {
    PyObject *et, *ev, *tb;
    PyObject *value = NULL;
    __Pyx_ErrFetch(&et, &ev, &tb);
    if (!et) {
        Py_XDECREF(tb);
        Py_XDECREF(ev);
        Py_INCREF(Py_None);
        *pvalue = Py_None;
        return 0;
    }
    if (likely(et == PyExc_StopIteration)) {
        if (!ev) {
            Py_INCREF(Py_None);
            value = Py_None;
        }
#if PY_VERSION_HEX >= 0x030300A0
        else if (Py_TYPE(ev) == (PyTypeObject*)PyExc_StopIteration) {
            value = ((PyStopIterationObject *)ev)->value;
            Py_INCREF(value);
            Py_DECREF(ev);
        }
#endif
        else if (unlikely(PyTuple_Check(ev))) {
            if (PyTuple_GET_SIZE(ev) >= 1) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
                value = PyTuple_GET_ITEM(ev, 0);
                Py_INCREF(value);
#else
                value = PySequence_ITEM(ev, 0);
#endif
            } else {
                Py_INCREF(Py_None);
                value = Py_None;
            }
            Py_DECREF(ev);
        }
        else if (!__Pyx_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration)) {
            value = ev;
        }
        if (likely(value)) {
            Py_XDECREF(tb);
            Py_DECREF(et);
            *pvalue = value;
            return 0;
        }
    } else if (!__Pyx_PyErr_GivenExceptionMatches(et, PyExc_StopIteration)) {
        __Pyx_ErrRestore(et, ev, tb);
        return -1;
    }
    PyErr_NormalizeException(&et, &ev, &tb);
    if (unlikely(!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration))) {
        __Pyx_ErrRestore(et, ev, tb);
        return -1;
    }
    Py_XDECREF(tb);
    Py_DECREF(et);
#if PY_VERSION_HEX >= 0x030300A0
    value = ((PyStopIterationObject *)ev)->value;
    Py_INCREF(value);
    Py_DECREF(ev);
#else
    {
        PyObject* args = __Pyx_PyObject_GetAttrStr(ev, __pyx_n_s_args);
        Py_DECREF(ev);
        if (likely(args)) {
            value = PySequence_GetItem(args, 0);
            Py_DECREF(args);
        }
        if (unlikely(!value)) {
            __Pyx_ErrRestore(NULL, NULL, NULL);
            Py_INCREF(Py_None);
            value = Py_None;
        }
    }
#endif
    *pvalue = value;
    return 0;
}
static CYTHON_INLINE
void __Pyx_Coroutine_ExceptionClear(__Pyx_ExcInfoStruct *exc_state) {
    PyObject *t, *v, *tb;
    t = exc_state->exc_type;
    v = exc_state->exc_value;
    tb = exc_state->exc_traceback;
    exc_state->exc_type = NULL;
    exc_state->exc_value = NULL;
    exc_state->exc_traceback = NULL;
    Py_XDECREF(t);
    Py_XDECREF(v);
    Py_XDECREF(tb);
}
#define __Pyx_Coroutine_AlreadyRunningError(gen)  (__Pyx__Coroutine_AlreadyRunningError(gen), (PyObject*)NULL)
static void __Pyx__Coroutine_AlreadyRunningError(CYTHON_UNUSED __pyx_CoroutineObject *gen) {
    const char *msg;
    if ((0)) {
    #ifdef __Pyx_Coroutine_USED
    } else if (__Pyx_Coroutine_Check((PyObject*)gen)) {
        msg = "coroutine already executing";
    #endif
    #ifdef __Pyx_AsyncGen_USED
    } else if (__Pyx_AsyncGen_CheckExact((PyObject*)gen)) {
        msg = "async generator already executing";
    #endif
    } else {
        msg = "generator already executing";
    }
    PyErr_SetString(PyExc_ValueError, msg);
}
#define __Pyx_Coroutine_NotStartedError(gen)  (__Pyx__Coroutine_NotStartedError(gen), (PyObject*)NULL)
static void __Pyx__Coroutine_NotStartedError(CYTHON_UNUSED PyObject *gen) {
    const char *msg;
    if ((0)) {
    #ifdef __Pyx_Coroutine_USED
    } else if (__Pyx_Coroutine_Check(gen)) {
        msg = "can't send non-None value to a just-started coroutine";
    #endif
    #ifdef __Pyx_AsyncGen_USED
    } else if (__Pyx_AsyncGen_CheckExact(gen)) {
        msg = "can't send non-None value to a just-started async generator";
    #endif
    } else {
        msg = "can't send non-None value to a just-started generator";
    }
    PyErr_SetString(PyExc_TypeError, msg);
}
#define __Pyx_Coroutine_AlreadyTerminatedError(gen, value, closing)  (__Pyx__Coroutine_AlreadyTerminatedError(gen, value, closing), (PyObject*)NULL)
static void __Pyx__Coroutine_AlreadyTerminatedError(CYTHON_UNUSED PyObject *gen, PyObject *value, CYTHON_UNUSED int closing) {
    #ifdef __Pyx_Coroutine_USED
    if (!closing && __Pyx_Coroutine_Check(gen)) {
        PyErr_SetString(PyExc_RuntimeError, "cannot reuse already awaited coroutine");
    } else
    #endif
    if (value) {
        #ifdef __Pyx_AsyncGen_USED
        if (__Pyx_AsyncGen_CheckExact(gen))
            PyErr_SetNone(__Pyx_PyExc_StopAsyncIteration);
        else
        #endif
        PyErr_SetNone(PyExc_StopIteration);
    }
}
static
PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value, int closing) {
    __Pyx_PyThreadState_declare
    PyThreadState *tstate;
    __Pyx_ExcInfoStruct *exc_state;
    PyObject *retval;
    assert(!self->is_running);
    if (unlikely(self->resume_label == 0)) {
        if (unlikely(value && value != Py_None)) {
            return __Pyx_Coroutine_NotStartedError((PyObject*)self);
        }
    }
    if (unlikely(self->resume_label == -1)) {
        return __Pyx_Coroutine_AlreadyTerminatedError((PyObject*)self, value, closing);
    }
#if CYTHON_FAST_THREAD_STATE
    __Pyx_PyThreadState_assign
    tstate = __pyx_tstate;
#else
    tstate = __Pyx_PyThreadState_Current;
#endif
    exc_state = &self->gi_exc_state;
    if (exc_state->exc_type) {
        #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON
        #else
        if (exc_state->exc_traceback) {
            PyTracebackObject *tb = (PyTracebackObject *) exc_state->exc_traceback;
            PyFrameObject *f = tb->tb_frame;
            assert(f->f_back == NULL);
            #if PY_VERSION_HEX >= 0x030B00A1
            f->f_back = PyThreadState_GetFrame(tstate);
            #else
            Py_XINCREF(tstate->frame);
            f->f_back = tstate->frame;
            #endif
        }
        #endif
    }
#if CYTHON_USE_EXC_INFO_STACK
    exc_state->previous_item = tstate->exc_info;
    tstate->exc_info = exc_state;
#else
    if (exc_state->exc_type) {
        __Pyx_ExceptionSwap(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback);
    } else {
        __Pyx_Coroutine_ExceptionClear(exc_state);
        __Pyx_ExceptionSave(&exc_state->exc_type, &exc_state->exc_value, &exc_state->exc_traceback);
    }
#endif
    self->is_running = 1;
    retval = self->body((PyObject *) self, tstate, value);
    self->is_running = 0;
#if CYTHON_USE_EXC_INFO_STACK
    exc_state = &self->gi_exc_state;
    tstate->exc_info = exc_state->previous_item;
    exc_state->previous_item = NULL;
    __Pyx_Coroutine_ResetFrameBackpointer(exc_state);
#endif
    return retval;
}
static CYTHON_INLINE void __Pyx_Coroutine_ResetFrameBackpointer(__Pyx_ExcInfoStruct *exc_state) {
    PyObject *exc_tb = exc_state->exc_traceback;
    if (likely(exc_tb)) {
#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON
#else
        PyTracebackObject *tb = (PyTracebackObject *) exc_tb;
        PyFrameObject *f = tb->tb_frame;
        Py_CLEAR(f->f_back);
#endif
    }
}
static CYTHON_INLINE
PyObject *__Pyx_Coroutine_MethodReturn(CYTHON_UNUSED PyObject* gen, PyObject *retval) {
    if (unlikely(!retval)) {
        __Pyx_PyThreadState_declare
        __Pyx_PyThreadState_assign
        if (!__Pyx_PyErr_Occurred()) {
            PyObject *exc = PyExc_StopIteration;
            #ifdef __Pyx_AsyncGen_USED
            if (__Pyx_AsyncGen_CheckExact(gen))
                exc = __Pyx_PyExc_StopAsyncIteration;
            #endif
            __Pyx_PyErr_SetNone(exc);
        }
    }
    return retval;
}
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
static CYTHON_INLINE
PyObject *__Pyx_PyGen_Send(PyGenObject *gen, PyObject *arg) {
#if PY_VERSION_HEX <= 0x030A00A1
    return _PyGen_Send(gen, arg);
#else
    PyObject *result;
    if (PyIter_Send((PyObject*)gen, arg ? arg : Py_None, &result) == PYGEN_RETURN) {
        if (PyAsyncGen_CheckExact(gen)) {
            assert(result == Py_None);
            PyErr_SetNone(PyExc_StopAsyncIteration);
        }
        else if (result == Py_None) {
            PyErr_SetNone(PyExc_StopIteration);
        }
        else {
            _PyGen_SetStopIterationValue(result);
        }
        Py_CLEAR(result);
    }
    return result;
#endif
}
#endif
static CYTHON_INLINE
PyObject *__Pyx_Coroutine_FinishDelegation(__pyx_CoroutineObject *gen) {
    PyObject *ret;
    PyObject *val = NULL;
    __Pyx_Coroutine_Undelegate(gen);
    __Pyx_PyGen__FetchStopIterationValue(__Pyx_PyThreadState_Current, &val);
    ret = __Pyx_Coroutine_SendEx(gen, val, 0);
    Py_XDECREF(val);
    return ret;
}
static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) {
    PyObject *retval;
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self;
    PyObject *yf = gen->yieldfrom;
    if (unlikely(gen->is_running))
        return __Pyx_Coroutine_AlreadyRunningError(gen);
    if (yf) {
        PyObject *ret;
        gen->is_running = 1;
        #ifdef __Pyx_Generator_USED
        if (__Pyx_Generator_CheckExact(yf)) {
            ret = __Pyx_Coroutine_Send(yf, value);
        } else
        #endif
        #ifdef __Pyx_Coroutine_USED
        if (__Pyx_Coroutine_Check(yf)) {
            ret = __Pyx_Coroutine_Send(yf, value);
        } else
        #endif
        #ifdef __Pyx_AsyncGen_USED
        if (__pyx_PyAsyncGenASend_CheckExact(yf)) {
            ret = __Pyx_async_gen_asend_send(yf, value);
        } else
        #endif
        #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
        if (PyGen_CheckExact(yf)) {
            ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
        } else
        #endif
        #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03050000 && defined(PyCoro_CheckExact) && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
        if (PyCoro_CheckExact(yf)) {
            ret = __Pyx_PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
        } else
        #endif
        {
            if (value == Py_None)
                ret = Py_TYPE(yf)->tp_iternext(yf);
            else
                ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value);
        }
        gen->is_running = 0;
        if (likely(ret)) {
            return ret;
        }
        retval = __Pyx_Coroutine_FinishDelegation(gen);
    } else {
        retval = __Pyx_Coroutine_SendEx(gen, value, 0);
    }
    return __Pyx_Coroutine_MethodReturn(self, retval);
}
static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) {
    PyObject *retval = NULL;
    int err = 0;
    #ifdef __Pyx_Generator_USED
    if (__Pyx_Generator_CheckExact(yf)) {
        retval = __Pyx_Coroutine_Close(yf);
        if (!retval)
            return -1;
    } else
    #endif
    #ifdef __Pyx_Coroutine_USED
    if (__Pyx_Coroutine_Check(yf)) {
        retval = __Pyx_Coroutine_Close(yf);
        if (!retval)
            return -1;
    } else
    if (__Pyx_CoroutineAwait_CheckExact(yf)) {
        retval = __Pyx_CoroutineAwait_Close((__pyx_CoroutineAwaitObject*)yf, NULL);
        if (!retval)
            return -1;
    } else
    #endif
    #ifdef __Pyx_AsyncGen_USED
    if (__pyx_PyAsyncGenASend_CheckExact(yf)) {
        retval = __Pyx_async_gen_asend_close(yf, NULL);
    } else
    if (__pyx_PyAsyncGenAThrow_CheckExact(yf)) {
        retval = __Pyx_async_gen_athrow_close(yf, NULL);
    } else
    #endif
    {
        PyObject *meth;
        gen->is_running = 1;
        meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_close);
        if (unlikely(!meth)) {
            if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
                PyErr_WriteUnraisable(yf);
            }
            PyErr_Clear();
        } else {
            retval = PyObject_CallFunction(meth, NULL);
            Py_DECREF(meth);
            if (!retval)
                err = -1;
        }
        gen->is_running = 0;
    }
    Py_XDECREF(retval);
    return err;
}
static PyObject *__Pyx_Generator_Next(PyObject *self) {
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self;
    PyObject *yf = gen->yieldfrom;
    if (unlikely(gen->is_running))
        return __Pyx_Coroutine_AlreadyRunningError(gen);
    if (yf) {
        PyObject *ret;
        gen->is_running = 1;
        #ifdef __Pyx_Generator_USED
        if (__Pyx_Generator_CheckExact(yf)) {
            ret = __Pyx_Generator_Next(yf);
        } else
        #endif
        #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03030000 && (defined(__linux__) || PY_VERSION_HEX >= 0x030600B3)
        if (PyGen_CheckExact(yf)) {
            ret = __Pyx_PyGen_Send((PyGenObject*)yf, NULL);
        } else
        #endif
        #ifdef __Pyx_Coroutine_USED
        if (__Pyx_Coroutine_Check(yf)) {
            ret = __Pyx_Coroutine_Send(yf, Py_None);
        } else
        #endif
            ret = Py_TYPE(yf)->tp_iternext(yf);
        gen->is_running = 0;
        if (likely(ret)) {
            return ret;
        }
        return __Pyx_Coroutine_FinishDelegation(gen);
    }
    return __Pyx_Coroutine_SendEx(gen, Py_None, 0);
}
static PyObject *__Pyx_Coroutine_Close_Method(PyObject *self, CYTHON_UNUSED PyObject *arg) {
    return __Pyx_Coroutine_Close(self);
}
static PyObject *__Pyx_Coroutine_Close(PyObject *self) {
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
    PyObject *retval, *raised_exception;
    PyObject *yf = gen->yieldfrom;
    int err = 0;
    if (unlikely(gen->is_running))
        return __Pyx_Coroutine_AlreadyRunningError(gen);
    if (yf) {
        Py_INCREF(yf);
        err = __Pyx_Coroutine_CloseIter(gen, yf);
        __Pyx_Coroutine_Undelegate(gen);
        Py_DECREF(yf);
    }
    if (err == 0)
        PyErr_SetNone(PyExc_GeneratorExit);
    retval = __Pyx_Coroutine_SendEx(gen, NULL, 1);
    if (unlikely(retval)) {
        const char *msg;
        Py_DECREF(retval);
        if ((0)) {
        #ifdef __Pyx_Coroutine_USED
        } else if (__Pyx_Coroutine_Check(self)) {
            msg = "coroutine ignored GeneratorExit";
        #endif
        #ifdef __Pyx_AsyncGen_USED
        } else if (__Pyx_AsyncGen_CheckExact(self)) {
#if PY_VERSION_HEX < 0x03060000
            msg = "async generator ignored GeneratorExit - might require Python 3.6+ finalisation (PEP 525)";
#else
            msg = "async generator ignored GeneratorExit";
#endif
        #endif
        } else {
            msg = "generator ignored GeneratorExit";
        }
        PyErr_SetString(PyExc_RuntimeError, msg);
        return NULL;
    }
    raised_exception = PyErr_Occurred();
    if (likely(!raised_exception || __Pyx_PyErr_GivenExceptionMatches2(raised_exception, PyExc_GeneratorExit, PyExc_StopIteration))) {
        if (raised_exception) PyErr_Clear();
        Py_INCREF(Py_None);
        return Py_None;
    }
    return NULL;
}
static PyObject *__Pyx__Coroutine_Throw(PyObject *self, PyObject *typ, PyObject *val, PyObject *tb,
                                        PyObject *args, int close_on_genexit) {
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
    PyObject *yf = gen->yieldfrom;
    if (unlikely(gen->is_running))
        return __Pyx_Coroutine_AlreadyRunningError(gen);
    if (yf) {
        PyObject *ret;
        Py_INCREF(yf);
        if (__Pyx_PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit) && close_on_genexit) {
            int err = __Pyx_Coroutine_CloseIter(gen, yf);
            Py_DECREF(yf);
            __Pyx_Coroutine_Undelegate(gen);
            if (err < 0)
                return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0));
            goto throw_here;
        }
        gen->is_running = 1;
        if (0
        #ifdef __Pyx_Generator_USED
            || __Pyx_Generator_CheckExact(yf)
        #endif
        #ifdef __Pyx_Coroutine_USED
            || __Pyx_Coroutine_Check(yf)
        #endif
            ) {
            ret = __Pyx__Coroutine_Throw(yf, typ, val, tb, args, close_on_genexit);
        #ifdef __Pyx_Coroutine_USED
        } else if (__Pyx_CoroutineAwait_CheckExact(yf)) {
            ret = __Pyx__Coroutine_Throw(((__pyx_CoroutineAwaitObject*)yf)->coroutine, typ, val, tb, args, close_on_genexit);
        #endif
        } else {
            PyObject *meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_throw);
            if (unlikely(!meth)) {
                Py_DECREF(yf);
                if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
                    gen->is_running = 0;
                    return NULL;
                }
                PyErr_Clear();
                __Pyx_Coroutine_Undelegate(gen);
                gen->is_running = 0;
                goto throw_here;
            }
            if (likely(args)) {
                ret = PyObject_CallObject(meth, args);
            } else {
                ret = PyObject_CallFunctionObjArgs(meth, typ, val, tb, NULL);
            }
            Py_DECREF(meth);
        }
        gen->is_running = 0;
        Py_DECREF(yf);
        if (!ret) {
            ret = __Pyx_Coroutine_FinishDelegation(gen);
        }
        return __Pyx_Coroutine_MethodReturn(self, ret);
    }
throw_here:
    __Pyx_Raise(typ, val, tb, NULL);
    return __Pyx_Coroutine_MethodReturn(self, __Pyx_Coroutine_SendEx(gen, NULL, 0));
}
static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) {
    PyObject *typ;
    PyObject *val = NULL;
    PyObject *tb = NULL;
    if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
        return NULL;
    return __Pyx__Coroutine_Throw(self, typ, val, tb, args, 1);
}
static CYTHON_INLINE int __Pyx_Coroutine_traverse_excstate(__Pyx_ExcInfoStruct *exc_state, visitproc visit, void *arg) {
    Py_VISIT(exc_state->exc_type);
    Py_VISIT(exc_state->exc_value);
    Py_VISIT(exc_state->exc_traceback);
    return 0;
}
static int __Pyx_Coroutine_traverse(__pyx_CoroutineObject *gen, visitproc visit, void *arg) {
    Py_VISIT(gen->closure);
    Py_VISIT(gen->classobj);
    Py_VISIT(gen->yieldfrom);
    return __Pyx_Coroutine_traverse_excstate(&gen->gi_exc_state, visit, arg);
}
static int __Pyx_Coroutine_clear(PyObject *self) {
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
    Py_CLEAR(gen->closure);
    Py_CLEAR(gen->classobj);
    Py_CLEAR(gen->yieldfrom);
    __Pyx_Coroutine_ExceptionClear(&gen->gi_exc_state);
#ifdef __Pyx_AsyncGen_USED
    if (__Pyx_AsyncGen_CheckExact(self)) {
        Py_CLEAR(((__pyx_PyAsyncGenObject*)gen)->ag_finalizer);
    }
#endif
    Py_CLEAR(gen->gi_code);
    Py_CLEAR(gen->gi_frame);
    Py_CLEAR(gen->gi_name);
    Py_CLEAR(gen->gi_qualname);
    Py_CLEAR(gen->gi_modulename);
    return 0;
}
static void __Pyx_Coroutine_dealloc(PyObject *self) {
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
    PyObject_GC_UnTrack(gen);
    if (gen->gi_weakreflist != NULL)
        PyObject_ClearWeakRefs(self);
    if (gen->resume_label >= 0) {
        PyObject_GC_Track(self);
#if PY_VERSION_HEX >= 0x030400a1 && CYTHON_USE_TP_FINALIZE
        if (PyObject_CallFinalizerFromDealloc(self))
#else
        Py_TYPE(gen)->tp_del(self);
        if (Py_REFCNT(self) > 0)
#endif
        {
            return;
        }
        PyObject_GC_UnTrack(self);
    }
#ifdef __Pyx_AsyncGen_USED
    if (__Pyx_AsyncGen_CheckExact(self)) {
        /* We have to handle this case for asynchronous generators
           right here, because this code has to be between UNTRACK
           and GC_Del. */
        Py_CLEAR(((__pyx_PyAsyncGenObject*)self)->ag_finalizer);
    }
#endif
    __Pyx_Coroutine_clear(self);
    PyObject_GC_Del(gen);
}
static void __Pyx_Coroutine_del(PyObject *self) {
    PyObject *error_type, *error_value, *error_traceback;
    __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self;
    __Pyx_PyThreadState_declare
    if (gen->resume_label < 0) {
        return;
    }
#if !CYTHON_USE_TP_FINALIZE
    assert(self->ob_refcnt == 0);
    __Pyx_SET_REFCNT(self, 1);
#endif
    __Pyx_PyThreadState_assign
    __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
#ifdef __Pyx_AsyncGen_USED
    if (__Pyx_AsyncGen_CheckExact(self)) {
        __pyx_PyAsyncGenObject *agen = (__pyx_PyAsyncGenObject*)self;
        PyObject *finalizer = agen->ag_finalizer;
        if (finalizer && !agen->ag_closed) {
            PyObject *res = __Pyx_PyObject_CallOneArg(finalizer, self);
            if (unlikely(!res)) {
                PyErr_WriteUnraisable(self);
            } else {
                Py_DECREF(res);
            }
            __Pyx_ErrRestore(error_type, error_value, error_traceback);
            return;
        }
    }
#endif
    if (unlikely(gen->resume_label == 0 && !error_value)) {
#ifdef __Pyx_Coroutine_USED
#ifdef __Pyx_Generator_USED
    if (!__Pyx_Generator_CheckExact(self))
#endif
        {
        PyObject_GC_UnTrack(self);
#if PY_MAJOR_VERSION >= 3  || defined(PyErr_WarnFormat)
        if (unlikely(PyErr_WarnFormat(PyExc_RuntimeWarning, 1, "coroutine '%.50S' was never awaited", gen->gi_qualname) < 0))
            PyErr_WriteUnraisable(self);
#else
        {PyObject *msg;
        char *cmsg;
        #if CYTHON_COMPILING_IN_PYPY
        msg = NULL;
        cmsg = (char*) "coroutine was never awaited";
        #else
        char *cname;
        PyObject *qualname;
        qualname = gen->gi_qualname;
        cname = PyString_AS_STRING(qualname);
        msg = PyString_FromFormat("coroutine '%.50s' was never awaited", cname);
        if (unlikely(!msg)) {
            PyErr_Clear();
            cmsg = (char*) "coroutine was never awaited";
        } else {
            cmsg = PyString_AS_STRING(msg);
        }
        #endif
        if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, cmsg, 1) < 0))
            PyErr_WriteUnraisable(self);
        Py_XDECREF(msg);}
#endif
        PyObject_GC_Track(self);
        }
#endif
    } else {
        PyObject *res = __Pyx_Coroutine_Close(self);
        if (unlikely(!res)) {
            if (PyErr_Occurred())
                PyErr_WriteUnraisable(self);
        } else {
            Py_DECREF(res);
        }
    }
    __Pyx_ErrRestore(error_type, error_value, error_traceback);
#if !CYTHON_USE_TP_FINALIZE
    assert(Py_REFCNT(self) > 0);
    if (--self->ob_refcnt == 0) {
        return;
    }
    {
        Py_ssize_t refcnt = Py_REFCNT(self);
        _Py_NewReference(self);
        __Pyx_SET_REFCNT(self, refcnt);
    }
#if CYTHON_COMPILING_IN_CPYTHON
    assert(PyType_IS_GC(Py_TYPE(self)) &&
           _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
    _Py_DEC_REFTOTAL;
#endif
#ifdef COUNT_ALLOCS
    --Py_TYPE(self)->tp_frees;
    --Py_TYPE(self)->tp_allocs;
#endif
#endif
}
static PyObject *
__Pyx_Coroutine_get_name(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context)
{
    PyObject *name = self->gi_name;
    if (unlikely(!name)) name = Py_None;
    Py_INCREF(name);
    return name;
}
static int
__Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context)
{
    PyObject *tmp;
#if PY_MAJOR_VERSION >= 3
    if (unlikely(value == NULL || !PyUnicode_Check(value)))
#else
    if (unlikely(value == NULL || !PyString_Check(value)))
#endif
    {
        PyErr_SetString(PyExc_TypeError,
                        "__name__ must be set to a string object");
        return -1;
    }
    tmp = self->gi_name;
    Py_INCREF(value);
    self->gi_name = value;
    Py_XDECREF(tmp);
    return 0;
}
static PyObject *
__Pyx_Coroutine_get_qualname(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context)
{
    PyObject *name = self->gi_qualname;
    if (unlikely(!name)) name = Py_None;
    Py_INCREF(name);
    return name;
}
static int
__Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value, CYTHON_UNUSED void *context)
{
    PyObject *tmp;
#if PY_MAJOR_VERSION >= 3
    if (unlikely(value == NULL || !PyUnicode_Check(value)))
#else
    if (unlikely(value == NULL || !PyString_Check(value)))
#endif
    {
        PyErr_SetString(PyExc_TypeError,
                        "__qualname__ must be set to a string object");
        return -1;
    }
    tmp = self->gi_qualname;
    Py_INCREF(value);
    self->gi_qualname = value;
    Py_XDECREF(tmp);
    return 0;
}
static PyObject *
__Pyx_Coroutine_get_frame(__pyx_CoroutineObject *self, CYTHON_UNUSED void *context)
{
    PyObject *frame = self->gi_frame;
    if (!frame) {
        if (unlikely(!self->gi_code)) {
            Py_RETURN_NONE;
        }
        frame = (PyObject *) PyFrame_New(
            PyThreadState_Get(),            /*PyThreadState *tstate,*/
            (PyCodeObject*) self->gi_code,  /*PyCodeObject *code,*/
            __pyx_d,                 /*PyObject *globals,*/
            0                               /*PyObject *locals*/
        );
        if (unlikely(!frame))
            return NULL;
        self->gi_frame = frame;
    }
    Py_INCREF(frame);
    return frame;
}
static __pyx_CoroutineObject *__Pyx__Coroutine_New(
            PyTypeObject* type, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
            PyObject *name, PyObject *qualname, PyObject *module_name) {
    __pyx_CoroutineObject *gen = PyObject_GC_New(__pyx_CoroutineObject, type);
    if (unlikely(!gen))
        return NULL;
    return __Pyx__Coroutine_NewInit(gen, body, code, closure, name, qualname, module_name);
}
static __pyx_CoroutineObject *__Pyx__Coroutine_NewInit(
            __pyx_CoroutineObject *gen, __pyx_coroutine_body_t body, PyObject *code, PyObject *closure,
            PyObject *name, PyObject *qualname, PyObject *module_name) {
    gen->body = body;
    gen->closure = closure;
    Py_XINCREF(closure);
    gen->is_running = 0;
    gen->resume_label = 0;
    gen->classobj = NULL;
    gen->yieldfrom = NULL;
    gen->gi_exc_state.exc_type = NULL;
    gen->gi_exc_state.exc_value = NULL;
    gen->gi_exc_state.exc_traceback = NULL;
#if CYTHON_USE_EXC_INFO_STACK
    gen->gi_exc_state.previous_item = NULL;
#endif
    gen->gi_weakreflist = NULL;
    Py_XINCREF(qualname);
    gen->gi_qualname = qualname;
    Py_XINCREF(name);
    gen->gi_name = name;
    Py_XINCREF(module_name);
    gen->gi_modulename = module_name;
    Py_XINCREF(code);
    gen->gi_code = code;
    gen->gi_frame = NULL;
    PyObject_GC_Track(gen);
    return gen;
}

/* PatchModuleWithCoroutine */
static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code) {
#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
    int result;
    PyObject *globals, *result_obj;
    globals = PyDict_New();  if (unlikely(!globals)) goto ignore;
    result = PyDict_SetItemString(globals, "_cython_coroutine_type",
    #ifdef __Pyx_Coroutine_USED
        (PyObject*)__pyx_CoroutineType);
    #else
        Py_None);
    #endif
    if (unlikely(result < 0)) goto ignore;
    result = PyDict_SetItemString(globals, "_cython_generator_type",
    #ifdef __Pyx_Generator_USED
        (PyObject*)__pyx_GeneratorType);
    #else
        Py_None);
    #endif
    if (unlikely(result < 0)) goto ignore;
    if (unlikely(PyDict_SetItemString(globals, "_module", module) < 0)) goto ignore;
    if (unlikely(PyDict_SetItemString(globals, "__builtins__", __pyx_b) < 0)) goto ignore;
    result_obj = PyRun_String(py_code, Py_file_input, globals, globals);
    if (unlikely(!result_obj)) goto ignore;
    Py_DECREF(result_obj);
    Py_DECREF(globals);
    return module;
ignore:
    Py_XDECREF(globals);
    PyErr_WriteUnraisable(module);
    if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, "Cython module failed to patch module with custom type", 1) < 0)) {
        Py_DECREF(module);
        module = NULL;
    }
#else
    py_code++;
#endif
    return module;
}

/* PatchGeneratorABC */
#ifndef CYTHON_REGISTER_ABCS
#define CYTHON_REGISTER_ABCS 1
#endif
#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
static PyObject* __Pyx_patch_abc_module(PyObject *module);
static PyObject* __Pyx_patch_abc_module(PyObject *module) {
    module = __Pyx_Coroutine_patch_module(
        module, ""
"if _cython_generator_type is not None:\n"
"    try: Generator = _module.Generator\n"
"    except AttributeError: pass\n"
"    else: Generator.register(_cython_generator_type)\n"
"if _cython_coroutine_type is not None:\n"
"    try: Coroutine = _module.Coroutine\n"
"    except AttributeError: pass\n"
"    else: Coroutine.register(_cython_coroutine_type)\n"
    );
    return module;
}
#endif
static int __Pyx_patch_abc(void) {
#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
    static int abc_patched = 0;
    if (CYTHON_REGISTER_ABCS && !abc_patched) {
        PyObject *module;
        module = PyImport_ImportModule((PY_MAJOR_VERSION >= 3) ? "collections.abc" : "collections");
        if (!module) {
            PyErr_WriteUnraisable(NULL);
            if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning,
                    ((PY_MAJOR_VERSION >= 3) ?
                        "Cython module failed to register with collections.abc module" :
                        "Cython module failed to register with collections module"), 1) < 0)) {
                return -1;
            }
        } else {
            module = __Pyx_patch_abc_module(module);
            abc_patched = 1;
            if (unlikely(!module))
                return -1;
            Py_DECREF(module);
        }
        module = PyImport_ImportModule("backports_abc");
        if (module) {
            module = __Pyx_patch_abc_module(module);
            Py_XDECREF(module);
        }
        if (!module) {
            PyErr_Clear();
        }
    }
#else
    if ((0)) __Pyx_Coroutine_patch_module(NULL, NULL);
#endif
    return 0;
}

/* Generator */
static PyMethodDef __pyx_Generator_methods[] = {
    {"send", (PyCFunction) __Pyx_Coroutine_Send, METH_O,
     (char*) PyDoc_STR("send(arg) -> send 'arg' into generator,\nreturn next yielded value or raise StopIteration.")},
    {"throw", (PyCFunction) __Pyx_Coroutine_Throw, METH_VARARGS,
     (char*) PyDoc_STR("throw(typ[,val[,tb]]) -> raise exception in generator,\nreturn next yielded value or raise StopIteration.")},
    {"close", (PyCFunction) __Pyx_Coroutine_Close_Method, METH_NOARGS,
     (char*) PyDoc_STR("close() -> raise GeneratorExit inside generator.")},
    {0, 0, 0, 0}
};
static PyMemberDef __pyx_Generator_memberlist[] = {
    {(char *) "gi_running", T_BOOL, offsetof(__pyx_CoroutineObject, is_running), READONLY, NULL},
    {(char*) "gi_yieldfrom", T_OBJECT, offsetof(__pyx_CoroutineObject, yieldfrom), READONLY,
     (char*) PyDoc_STR("object being iterated by 'yield from', or None")},
    {(char*) "gi_code", T_OBJECT, offsetof(__pyx_CoroutineObject, gi_code), READONLY, NULL},
    {0, 0, 0, 0, 0}
};
static PyGetSetDef __pyx_Generator_getsets[] = {
    {(char *) "__name__", (getter)__Pyx_Coroutine_get_name, (setter)__Pyx_Coroutine_set_name,
     (char*) PyDoc_STR("name of the generator"), 0},
    {(char *) "__qualname__", (getter)__Pyx_Coroutine_get_qualname, (setter)__Pyx_Coroutine_set_qualname,
     (char*) PyDoc_STR("qualified name of the generator"), 0},
    {(char *) "gi_frame", (getter)__Pyx_Coroutine_get_frame, NULL,
     (char*) PyDoc_STR("Frame of the generator"), 0},
    {0, 0, 0, 0, 0}
};
static PyTypeObject __pyx_GeneratorType_type = {
    PyVarObject_HEAD_INIT(0, 0)
    "generator",
    sizeof(__pyx_CoroutineObject),
    0,
    (destructor) __Pyx_Coroutine_dealloc,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE,
    0,
    (traverseproc) __Pyx_Coroutine_traverse,
    0,
    0,
    offsetof(__pyx_CoroutineObject, gi_weakreflist),
    0,
    (iternextfunc) __Pyx_Generator_Next,
    __pyx_Generator_methods,
    __pyx_Generator_memberlist,
    __pyx_Generator_getsets,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
    0,
#if CYTHON_USE_TP_FINALIZE
    0,
#else
    __Pyx_Coroutine_del,
#endif
    0,
#if CYTHON_USE_TP_FINALIZE
    __Pyx_Coroutine_del,
#elif PY_VERSION_HEX >= 0x030400a1
    0,
#endif
#if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
    0,
#endif
#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
    0,
#endif
#if PY_VERSION_HEX >= 0x030C0000
    0,
#endif
#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
    0,
#endif
};
static int __pyx_Generator_init(void) {
    __pyx_GeneratorType_type.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
    __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
    __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type);
    if (unlikely(!__pyx_GeneratorType)) {
        return -1;
    }
    return 0;
}

/* CheckBinaryVersion */
static int __Pyx_check_binary_version(void) {
    char ctversion[5];
    int same=1, i, found_dot;
    const char* rt_from_call = Py_GetVersion();
    PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
    found_dot = 0;
    for (i = 0; i < 4; i++) {
        if (!ctversion[i]) {
            same = (rt_from_call[i] < '0' || rt_from_call[i] > '9');
            break;
        }
        if (rt_from_call[i] != ctversion[i]) {
            same = 0;
            break;
        }
    }
    if (!same) {
        char rtversion[5] = {'\0'};
        char message[200];
        for (i=0; i<4; ++i) {
            if (rt_from_call[i] == '.') {
                if (found_dot) break;
                found_dot = 1;
            } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') {
                break;
            }
            rtversion[i] = rt_from_call[i];
        }
        PyOS_snprintf(message, sizeof(message),
                      "compiletime version %s of module '%.100s' "
                      "does not match runtime version %s",
                      ctversion, __Pyx_MODULE_NAME, rtversion);
        return PyErr_WarnEx(NULL, message, 1);
    }
    return 0;
}

/* InitStrings */
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
    while (t->p) {
        #if PY_MAJOR_VERSION < 3
        if (t->is_unicode) {
            *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
        } else if (t->intern) {
            *t->p = PyString_InternFromString(t->s);
        } else {
            *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
        }
        #else
        if (t->is_unicode | t->is_str) {
            if (t->intern) {
                *t->p = PyUnicode_InternFromString(t->s);
            } else if (t->encoding) {
                *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
            } else {
                *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
            }
        } else {
            *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
        }
        #endif
        if (!*t->p)
            return -1;
        if (PyObject_Hash(*t->p) == -1)
            return -1;
        ++t;
    }
    return 0;
}

static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
}
static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
    Py_ssize_t ignore;
    return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
#if !CYTHON_PEP393_ENABLED
static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
    char* defenc_c;
    PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
    if (!defenc) return NULL;
    defenc_c = PyBytes_AS_STRING(defenc);
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
    {
        char* end = defenc_c + PyBytes_GET_SIZE(defenc);
        char* c;
        for (c = defenc_c; c < end; c++) {
            if ((unsigned char) (*c) >= 128) {
                PyUnicode_AsASCIIString(o);
                return NULL;
            }
        }
    }
#endif
    *length = PyBytes_GET_SIZE(defenc);
    return defenc_c;
}
#else
static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
    if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
    if (likely(PyUnicode_IS_ASCII(o))) {
        *length = PyUnicode_GET_LENGTH(o);
        return PyUnicode_AsUTF8(o);
    } else {
        PyUnicode_AsASCIIString(o);
        return NULL;
    }
#else
    return PyUnicode_AsUTF8AndSize(o, length);
#endif
}
#endif
#endif
static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
    if (
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
            __Pyx_sys_getdefaultencoding_not_ascii &&
#endif
            PyUnicode_Check(o)) {
        return __Pyx_PyUnicode_AsStringAndSize(o, length);
    } else
#endif
#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
    if (PyByteArray_Check(o)) {
        *length = PyByteArray_GET_SIZE(o);
        return PyByteArray_AS_STRING(o);
    } else
#endif
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (unlikely(r < 0)) {
            return NULL;
        } else {
            return result;
        }
    }
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
    int retval;
    if (unlikely(!x)) return -1;
    retval = __Pyx_PyObject_IsTrue(x);
    Py_DECREF(x);
    return retval;
}
static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
#if PY_MAJOR_VERSION >= 3
    if (PyLong_Check(result)) {
        if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
                "__int__ returned non-int (type %.200s).  "
                "The ability to return an instance of a strict subclass of int "
                "is deprecated, and may be removed in a future version of Python.",
                Py_TYPE(result)->tp_name)) {
            Py_DECREF(result);
            return NULL;
        }
        return result;
    }
#endif
    PyErr_Format(PyExc_TypeError,
                 "__%.4s__ returned non-%.4s (type %.200s)",
                 type_name, type_name, Py_TYPE(result)->tp_name);
    Py_DECREF(result);
    return NULL;
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
#if CYTHON_USE_TYPE_SLOTS
  PyNumberMethods *m;
#endif
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_Check(x) || PyLong_Check(x)))
#else
  if (likely(PyLong_Check(x)))
#endif
    return __Pyx_NewRef(x);
#if CYTHON_USE_TYPE_SLOTS
  m = Py_TYPE(x)->tp_as_number;
  #if PY_MAJOR_VERSION < 3
  if (m && m->nb_int) {
    name = "int";
    res = m->nb_int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = m->nb_long(x);
  }
  #else
  if (likely(m && m->nb_int)) {
    name = "int";
    res = m->nb_int(x);
  }
  #endif
#else
  if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
    res = PyNumber_Int(x);
  }
#endif
  if (likely(res)) {
#if PY_MAJOR_VERSION < 3
    if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
#else
    if (unlikely(!PyLong_CheckExact(res))) {
#endif
        return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
    }
  }
  else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_TypeError,
                    "an integer is required");
  }
  return res;
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
  Py_ssize_t ival;
  PyObject *x;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_CheckExact(b))) {
    if (sizeof(Py_ssize_t) >= sizeof(long))
        return PyInt_AS_LONG(b);
    else
        return PyInt_AsSsize_t(b);
  }
#endif
  if (likely(PyLong_CheckExact(b))) {
    #if CYTHON_USE_PYLONG_INTERNALS
    const digit* digits = ((PyLongObject*)b)->ob_digit;
    const Py_ssize_t size = Py_SIZE(b);
    if (likely(__Pyx_sst_abs(size) <= 1)) {
        ival = likely(size) ? digits[0] : 0;
        if (size == -1) ival = -ival;
        return ival;
    } else {
      switch (size) {
         case 2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
      }
    }
    #endif
    return PyLong_AsSsize_t(b);
  }
  x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
  if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
    return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
#if PY_MAJOR_VERSION < 3
  } else if (likely(PyInt_CheckExact(o))) {
    return PyInt_AS_LONG(o);
#endif
  } else {
    Py_ssize_t ival;
    PyObject *x;
    x = PyNumber_Index(o);
    if (!x) return -1;
    ival = PyInt_AsLong(x);
    Py_DECREF(x);
    return ival;
  }
}
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
  return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
    return PyInt_FromSize_t(ival);
}


#endif /* Py_PYTHON_H */
