/* Generated by Cython 0.29.4 */

#define 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_4"
#define CYTHON_HEX_VERSION 0x001D04F0
#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
  #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
  #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
#elif defined(PYSTON_VERSION)
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 1
  #define CYTHON_COMPILING_IN_CPYTHON 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
#else
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 1
  #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 1
  #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
    #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
  #ifndef CYTHON_FAST_THREAD_STATE
    #define CYTHON_FAST_THREAD_STATE 1
  #endif
  #ifndef CYTHON_FAST_PYCALL
    #define CYTHON_FAST_PYCALL 1
  #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)
  #endif
  #ifndef CYTHON_USE_EXC_INFO_STACK
    #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
  #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
  #include "longintrepr.h"
  #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 CYTHON_INLINE
  #if defined(__clang__)
    #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
  #elif defined(__GNUC__)
    #define CYTHON_INLINE __inline__
  #elif defined(_MSC_VER)
    #define CYTHON_INLINE __inline
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_INLINE inline
  #else
    #define CYTHON_INLINE
  #endif
#endif

#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_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 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_USE_DICT_VERSIONS
#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);\
        }\
    }
#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
#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
  #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ?\
                                              0 : _PyUnicode_Ready((PyObject *)(op)))
  #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)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#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
  #define PyObject_Unicode             PyObject_Str
#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 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   PyInt_AsLong
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), 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(MS_WINDOWS)
  #define _USE_MATH_DEFINES
#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_ERR(f_index, lineno, Ln_error) \
{ \
  __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; 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__chaplotype
#define __PYX_HAVE_API__chaplotype
/* Early includes */
#include <string.h>
#include <stdio.h>
#include "pythread.h"
#include "stdlib.h"
#include "math.h"
#include "stdio.h"
#include "ctype.h"
#include "string.h"
#include "stdint.h"
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "htslib/sam.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_DEFAULT 0
#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);
#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[] = {
  "cython/chaplotype.pyx",
  "stringsource",
  "cython/fastafile.pxd",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "cython/htslibWrapper.pxd",
  "cython/variant.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_9fastafile_FastaIndex;
struct __pyx_obj_9fastafile_FastaFile;
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_13htslibWrapper_ReadIterator;
struct __pyx_obj_7variant_Variant;
struct __pyx_obj_7variant_VariantCandidateGenerator;
struct __pyx_obj_10chaplotype_Haplotype;
struct __pyx_t_13htslibWrapper_cAlignedRead;
typedef struct __pyx_t_13htslibWrapper_cAlignedRead __pyx_t_13htslibWrapper_cAlignedRead;
struct __pyx_opt_args_13htslibWrapper_7Samfile__open;

/* "htslibWrapper.pxd":187
 *     int bam_cigar_oplen(uint32_t c)
 * 
 * ctypedef struct cAlignedRead:             # <<<<<<<<<<<<<<
 *     char* seq
 *     char* qual
 */
struct __pyx_t_13htslibWrapper_cAlignedRead {
  char *seq;
  char *qual;
  short *cigarOps;
  short *hash;
  short mateChromID;
  short cigarLen;
  short chromID;
  short rlen;
  int pos;
  int end;
  int insertSize;
  int matePos;
  int bitFlag;
  unsigned char mapq;
};

/* "htslibWrapper.pxd":211
 *     cdef _hasIndex(self)
 *     cdef void openBAMFile(self, mode)
 *     cpdef _open(self, mode, loadIndex=*)             # <<<<<<<<<<<<<<
 *     cdef char* getrname(self, int tid)
 *     cpdef ReadIterator fetch(self, const char *region)
 */
struct __pyx_opt_args_13htslibWrapper_7Samfile__open {
  int __pyx_n;
  PyObject *loadIndex;
};
struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence;

/* "chaplotype.pxd":46
 *         double* alignReads(self, int individualIndex, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenReadsStart, cAlignedRead** brokenReadsEnd, int useMapQualCap)
 *         double alignSingleRead(self, cAlignedRead* theRead, int useMapQualCap)
 *         char* getReferenceSequence(self, prefix=*)             # <<<<<<<<<<<<<<
 *         char* getMutatedSequence(self)
 *         char* getShortHaplotypeSequence(self)
 */
struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence {
  int __pyx_n;
  PyObject *prefix;
};

/* "fastafile.pxd":1
 * cdef class FastaIndex:             # <<<<<<<<<<<<<<
 *     cdef object theFile
 *     cdef dict getRefs(self, int parseNCBI)
 */
struct __pyx_obj_9fastafile_FastaIndex {
  PyObject_HEAD
  struct __pyx_vtabstruct_9fastafile_FastaIndex *__pyx_vtab;
  PyObject *theFile;
};


/* "fastafile.pxd":5
 *     cdef dict getRefs(self, int parseNCBI)
 * 
 * cdef class FastaFile(object):             # <<<<<<<<<<<<<<
 *     cdef object theFile
 *     cdef FastaIndex theIndex
 */
struct __pyx_obj_9fastafile_FastaFile {
  PyObject_HEAD
  struct __pyx_vtabstruct_9fastafile_FastaFile *__pyx_vtab;
  PyObject *theFile;
  struct __pyx_obj_9fastafile_FastaIndex *theIndex;
  PyObject *refs;
  PyObject *cache;
  PyObject *cacheRefName;
  PY_LONG_LONG cacheStartPos;
  PY_LONG_LONG cacheEndPos;
};


/* "htslibWrapper.pxd":203
 *     unsigned char mapq
 * 
 * cdef class Samfile:             # <<<<<<<<<<<<<<
 *     cdef void clearHeader(self)
 *     cdef void clearIndex(self)
 */
struct __pyx_obj_13htslibWrapper_Samfile {
  PyObject_HEAD
  struct __pyx_vtabstruct_13htslibWrapper_Samfile *__pyx_vtab;
  char *filename;
  samFile *samfile;
  bam_hdr_t *theHeader;
  hts_idx_t *index;
  PyObject *lock;
};


/* "htslibWrapper.pxd":222
 *     cdef object lock
 * 
 * cdef class ReadIterator:             # <<<<<<<<<<<<<<
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID)
 *     cdef int cnext(self) nogil
 */
struct __pyx_obj_13htslibWrapper_ReadIterator {
  PyObject_HEAD
  struct __pyx_vtabstruct_13htslibWrapper_ReadIterator *__pyx_vtab;
  samFile *theSamfile;
  hts_itr_t *theIterator;
  bam1_t *b;
};


/* "variant.pxd":17
 * 
 * @cython.final
 * cdef class Variant:             # <<<<<<<<<<<<<<
 *     cdef:
 *         public bytes refName
 */
struct __pyx_obj_7variant_Variant {
  PyObject_HEAD
  struct __pyx_vtabstruct_7variant_Variant *__pyx_vtab;
  PyObject *refName;
  PyObject *added;
  PyObject *removed;
  PyObject *bamAdded;
  PyObject *bamRemoved;
  int refPos;
  int bamMinPos;
  int bamMaxPos;
  int minRefPos;
  int maxRefPos;
  int nSupportingReads;
  int varSource;
  int hashValue;
  int nAdded;
  int nRemoved;
  int varType;
};


/* "variant.pxd":44
 * 
 * @cython.final
 * cdef class VariantCandidateGenerator:             # <<<<<<<<<<<<<<
 *     cdef int CIGAR_M
 *     cdef int CIGAR_I
 */
struct __pyx_obj_7variant_VariantCandidateGenerator {
  PyObject_HEAD
  struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtab;
  int CIGAR_M;
  int CIGAR_I;
  int CIGAR_D;
  int CIGAR_N;
  int CIGAR_S;
  int CIGAR_H;
  int CIGAR_P;
  int CIGAR_EQ;
  int CIGAR_X;
  int minMapQual;
  int minBaseQual;
  int minFlank;
  int refId;
  int maxCoverage;
  int verbosity;
  int genSNPs;
  int genIndels;
  int maxReadLength;
  long rStart;
  long rEnd;
  long refSeqStart;
  long refSeqEnd;
  char *refSeq;
  PyObject *variantHeap;
  PyObject *pyRefSeq;
  PyObject *rname;
  struct __pyx_obj_9fastafile_FastaFile *refFile;
  PyObject *options;
  int qualBinSize;
};


/* "chaplotype.pxd":14
 * 
 * @cython.final
 * cdef class Haplotype:             # <<<<<<<<<<<<<<
 *     cdef:
 *         bytes refName
 */
struct __pyx_obj_10chaplotype_Haplotype {
  PyObject_HEAD
  struct __pyx_vtabstruct_10chaplotype_Haplotype *__pyx_vtab;
  PyObject *refName;
  int startPos;
  int endPos;
  int maxReadLength;
  int minVarPos;
  int maxVarPos;
  PyObject *variants;
  PyObject *haplotypeSequence;
  PyObject *shortHaplotypeSequence;
  char *cHaplotypeSequence;
  struct __pyx_obj_9fastafile_FastaFile *refFile;
  PyObject *options;
  double *likelihoodCache;
  int lenCache;
  int lastIndividualIndex;
  PyObject *referenceSequence;
  PyObject *shortReferenceSequence;
  struct __pyx_obj_7variant_Variant *longVar;
  int hash;
  int hapLen;
  int verbosity;
  int endBufferSize;
  char *cHomopolQ;
  char *localGapOpen;
  short *hapSequenceHash;
  short *hapSequenceNextArray;
  int *mapCounts;
  int mapCountsLen;
};



/* "fastafile.pxd":1
 * cdef class FastaIndex:             # <<<<<<<<<<<<<<
 *     cdef object theFile
 *     cdef dict getRefs(self, int parseNCBI)
 */

struct __pyx_vtabstruct_9fastafile_FastaIndex {
  PyObject *(*getRefs)(struct __pyx_obj_9fastafile_FastaIndex *, int);
};
static struct __pyx_vtabstruct_9fastafile_FastaIndex *__pyx_vtabptr_9fastafile_FastaIndex;


/* "fastafile.pxd":5
 *     cdef dict getRefs(self, int parseNCBI)
 * 
 * cdef class FastaFile(object):             # <<<<<<<<<<<<<<
 *     cdef object theFile
 *     cdef FastaIndex theIndex
 */

struct __pyx_vtabstruct_9fastafile_FastaFile {
  PyObject *(*getCharacter)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG);
  PyObject *(*getSequence)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG, PY_LONG_LONG);
  void (*setCacheSequence)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG, PY_LONG_LONG);
};
static struct __pyx_vtabstruct_9fastafile_FastaFile *__pyx_vtabptr_9fastafile_FastaFile;


/* "htslibWrapper.pxd":203
 *     unsigned char mapq
 * 
 * cdef class Samfile:             # <<<<<<<<<<<<<<
 *     cdef void clearHeader(self)
 *     cdef void clearIndex(self)
 */

struct __pyx_vtabstruct_13htslibWrapper_Samfile {
  void (*clearHeader)(struct __pyx_obj_13htslibWrapper_Samfile *);
  void (*clearIndex)(struct __pyx_obj_13htslibWrapper_Samfile *);
  int (*_isBam)(struct __pyx_obj_13htslibWrapper_Samfile *);
  int (*_isCram)(struct __pyx_obj_13htslibWrapper_Samfile *);
  int (*_isOpen)(struct __pyx_obj_13htslibWrapper_Samfile *);
  PyObject *(*_hasIndex)(struct __pyx_obj_13htslibWrapper_Samfile *);
  void (*openBAMFile)(struct __pyx_obj_13htslibWrapper_Samfile *, PyObject *);
  PyObject *(*_open)(struct __pyx_obj_13htslibWrapper_Samfile *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_13htslibWrapper_7Samfile__open *__pyx_optional_args);
  char *(*getrname)(struct __pyx_obj_13htslibWrapper_Samfile *, int);
  struct __pyx_obj_13htslibWrapper_ReadIterator *(*fetch)(struct __pyx_obj_13htslibWrapper_Samfile *, char const *, int __pyx_skip_dispatch);
  PyObject *(*close)(struct __pyx_obj_13htslibWrapper_Samfile *, int __pyx_skip_dispatch);
};
static struct __pyx_vtabstruct_13htslibWrapper_Samfile *__pyx_vtabptr_13htslibWrapper_Samfile;


/* "htslibWrapper.pxd":222
 *     cdef object lock
 * 
 * cdef class ReadIterator:             # <<<<<<<<<<<<<<
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID)
 *     cdef int cnext(self) nogil
 */

struct __pyx_vtabstruct_13htslibWrapper_ReadIterator {
  __pyx_t_13htslibWrapper_cAlignedRead *(*get)(struct __pyx_obj_13htslibWrapper_ReadIterator *, int, char **);
  int (*cnext)(struct __pyx_obj_13htslibWrapper_ReadIterator *);
  char (*_getBase)(struct __pyx_obj_13htslibWrapper_ReadIterator *, uint8_t *, int);
};
static struct __pyx_vtabstruct_13htslibWrapper_ReadIterator *__pyx_vtabptr_13htslibWrapper_ReadIterator;


/* "variant.pxd":17
 * 
 * @cython.final
 * cdef class Variant:             # <<<<<<<<<<<<<<
 *     cdef:
 *         public bytes refName
 */

struct __pyx_vtabstruct_7variant_Variant {
  double (*indelPrior)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_9fastafile_FastaFile *, int);
  double (*calculatePrior)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_9fastafile_FastaFile *);
  void (*addVariant)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_7variant_Variant *);
  int (*overlaps)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_7variant_Variant *);
};
static struct __pyx_vtabstruct_7variant_Variant *__pyx_vtabptr_7variant_Variant;


/* "variant.pxd":44
 * 
 * @cython.final
 * cdef class VariantCandidateGenerator:             # <<<<<<<<<<<<<<
 *     cdef int CIGAR_M
 *     cdef int CIGAR_I
 */

struct __pyx_vtabstruct_7variant_VariantCandidateGenerator {
  void (*addVariantToList)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_7variant_Variant *);
  void (*getSnpCandidatesFromReadSegment)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *, char *, char *, int, int, int, int, int);
  void (*getVariantCandidatesFromSingleRead)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *);
  void (*addCandidatesFromReads)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **);
  PyObject *(*getCandidates)(struct __pyx_obj_7variant_VariantCandidateGenerator *, int);
};
static struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtabptr_7variant_VariantCandidateGenerator;


/* "chaplotype.pyx":120
 * 
 * @cython.final
 * cdef class Haplotype:             # <<<<<<<<<<<<<<
 *     """
 *     Class to encapsulate a single haplotype. This will store all the
 */

struct __pyx_vtabstruct_10chaplotype_Haplotype {
  double *(*alignReads)(struct __pyx_obj_10chaplotype_Haplotype *, int, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, int);
  double (*alignSingleRead)(struct __pyx_obj_10chaplotype_Haplotype *, __pyx_t_13htslibWrapper_cAlignedRead *, int);
  char *(*getReferenceSequence)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args);
  char *(*getMutatedSequence)(struct __pyx_obj_10chaplotype_Haplotype *);
  char *(*getShortHaplotypeSequence)(struct __pyx_obj_10chaplotype_Haplotype *);
  PyObject *(*vcfINFO)(struct __pyx_obj_10chaplotype_Haplotype *);
  PyObject *(*getSequenceContext)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
  int (*homopolymerLengthForOneVariant)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
  PyObject *(*homopolymerLengths)(struct __pyx_obj_10chaplotype_Haplotype *);
  void (*annotateWithGapOpen)(struct __pyx_obj_10chaplotype_Haplotype *);
};
static struct __pyx_vtabstruct_10chaplotype_Haplotype *__pyx_vtabptr_10chaplotype_Haplotype;
static double *__pyx_f_10chaplotype_9Haplotype_alignReads(struct __pyx_obj_10chaplotype_Haplotype *, int, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, int);
static double __pyx_f_10chaplotype_9Haplotype_alignSingleRead(struct __pyx_obj_10chaplotype_Haplotype *, __pyx_t_13htslibWrapper_cAlignedRead *, int);
static char *__pyx_f_10chaplotype_9Haplotype_getReferenceSequence(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args);
static char *__pyx_f_10chaplotype_9Haplotype_getMutatedSequence(struct __pyx_obj_10chaplotype_Haplotype *);
static char *__pyx_f_10chaplotype_9Haplotype_getShortHaplotypeSequence(struct __pyx_obj_10chaplotype_Haplotype *);
static PyObject *__pyx_f_10chaplotype_9Haplotype_vcfINFO(struct __pyx_obj_10chaplotype_Haplotype *);
static PyObject *__pyx_f_10chaplotype_9Haplotype_getSequenceContext(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
static int __pyx_f_10chaplotype_9Haplotype_homopolymerLengthForOneVariant(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
static PyObject *__pyx_f_10chaplotype_9Haplotype_homopolymerLengths(struct __pyx_obj_10chaplotype_Haplotype *);
static void __pyx_f_10chaplotype_9Haplotype_annotateWithGapOpen(struct __pyx_obj_10chaplotype_Haplotype *);

/* --- 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);

/* 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);

/* PyIntBinop.proto */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
#else
#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\
    (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2))
#endif

/* 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

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

/* 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);
        Py_SIZE(list) = len+1;
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
#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, int 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
  static size_t __pyx_pyframe_localsplus_offset = 0;
  #include "frameobject.h"
  #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

/* 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);

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

/* GetModuleGlobalName.proto */
#if CYTHON_USE_DICT_VERSIONS
#define __Pyx_GetModuleGlobalName(var, name)  {\
    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);\
}
#define __Pyx_GetModuleGlobalNameUncached(var, name)  {\
    PY_UINT64_T __pyx_dict_version;\
    PyObject *__pyx_dict_cached_value;\
    (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
}
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

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

/* 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);

/* BytesEquals.proto */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);

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

/* PyIntCompare.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, long inplace);

/* 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);
        Py_SIZE(list) = len+1;
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif

/* PyIntBinop.proto */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
#else
#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\
    (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2))
#endif

/* StringJoin.proto */
#if PY_MAJOR_VERSION < 3
#define __Pyx_PyString_Join __Pyx_PyBytes_Join
#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v))
#else
#define __Pyx_PyString_Join PyUnicode_Join
#define __Pyx_PyBaseString_Join PyUnicode_Join
#endif
#if CYTHON_COMPILING_IN_CPYTHON
    #if PY_MAJOR_VERSION < 3
    #define __Pyx_PyBytes_Join _PyString_Join
    #else
    #define __Pyx_PyBytes_Join _PyBytes_Join
    #endif
#else
static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values);
#endif

/* 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);

/* 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

/* 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

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

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

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

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

/* UnicodeEquals.proto */
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);

/* StrEquals.proto */
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
#else
#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
#endif

/* 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

/* SetVTable.proto */
static int __Pyx_SetVtable(PyObject *dict, void *vtable);

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

/* TypeImport.proto */
#ifndef __PYX_HAVE_RT_ImportType_proto
#define __PYX_HAVE_RT_ImportType_proto
enum __Pyx_ImportType_CheckSize {
   __Pyx_ImportType_CheckSize_Error = 0,
   __Pyx_ImportType_CheckSize_Warn = 1,
   __Pyx_ImportType_CheckSize_Ignore = 2
};
static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size);
#endif

/* GetVTable.proto */
static void* __Pyx_GetVtable(PyObject *dict);

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

/* PyFloatBinop.proto */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyFloat_AddCObj(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check);
#else
#define __Pyx_PyFloat_AddCObj(op1, op2, floatval, inplace, zerodivision_check)\
    (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2))
#endif

/* PyIntFromDouble.proto */
#if PY_MAJOR_VERSION < 3
static CYTHON_INLINE PyObject* __Pyx_PyInt_FromDouble(double value);
#else
#define __Pyx_PyInt_FromDouble(value) PyLong_FromDouble(value)
#endif

/* 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);

/* 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_char(char value);

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

/* CIntFromPy.proto */
static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_As_PY_LONG_LONG(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)

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

/* FunctionExport.proto */
static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig);

/* VoidPtrImport.proto */
static int __Pyx_ImportVoidPtr(PyObject *module, const char *name, void **p, const char *sig);

/* FunctionImport.proto */
static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig);

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

static char *__pyx_f_10chaplotype_9Haplotype_getShortHaplotypeSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto*/
static double *__pyx_f_10chaplotype_9Haplotype_alignReads(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, int __pyx_v_individualIndex, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_start, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_end, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_badReadsStart, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_badReadsEnd, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_brokenReadsStart, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_brokenReadsEnd, int __pyx_v_useMapQualCap); /* proto*/
static double __pyx_f_10chaplotype_9Haplotype_alignSingleRead(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, __pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead, int __pyx_v_useMapQualCap); /* proto*/
static char *__pyx_f_10chaplotype_9Haplotype_getReferenceSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args); /* proto*/
static char *__pyx_f_10chaplotype_9Haplotype_getMutatedSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_10chaplotype_9Haplotype_homopolymerLengths(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto*/
static int __pyx_f_10chaplotype_9Haplotype_homopolymerLengthForOneVariant(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_7variant_Variant *__pyx_v_variant); /* proto*/
static PyObject *__pyx_f_10chaplotype_9Haplotype_getSequenceContext(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_7variant_Variant *__pyx_v_variant); /* proto*/
static PyObject *__pyx_f_10chaplotype_9Haplotype_vcfINFO(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto*/
static void __pyx_f_10chaplotype_9Haplotype_annotateWithGapOpen(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto*/

/* Module declarations from 'cython' */

/* Module declarations from 'fastafile' */
static PyTypeObject *__pyx_ptype_9fastafile_FastaIndex = 0;
static PyTypeObject *__pyx_ptype_9fastafile_FastaFile = 0;

/* Module declarations from 'cpython.version' */

/* Module declarations from '__builtin__' */

/* Module declarations from 'cpython.type' */
static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;

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

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

/* Module declarations from 'cpython.object' */

/* Module declarations from 'cpython.ref' */

/* Module declarations from 'cpython.exc' */

/* Module declarations from 'cpython.module' */

/* Module declarations from 'cpython.mem' */

/* Module declarations from 'cpython.tuple' */

/* Module declarations from 'cpython.list' */

/* Module declarations from 'cpython.sequence' */

/* Module declarations from 'cpython.mapping' */

/* Module declarations from 'cpython.iterator' */

/* Module declarations from 'cpython.number' */

/* Module declarations from 'cpython.int' */

/* Module declarations from '__builtin__' */

/* Module declarations from 'cpython.bool' */
static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;

/* Module declarations from 'cpython.long' */

/* Module declarations from 'cpython.float' */

/* Module declarations from '__builtin__' */

/* Module declarations from 'cpython.complex' */
static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;

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

/* Module declarations from 'cpython.unicode' */

/* Module declarations from 'cpython.dict' */

/* Module declarations from 'cpython.instance' */

/* Module declarations from 'cpython.function' */

/* Module declarations from 'cpython.method' */

/* Module declarations from 'cpython.weakref' */

/* Module declarations from 'cpython.getargs' */

/* Module declarations from 'cpython.pythread' */

/* Module declarations from 'cpython.pystate' */

/* Module declarations from 'cpython.cobject' */

/* Module declarations from 'cpython.oldbuffer' */

/* Module declarations from 'cpython.set' */

/* Module declarations from 'cpython.buffer' */

/* Module declarations from 'cpython.bytes' */

/* Module declarations from 'cpython.pycapsule' */

/* Module declarations from 'cpython' */

/* Module declarations from 'htslibWrapper' */
static PyTypeObject *__pyx_ptype_13htslibWrapper_Samfile = 0;
static PyTypeObject *__pyx_ptype_13htslibWrapper_ReadIterator = 0;
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReverse(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsPaired(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsProperPair(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsDuplicate(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsQCFail(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReadOne(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsSecondaryAlignment(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/

/* Module declarations from 'variant' */
static PyTypeObject *__pyx_ptype_7variant_Variant = 0;
static PyTypeObject *__pyx_ptype_7variant_VariantCandidateGenerator = 0;
static int *__pyx_vp_7variant_PLATYPUS_VAR = 0;
#define __pyx_v_7variant_PLATYPUS_VAR (*__pyx_vp_7variant_PLATYPUS_VAR)
static int *__pyx_vp_7variant_FILE_VAR = 0;
#define __pyx_v_7variant_FILE_VAR (*__pyx_vp_7variant_FILE_VAR)
static int *__pyx_vp_7variant_ASSEMBLER_VAR = 0;
#define __pyx_v_7variant_ASSEMBLER_VAR (*__pyx_vp_7variant_ASSEMBLER_VAR)

/* Module declarations from 'calign' */
static int *__pyx_vp_6calign_hash_nucs = 0;
#define __pyx_v_6calign_hash_nucs (*__pyx_vp_6calign_hash_nucs)
static int *__pyx_vp_6calign_hash_size = 0;
#define __pyx_v_6calign_hash_size (*__pyx_vp_6calign_hash_size)
static int *__pyx_vp_6calign_max_sequence_length = 0;
#define __pyx_v_6calign_max_sequence_length (*__pyx_vp_6calign_max_sequence_length)
static short *(*__pyx_f_6calign_hash_sequence)(char *, int); /*proto*/
static void (*__pyx_f_6calign_hash_sequence_multihit)(char *, int, short **, short **); /*proto*/
static int (*__pyx_f_6calign_mapAndAlignReadToHaplotype)(char *, char *, int, int, int, int, short *, short *, short *, char *, int, int, char *, int *, int, int, int); /*proto*/
static void (*__pyx_f_6calign_hashReadForMapping)(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/

/* Module declarations from 'cerrormodel' */

/* Module declarations from 'chaplotype' */
static PyTypeObject *__pyx_ptype_10chaplotype_Haplotype = 0;
static double __pyx_v_10chaplotype_PI;
static double __pyx_v_10chaplotype_mLTOT;
static PyObject *__pyx_v_10chaplotype_per_base_indel_errors = 0;
static PyObject *__pyx_v_10chaplotype_homopolq = 0;
static int __pyx_f_10chaplotype_computeOverlapOfReadAndHaplotype(int, int, __pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static void __pyx_f_10chaplotype_my_free(void *); /*proto*/
static void *__pyx_f_10chaplotype_my_malloc(size_t); /*proto*/
static double __pyx_f_10chaplotype_alignReadToHaplotype(__pyx_t_13htslibWrapper_cAlignedRead *, struct __pyx_obj_10chaplotype_Haplotype *, int, int); /*proto*/
#define __Pyx_MODULE_NAME "chaplotype"
extern int __pyx_module_is_main_chaplotype;
int __pyx_module_is_main_chaplotype = 0;

/* Implementation of 'chaplotype' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_min;
static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_StandardError;
static PyObject *__pyx_builtin_reversed;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_zip;
static const char __pyx_k_[] = "";
static const char __pyx_k_n[] = "n";
static const char __pyx_k_q[] = "q";
static const char __pyx_k_HP[] = "HP";
static const char __pyx_k_SC[] = "SC";
static const char __pyx_k__2[] = ",";
static const char __pyx_k__5[] = " ";
static const char __pyx_k__6[] = "-";
static const char __pyx_k__7[] = "!";
static const char __pyx_k__8[] = ".";
static const char __pyx_k_pi[] = "pi";
static const char __pyx_k_Log[] = "Log";
static const char __pyx_k_chr[] = "chr";
static const char __pyx_k_idx[] = "idx";
static const char __pyx_k_max[] = "max";
static const char __pyx_k_min[] = "min";
static const char __pyx_k_pow[] = "pow";
static const char __pyx_k_str[] = "__str__";
static const char __pyx_k_zip[] = "zip";
static const char __pyx_k_join[] = "join";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_math[] = "math";
static const char __pyx_k_name[] = "__name__";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_debug[] = "debug";
static const char __pyx_k_error[] = "error";
static const char __pyx_k_lower[] = "lower";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_s_s_s[] = ") %s:%s-%s";
static const char __pyx_k_upper[] = "upper";
static const char __pyx_k_endPos[] = "endPos";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_logger[] = "logger";
static const char __pyx_k_random[] = "random";
static const char __pyx_k_reduce[] = "__reduce__";
static const char __pyx_k_Score_s[] = " Score = %s";
static const char __pyx_k_logging[] = "logging";
static const char __pyx_k_options[] = "options";
static const char __pyx_k_refFile[] = "refFile";
static const char __pyx_k_refName[] = "refName";
static const char __pyx_k_getstate[] = "__getstate__";
static const char __pyx_k_reversed[] = "reversed";
static const char __pyx_k_setstate[] = "__setstate__";
static const char __pyx_k_startPos[] = "startPos";
static const char __pyx_k_variants[] = "variants";
static const char __pyx_k_Haplotype[] = "  Haplotype(";
static const char __pyx_k_SeqLength[] = "SeqLength";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_enumerate[] = "enumerate";
static const char __pyx_k_getLogger[] = "getLogger";
static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
static const char __pyx_k_varSource[] = "varSource";
static const char __pyx_k_verbosity[] = "verbosity";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
static const char __pyx_k_Haplotype_2[] = "Haplotype";
static const char __pyx_k_minBaseQual[] = "minBaseQual";
static const char __pyx_k_StandardError[] = "StandardError";
static const char __pyx_k_maxReadLength[] = "maxReadLength";
static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_calculateFlankScore[] = "calculateFlankScore";
static const char __pyx_k_Oh_no_The_bridge_is_gone[] = "Oh no! The bridge is gone!";
static const char __pyx_k_Haplotype_Reference_s_s_s[] = "  Haplotype(*Reference*) %s:%s-%s";
static const char __pyx_k_Haplotype_with_vars_s_has_len_s[] = "Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s";
static const char __pyx_k_cpos_s_end_pos_s_Variants_are_s[] = "cpos = %s end pos = %s. Variants are %s";
static const char __pyx_k_module_containing_various_class[] = "\nmodule containing various classes and functions for use in generating\nand processing haplotypes.\n";
static const char __pyx_k_Could_not_allocate_haplotype_cac[] = "Could not allocate haplotype cache";
static const char __pyx_k_Could_not_reallocate_haplotype_c[] = "Could not reallocate haplotype cache";
static const char __pyx_k_Haplotype_is_too_long_Max_allowe[] = "Haplotype is too long. Max allowed length is %s";
static const char __pyx_k_Internal_error_encountered_negat[] = "Internal error: encountered negative gap open score (%s, at position %s)";
static const char __pyx_k_Op_code_s_not_implemented_in_hap[] = "Op code %s not implemented in haplotype__richcmp__()";
static const char __pyx_k_Out_of_memory_in_cHaplotype_alig[] = "Out of memory in cHaplotype.alignReads";
static const char __pyx_k_self_hapSequenceHash_self_hapSeq[] = "self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling";
static PyObject *__pyx_kp_s_;
static PyObject *__pyx_kp_s_Could_not_allocate_haplotype_cac;
static PyObject *__pyx_kp_s_Could_not_reallocate_haplotype_c;
static PyObject *__pyx_n_s_HP;
static PyObject *__pyx_kp_s_Haplotype;
static PyObject *__pyx_n_s_Haplotype_2;
static PyObject *__pyx_kp_s_Haplotype_Reference_s_s_s;
static PyObject *__pyx_kp_s_Haplotype_is_too_long_Max_allowe;
static PyObject *__pyx_kp_s_Haplotype_with_vars_s_has_len_s;
static PyObject *__pyx_kp_s_Internal_error_encountered_negat;
static PyObject *__pyx_n_s_Log;
static PyObject *__pyx_kp_s_Oh_no_The_bridge_is_gone;
static PyObject *__pyx_kp_s_Op_code_s_not_implemented_in_hap;
static PyObject *__pyx_kp_s_Out_of_memory_in_cHaplotype_alig;
static PyObject *__pyx_n_s_SC;
static PyObject *__pyx_kp_s_Score_s;
static PyObject *__pyx_n_s_SeqLength;
static PyObject *__pyx_n_s_StandardError;
static PyObject *__pyx_n_s_TypeError;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_kp_s__2;
static PyObject *__pyx_kp_s__5;
static PyObject *__pyx_kp_s__6;
static PyObject *__pyx_kp_s__7;
static PyObject *__pyx_kp_s__8;
static PyObject *__pyx_n_s_calculateFlankScore;
static PyObject *__pyx_n_s_chr;
static PyObject *__pyx_n_s_cline_in_traceback;
static PyObject *__pyx_kp_s_cpos_s_end_pos_s_Variants_are_s;
static PyObject *__pyx_n_s_debug;
static PyObject *__pyx_n_s_endPos;
static PyObject *__pyx_n_s_enumerate;
static PyObject *__pyx_n_s_error;
static PyObject *__pyx_n_s_getLogger;
static PyObject *__pyx_n_s_getstate;
static PyObject *__pyx_n_s_idx;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_join;
static PyObject *__pyx_n_s_logger;
static PyObject *__pyx_n_s_logging;
static PyObject *__pyx_n_s_lower;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_math;
static PyObject *__pyx_n_s_max;
static PyObject *__pyx_n_s_maxReadLength;
static PyObject *__pyx_n_s_min;
static PyObject *__pyx_n_s_minBaseQual;
static PyObject *__pyx_n_s_n;
static PyObject *__pyx_n_s_name;
static PyObject *__pyx_n_s_options;
static PyObject *__pyx_n_s_pi;
static PyObject *__pyx_n_s_pow;
static PyObject *__pyx_n_s_pyx_vtable;
static PyObject *__pyx_n_s_q;
static PyObject *__pyx_n_s_random;
static PyObject *__pyx_n_s_range;
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_refFile;
static PyObject *__pyx_n_s_refName;
static PyObject *__pyx_n_s_reversed;
static PyObject *__pyx_kp_s_s_s_s;
static PyObject *__pyx_kp_s_self_hapSequenceHash_self_hapSeq;
static PyObject *__pyx_n_s_setstate;
static PyObject *__pyx_n_s_setstate_cython;
static PyObject *__pyx_n_s_startPos;
static PyObject *__pyx_n_s_str;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_upper;
static PyObject *__pyx_n_s_varSource;
static PyObject *__pyx_n_s_variants;
static PyObject *__pyx_n_s_verbosity;
static PyObject *__pyx_n_s_zip;
static int __pyx_pf_10chaplotype_9Haplotype___init__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, PyObject *__pyx_v_refName, int __pyx_v_startPos, int __pyx_v_endPos, PyObject *__pyx_v_variants, struct __pyx_obj_9fastafile_FastaFile *__pyx_v_refFile, int __pyx_v_maxReadLength, PyObject *__pyx_v_options); /* proto */
static void __pyx_pf_10chaplotype_9Haplotype_2__dealloc__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_4__copy__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_6__richcmp__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_other, int __pyx_v_opCode); /* proto */
static Py_hash_t __pyx_pf_10chaplotype_9Haplotype_8__hash__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_10__str__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_12__repr__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_14__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_10chaplotype_9Haplotype_16__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
static PyObject *__pyx_tp_new_10chaplotype_Haplotype(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_float_1_0eneg_3;
static PyObject *__pyx_float_1_1eneg_4;
static PyObject *__pyx_float_1_4eneg_3;
static PyObject *__pyx_float_2_4eneg_4;
static PyObject *__pyx_float_2_9eneg_5;
static PyObject *__pyx_float_4_3eneg_4;
static PyObject *__pyx_float_4_3eneg_5;
static PyObject *__pyx_float_5_7eneg_4;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_10;
static PyObject *__pyx_int_11;
static PyObject *__pyx_int_20;
static PyObject *__pyx_int_21;
static PyObject *__pyx_tuple__3;
static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__9;
/* Late includes */

/* "chaplotype.pyx":71
 * ###################################################################################################
 * 
 * cdef void my_free(void* thePointer):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

static void __pyx_f_10chaplotype_my_free(void *__pyx_v_thePointer) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("my_free", 0);

  /* "chaplotype.pyx":75
 *     Cython wrapper. Used for profiling.
 *     """
 *     free(thePointer)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  free(__pyx_v_thePointer);

  /* "chaplotype.pyx":71
 * ###################################################################################################
 * 
 * cdef void my_free(void* thePointer):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

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

/* "chaplotype.pyx":79
 * ###################################################################################################
 * 
 * cdef void* my_malloc(size_t theSize):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

static void *__pyx_f_10chaplotype_my_malloc(size_t __pyx_v_theSize) {
  void *__pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("my_malloc", 0);

  /* "chaplotype.pyx":83
 *     Cython wrapper. Used for profiling.
 *     """
 *     return malloc(theSize)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = malloc(__pyx_v_theSize);
  goto __pyx_L0;

  /* "chaplotype.pyx":79
 * ###################################################################################################
 * 
 * cdef void* my_malloc(size_t theSize):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

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

/* "chaplotype.pyx":87
 * ###################################################################################################
 * 
 * cdef void* my_calloc(size_t theSize1, size_t theSize2):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

static void *__pyx_f_10chaplotype_my_calloc(size_t __pyx_v_theSize1, size_t __pyx_v_theSize2) {
  void *__pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("my_calloc", 0);

  /* "chaplotype.pyx":91
 *     Cython wrapper. Used for profiling.
 *     """
 *     return calloc(theSize1, theSize2)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = calloc(__pyx_v_theSize1, __pyx_v_theSize2);
  goto __pyx_L0;

  /* "chaplotype.pyx":87
 * ###################################################################################################
 * 
 * cdef void* my_calloc(size_t theSize1, size_t theSize2):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

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

/* "chaplotype.pyx":95
 * ###################################################################################################
 * 
 * cdef void* my_realloc(void* thePointer, size_t newSize):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

static void *__pyx_f_10chaplotype_my_realloc(void *__pyx_v_thePointer, size_t __pyx_v_newSize) {
  void *__pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("my_realloc", 0);

  /* "chaplotype.pyx":99
 *     Cython wrapper. Used for profiling.
 *     """
 *     return realloc(thePointer, newSize)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = realloc(__pyx_v_thePointer, __pyx_v_newSize);
  goto __pyx_L0;

  /* "chaplotype.pyx":95
 * ###################################################################################################
 * 
 * cdef void* my_realloc(void* thePointer, size_t newSize):             # <<<<<<<<<<<<<<
 *     """
 *     Cython wrapper. Used for profiling.
 */

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

/* "chaplotype.pyx":103
 * ###################################################################################################
 * 
 * cdef int computeOverlapOfReadAndHaplotype(int hapStart, int hapEnd, cAlignedRead* theRead):             # <<<<<<<<<<<<<<
 *     """
 *     Compute and return the number of bases by which a read overlaps the haplotype of interest.
 */

static int __pyx_f_10chaplotype_computeOverlapOfReadAndHaplotype(int __pyx_v_hapStart, int __pyx_v_hapEnd, __pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_v_readStart;
  int __pyx_v_readEnd;
  int __pyx_v_overlapStart;
  int __pyx_v_overlapEnd;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  __Pyx_RefNannySetupContext("computeOverlapOfReadAndHaplotype", 0);

  /* "chaplotype.pyx":107
 *     Compute and return the number of bases by which a read overlaps the haplotype of interest.
 *     """
 *     cdef int readStart = theRead[0].pos             # <<<<<<<<<<<<<<
 *     cdef int readEnd = theRead[0].end
 *     cdef int overlapStart = max(hapStart, readStart)
 */
  __pyx_t_1 = (__pyx_v_theRead[0]).pos;
  __pyx_v_readStart = __pyx_t_1;

  /* "chaplotype.pyx":108
 *     """
 *     cdef int readStart = theRead[0].pos
 *     cdef int readEnd = theRead[0].end             # <<<<<<<<<<<<<<
 *     cdef int overlapStart = max(hapStart, readStart)
 *     cdef int overlapEnd = min(hapEnd, readEnd)
 */
  __pyx_t_1 = (__pyx_v_theRead[0]).end;
  __pyx_v_readEnd = __pyx_t_1;

  /* "chaplotype.pyx":109
 *     cdef int readStart = theRead[0].pos
 *     cdef int readEnd = theRead[0].end
 *     cdef int overlapStart = max(hapStart, readStart)             # <<<<<<<<<<<<<<
 *     cdef int overlapEnd = min(hapEnd, readEnd)
 * 
 */
  __pyx_t_1 = __pyx_v_readStart;
  __pyx_t_2 = __pyx_v_hapStart;
  if (((__pyx_t_1 > __pyx_t_2) != 0)) {
    __pyx_t_3 = __pyx_t_1;
  } else {
    __pyx_t_3 = __pyx_t_2;
  }
  __pyx_v_overlapStart = __pyx_t_3;

  /* "chaplotype.pyx":110
 *     cdef int readEnd = theRead[0].end
 *     cdef int overlapStart = max(hapStart, readStart)
 *     cdef int overlapEnd = min(hapEnd, readEnd)             # <<<<<<<<<<<<<<
 * 
 *     if overlapEnd > overlapStart:
 */
  __pyx_t_3 = __pyx_v_readEnd;
  __pyx_t_1 = __pyx_v_hapEnd;
  if (((__pyx_t_3 < __pyx_t_1) != 0)) {
    __pyx_t_2 = __pyx_t_3;
  } else {
    __pyx_t_2 = __pyx_t_1;
  }
  __pyx_v_overlapEnd = __pyx_t_2;

  /* "chaplotype.pyx":112
 *     cdef int overlapEnd = min(hapEnd, readEnd)
 * 
 *     if overlapEnd > overlapStart:             # <<<<<<<<<<<<<<
 *         return overlapEnd - overlapStart
 *     else:
 */
  __pyx_t_4 = ((__pyx_v_overlapEnd > __pyx_v_overlapStart) != 0);
  if (__pyx_t_4) {

    /* "chaplotype.pyx":113
 * 
 *     if overlapEnd > overlapStart:
 *         return overlapEnd - overlapStart             # <<<<<<<<<<<<<<
 *     else:
 *         return -1
 */
    __pyx_r = (__pyx_v_overlapEnd - __pyx_v_overlapStart);
    goto __pyx_L0;

    /* "chaplotype.pyx":112
 *     cdef int overlapEnd = min(hapEnd, readEnd)
 * 
 *     if overlapEnd > overlapStart:             # <<<<<<<<<<<<<<
 *         return overlapEnd - overlapStart
 *     else:
 */
  }

  /* "chaplotype.pyx":115
 *         return overlapEnd - overlapStart
 *     else:
 *         return -1             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  /*else*/ {
    __pyx_r = -1;
    goto __pyx_L0;
  }

  /* "chaplotype.pyx":103
 * ###################################################################################################
 * 
 * cdef int computeOverlapOfReadAndHaplotype(int hapStart, int hapEnd, cAlignedRead* theRead):             # <<<<<<<<<<<<<<
 *     """
 *     Compute and return the number of bases by which a read overlaps the haplotype of interest.
 */

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

/* "chaplotype.pyx":127
 *     this haplotype in the reference.
 *     """
 *     def __init__(self, bytes refName, int startPos, int endPos, tuple variants, FastaFile refFile, int maxReadLength, options):             # <<<<<<<<<<<<<<
 *         """
 *         Constructor. Takes a tuple of variants and a
 */

/* Python wrapper */
static int __pyx_pw_10chaplotype_9Haplotype_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_10chaplotype_9Haplotype___init__[] = "\n        Constructor. Takes a tuple of variants and a\n        fasta file of the referene sequence.\n        Variants are sorted on instantiation\n        ";
#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_10chaplotype_9Haplotype___init__;
#endif
static int __pyx_pw_10chaplotype_9Haplotype_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_refName = 0;
  int __pyx_v_startPos;
  int __pyx_v_endPos;
  PyObject *__pyx_v_variants = 0;
  struct __pyx_obj_9fastafile_FastaFile *__pyx_v_refFile = 0;
  int __pyx_v_maxReadLength;
  PyObject *__pyx_v_options = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_refName,&__pyx_n_s_startPos,&__pyx_n_s_endPos,&__pyx_n_s_variants,&__pyx_n_s_refFile,&__pyx_n_s_maxReadLength,&__pyx_n_s_options,0};
    PyObject* values[7] = {0,0,0,0,0,0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
        CYTHON_FALLTHROUGH;
        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 (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_refName)) != 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_startPos)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 1); __PYX_ERR(0, 127, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  2:
        if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_endPos)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 2); __PYX_ERR(0, 127, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  3:
        if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_variants)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 3); __PYX_ERR(0, 127, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  4:
        if (likely((values[4] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_refFile)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 4); __PYX_ERR(0, 127, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  5:
        if (likely((values[5] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_maxReadLength)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 5); __PYX_ERR(0, 127, __pyx_L3_error)
        }
        CYTHON_FALLTHROUGH;
        case  6:
        if (likely((values[6] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_options)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 6); __PYX_ERR(0, 127, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 127, __pyx_L3_error)
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 7) {
      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);
      values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
      values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
      values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
      values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
    }
    __pyx_v_refName = ((PyObject*)values[0]);
    __pyx_v_startPos = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_startPos == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 127, __pyx_L3_error)
    __pyx_v_endPos = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_endPos == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 127, __pyx_L3_error)
    __pyx_v_variants = ((PyObject*)values[3]);
    __pyx_v_refFile = ((struct __pyx_obj_9fastafile_FastaFile *)values[4]);
    __pyx_v_maxReadLength = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_maxReadLength == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 127, __pyx_L3_error)
    __pyx_v_options = values[6];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 127, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("chaplotype.Haplotype.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_refName), (&PyBytes_Type), 1, "refName", 1))) __PYX_ERR(0, 127, __pyx_L1_error)
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_variants), (&PyTuple_Type), 1, "variants", 1))) __PYX_ERR(0, 127, __pyx_L1_error)
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_refFile), __pyx_ptype_9fastafile_FastaFile, 1, "refFile", 0))) __PYX_ERR(0, 127, __pyx_L1_error)
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype___init__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self), __pyx_v_refName, __pyx_v_startPos, __pyx_v_endPos, __pyx_v_variants, __pyx_v_refFile, __pyx_v_maxReadLength, __pyx_v_options);

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

static int __pyx_pf_10chaplotype_9Haplotype___init__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, PyObject *__pyx_v_refName, int __pyx_v_startPos, int __pyx_v_endPos, PyObject *__pyx_v_variants, struct __pyx_obj_9fastafile_FastaFile *__pyx_v_refFile, int __pyx_v_maxReadLength, PyObject *__pyx_v_options) {
  struct __pyx_obj_7variant_Variant *__pyx_v_v = 0;
  PyObject *__pyx_v_leftBuffer = NULL;
  PyObject *__pyx_v_rightBuffer = NULL;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  long __pyx_t_2;
  long __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  int __pyx_t_8;
  long __pyx_t_9;
  Py_ssize_t __pyx_t_10;
  char *__pyx_t_11;
  size_t __pyx_t_12;
  PyObject *__pyx_t_13 = NULL;
  PyObject *__pyx_t_14 = NULL;
  PyObject *__pyx_t_15 = NULL;
  __Pyx_RefNannySetupContext("__init__", 0);

  /* "chaplotype.pyx":133
 *         Variants are sorted on instantiation
 *         """
 *         self.refName             = refName             # <<<<<<<<<<<<<<
 *         self.refFile             = refFile
 *         self.variants            = variants
 */
  __Pyx_INCREF(__pyx_v_refName);
  __Pyx_GIVEREF(__pyx_v_refName);
  __Pyx_GOTREF(__pyx_v_self->refName);
  __Pyx_DECREF(__pyx_v_self->refName);
  __pyx_v_self->refName = __pyx_v_refName;

  /* "chaplotype.pyx":134
 *         """
 *         self.refName             = refName
 *         self.refFile             = refFile             # <<<<<<<<<<<<<<
 *         self.variants            = variants
 *         self.hash                = -1
 */
  __Pyx_INCREF(((PyObject *)__pyx_v_refFile));
  __Pyx_GIVEREF(((PyObject *)__pyx_v_refFile));
  __Pyx_GOTREF(__pyx_v_self->refFile);
  __Pyx_DECREF(((PyObject *)__pyx_v_self->refFile));
  __pyx_v_self->refFile = __pyx_v_refFile;

  /* "chaplotype.pyx":135
 *         self.refName             = refName
 *         self.refFile             = refFile
 *         self.variants            = variants             # <<<<<<<<<<<<<<
 *         self.hash                = -1
 *         self.localGapOpen        = NULL
 */
  __Pyx_INCREF(__pyx_v_variants);
  __Pyx_GIVEREF(__pyx_v_variants);
  __Pyx_GOTREF(__pyx_v_self->variants);
  __Pyx_DECREF(__pyx_v_self->variants);
  __pyx_v_self->variants = __pyx_v_variants;

  /* "chaplotype.pyx":136
 *         self.refFile             = refFile
 *         self.variants            = variants
 *         self.hash                = -1             # <<<<<<<<<<<<<<
 *         self.localGapOpen        = NULL
 *         self.haplotypeSequence   = None
 */
  __pyx_v_self->hash = -1;

  /* "chaplotype.pyx":137
 *         self.variants            = variants
 *         self.hash                = -1
 *         self.localGapOpen        = NULL             # <<<<<<<<<<<<<<
 *         self.haplotypeSequence   = None
 *         self.startPos            = max(0, startPos)
 */
  __pyx_v_self->localGapOpen = NULL;

  /* "chaplotype.pyx":138
 *         self.hash                = -1
 *         self.localGapOpen        = NULL
 *         self.haplotypeSequence   = None             # <<<<<<<<<<<<<<
 *         self.startPos            = max(0, startPos)
 *         self.endPos              = min(endPos, self.refFile.refs[self.refName].SeqLength-1)
 */
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  __Pyx_GOTREF(__pyx_v_self->haplotypeSequence);
  __Pyx_DECREF(__pyx_v_self->haplotypeSequence);
  __pyx_v_self->haplotypeSequence = ((PyObject*)Py_None);

  /* "chaplotype.pyx":139
 *         self.localGapOpen        = NULL
 *         self.haplotypeSequence   = None
 *         self.startPos            = max(0, startPos)             # <<<<<<<<<<<<<<
 *         self.endPos              = min(endPos, self.refFile.refs[self.refName].SeqLength-1)
 *         self.maxReadLength       = maxReadLength
 */
  __pyx_t_1 = __pyx_v_startPos;
  __pyx_t_2 = 0;
  if (((__pyx_t_1 > __pyx_t_2) != 0)) {
    __pyx_t_3 = __pyx_t_1;
  } else {
    __pyx_t_3 = __pyx_t_2;
  }
  __pyx_v_self->startPos = __pyx_t_3;

  /* "chaplotype.pyx":140
 *         self.haplotypeSequence   = None
 *         self.startPos            = max(0, startPos)
 *         self.endPos              = min(endPos, self.refFile.refs[self.refName].SeqLength-1)             # <<<<<<<<<<<<<<
 *         self.maxReadLength       = maxReadLength
 *         self.endBufferSize       = min(2*maxReadLength, 500) # Cap the buffer size at a reasonable length
 */
  if (unlikely(__pyx_v_self->refFile->refs == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
    __PYX_ERR(0, 140, __pyx_L1_error)
  }
  __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_self->refFile->refs, __pyx_v_self->refName); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_SeqLength); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __pyx_t_4 = __Pyx_PyInt_SubtractObjC(__pyx_t_5, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_t_1 = __pyx_v_endPos;
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_t_7 = PyObject_RichCompare(__pyx_t_4, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  if (__pyx_t_8) {
    __Pyx_INCREF(__pyx_t_4);
    __pyx_t_5 = __pyx_t_4;
  } else {
    __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 140, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_5 = __pyx_t_7;
    __pyx_t_7 = 0;
  }
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 140, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_v_self->endPos = __pyx_t_1;

  /* "chaplotype.pyx":141
 *         self.startPos            = max(0, startPos)
 *         self.endPos              = min(endPos, self.refFile.refs[self.refName].SeqLength-1)
 *         self.maxReadLength       = maxReadLength             # <<<<<<<<<<<<<<
 *         self.endBufferSize       = min(2*maxReadLength, 500) # Cap the buffer size at a reasonable length
 *         self.verbosity           = options.verbosity
 */
  __pyx_v_self->maxReadLength = __pyx_v_maxReadLength;

  /* "chaplotype.pyx":142
 *         self.endPos              = min(endPos, self.refFile.refs[self.refName].SeqLength-1)
 *         self.maxReadLength       = maxReadLength
 *         self.endBufferSize       = min(2*maxReadLength, 500) # Cap the buffer size at a reasonable length             # <<<<<<<<<<<<<<
 *         self.verbosity           = options.verbosity
 *         self.options             = options
 */
  __pyx_t_3 = 0x1F4;
  __pyx_t_2 = (2 * __pyx_v_maxReadLength);
  if (((__pyx_t_3 < __pyx_t_2) != 0)) {
    __pyx_t_9 = __pyx_t_3;
  } else {
    __pyx_t_9 = __pyx_t_2;
  }
  __pyx_v_self->endBufferSize = __pyx_t_9;

  /* "chaplotype.pyx":143
 *         self.maxReadLength       = maxReadLength
 *         self.endBufferSize       = min(2*maxReadLength, 500) # Cap the buffer size at a reasonable length
 *         self.verbosity           = options.verbosity             # <<<<<<<<<<<<<<
 *         self.options             = options
 *         self.lastIndividualIndex = -1
 */
  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_options, __pyx_n_s_verbosity); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 143, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 143, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_v_self->verbosity = __pyx_t_1;

  /* "chaplotype.pyx":144
 *         self.endBufferSize       = min(2*maxReadLength, 500) # Cap the buffer size at a reasonable length
 *         self.verbosity           = options.verbosity
 *         self.options             = options             # <<<<<<<<<<<<<<
 *         self.lastIndividualIndex = -1
 * 
 */
  __Pyx_INCREF(__pyx_v_options);
  __Pyx_GIVEREF(__pyx_v_options);
  __Pyx_GOTREF(__pyx_v_self->options);
  __Pyx_DECREF(__pyx_v_self->options);
  __pyx_v_self->options = __pyx_v_options;

  /* "chaplotype.pyx":145
 *         self.verbosity           = options.verbosity
 *         self.options             = options
 *         self.lastIndividualIndex = -1             # <<<<<<<<<<<<<<
 * 
 *         cdef Variant v
 */
  __pyx_v_self->lastIndividualIndex = -1;

  /* "chaplotype.pyx":149
 *         cdef Variant v
 * 
 *         self.shortReferenceSequence = self.getReferenceSequence()             # <<<<<<<<<<<<<<
 *         self.shortHaplotypeSequence = None
 * 
 */
  __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_f_10chaplotype_9Haplotype_getReferenceSequence(__pyx_v_self, NULL)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_GIVEREF(__pyx_t_5);
  __Pyx_GOTREF(__pyx_v_self->shortReferenceSequence);
  __Pyx_DECREF(__pyx_v_self->shortReferenceSequence);
  __pyx_v_self->shortReferenceSequence = ((PyObject*)__pyx_t_5);
  __pyx_t_5 = 0;

  /* "chaplotype.pyx":150
 * 
 *         self.shortReferenceSequence = self.getReferenceSequence()
 *         self.shortHaplotypeSequence = None             # <<<<<<<<<<<<<<
 * 
 *         if len(variants) > 0:
 */
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  __Pyx_GOTREF(__pyx_v_self->shortHaplotypeSequence);
  __Pyx_DECREF(__pyx_v_self->shortHaplotypeSequence);
  __pyx_v_self->shortHaplotypeSequence = ((PyObject*)Py_None);

  /* "chaplotype.pyx":152
 *         self.shortHaplotypeSequence = None
 * 
 *         if len(variants) > 0:             # <<<<<<<<<<<<<<
 *             self.minVarPos = min([v.minRefPos for v in variants])
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 */
  if (unlikely(__pyx_v_variants == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(0, 152, __pyx_L1_error)
  }
  __pyx_t_10 = PyTuple_GET_SIZE(__pyx_v_variants); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 152, __pyx_L1_error)
  __pyx_t_8 = ((__pyx_t_10 > 0) != 0);
  if (__pyx_t_8) {

    /* "chaplotype.pyx":153
 * 
 *         if len(variants) > 0:
 *             self.minVarPos = min([v.minRefPos for v in variants])             # <<<<<<<<<<<<<<
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 *             if self.minVarPos == self.maxVarPos:
 */
    __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 153, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__pyx_v_variants == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
      __PYX_ERR(0, 153, __pyx_L1_error)
    }
    __pyx_t_4 = __pyx_v_variants; __Pyx_INCREF(__pyx_t_4); __pyx_t_10 = 0;
    for (;;) {
      if (__pyx_t_10 >= 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_10); __Pyx_INCREF(__pyx_t_7); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 153, __pyx_L1_error)
      #else
      __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 153, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      #endif
      if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 153, __pyx_L1_error)
      __Pyx_XDECREF_SET(__pyx_v_v, ((struct __pyx_obj_7variant_Variant *)__pyx_t_7));
      __pyx_t_7 = 0;
      __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_v->minRefPos); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 153, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) __PYX_ERR(0, 153, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    }
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_min, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 153, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 153, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_v_self->minVarPos = __pyx_t_1;

    /* "chaplotype.pyx":154
 *         if len(variants) > 0:
 *             self.minVarPos = min([v.minRefPos for v in variants])
 *             self.maxVarPos = max([v.maxRefPos for v in variants])             # <<<<<<<<<<<<<<
 *             if self.minVarPos == self.maxVarPos:
 *                 self.maxVarPos += 1
 */
    __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 154, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    if (unlikely(__pyx_v_variants == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
      __PYX_ERR(0, 154, __pyx_L1_error)
    }
    __pyx_t_5 = __pyx_v_variants; __Pyx_INCREF(__pyx_t_5); __pyx_t_10 = 0;
    for (;;) {
      if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_10); __Pyx_INCREF(__pyx_t_7); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 154, __pyx_L1_error)
      #else
      __pyx_t_7 = PySequence_ITEM(__pyx_t_5, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 154, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      #endif
      if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 154, __pyx_L1_error)
      __Pyx_XDECREF_SET(__pyx_v_v, ((struct __pyx_obj_7variant_Variant *)__pyx_t_7));
      __pyx_t_7 = 0;
      __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_v->maxRefPos); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 154, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_7))) __PYX_ERR(0, 154, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    }
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_max, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 154, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_1 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 154, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_v_self->maxVarPos = __pyx_t_1;

    /* "chaplotype.pyx":155
 *             self.minVarPos = min([v.minRefPos for v in variants])
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 *             if self.minVarPos == self.maxVarPos:             # <<<<<<<<<<<<<<
 *                 self.maxVarPos += 1
 *             self.shortHaplotypeSequence = self.getMutatedSequence()
 */
    __pyx_t_8 = ((__pyx_v_self->minVarPos == __pyx_v_self->maxVarPos) != 0);
    if (__pyx_t_8) {

      /* "chaplotype.pyx":156
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 *             if self.minVarPos == self.maxVarPos:
 *                 self.maxVarPos += 1             # <<<<<<<<<<<<<<
 *             self.shortHaplotypeSequence = self.getMutatedSequence()
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence , self.shortHaplotypeSequence, 0, variants[0].varSource)
 */
      __pyx_v_self->maxVarPos = (__pyx_v_self->maxVarPos + 1);

      /* "chaplotype.pyx":155
 *             self.minVarPos = min([v.minRefPos for v in variants])
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 *             if self.minVarPos == self.maxVarPos:             # <<<<<<<<<<<<<<
 *                 self.maxVarPos += 1
 *             self.shortHaplotypeSequence = self.getMutatedSequence()
 */
    }

    /* "chaplotype.pyx":157
 *             if self.minVarPos == self.maxVarPos:
 *                 self.maxVarPos += 1
 *             self.shortHaplotypeSequence = self.getMutatedSequence()             # <<<<<<<<<<<<<<
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence , self.shortHaplotypeSequence, 0, variants[0].varSource)
 *         else:
 */
    __pyx_t_5 = __Pyx_PyBytes_FromString(__pyx_f_10chaplotype_9Haplotype_getMutatedSequence(__pyx_v_self)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 157, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_GIVEREF(__pyx_t_5);
    __Pyx_GOTREF(__pyx_v_self->shortHaplotypeSequence);
    __Pyx_DECREF(__pyx_v_self->shortHaplotypeSequence);
    __pyx_v_self->shortHaplotypeSequence = ((PyObject*)__pyx_t_5);
    __pyx_t_5 = 0;

    /* "chaplotype.pyx":158
 *                 self.maxVarPos += 1
 *             self.shortHaplotypeSequence = self.getMutatedSequence()
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence , self.shortHaplotypeSequence, 0, variants[0].varSource)             # <<<<<<<<<<<<<<
 *         else:
 *             self.minVarPos = self.startPos
 */
    __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_startPos); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 158, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(__pyx_v_variants == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
      __PYX_ERR(0, 158, __pyx_L1_error)
    }
    __pyx_t_4 = __Pyx_PyObject_GetAttrStr(PyTuple_GET_ITEM(__pyx_v_variants, 0), __pyx_n_s_varSource); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 158, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 158, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_INCREF(__pyx_v_refName);
    __Pyx_GIVEREF(__pyx_v_refName);
    PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_refName);
    __Pyx_GIVEREF(__pyx_t_5);
    PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_5);
    __Pyx_INCREF(__pyx_v_self->shortReferenceSequence);
    __Pyx_GIVEREF(__pyx_v_self->shortReferenceSequence);
    PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_self->shortReferenceSequence);
    __Pyx_INCREF(__pyx_v_self->shortHaplotypeSequence);
    __Pyx_GIVEREF(__pyx_v_self->shortHaplotypeSequence);
    PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_v_self->shortHaplotypeSequence);
    __Pyx_INCREF(__pyx_int_0);
    __Pyx_GIVEREF(__pyx_int_0);
    PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_0);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_t_4);
    __pyx_t_5 = 0;
    __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_7variant_Variant), __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 158, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_GIVEREF(__pyx_t_4);
    __Pyx_GOTREF(__pyx_v_self->longVar);
    __Pyx_DECREF(((PyObject *)__pyx_v_self->longVar));
    __pyx_v_self->longVar = ((struct __pyx_obj_7variant_Variant *)__pyx_t_4);
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":152
 *         self.shortHaplotypeSequence = None
 * 
 *         if len(variants) > 0:             # <<<<<<<<<<<<<<
 *             self.minVarPos = min([v.minRefPos for v in variants])
 *             self.maxVarPos = max([v.maxRefPos for v in variants])
 */
    goto __pyx_L3;
  }

  /* "chaplotype.pyx":160
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence , self.shortHaplotypeSequence, 0, variants[0].varSource)
 *         else:
 *             self.minVarPos = self.startPos             # <<<<<<<<<<<<<<
 *             self.maxVarPos = self.endPos
 *             self.shortHaplotypeSequence = self.shortReferenceSequence
 */
  /*else*/ {
    __pyx_t_1 = __pyx_v_self->startPos;
    __pyx_v_self->minVarPos = __pyx_t_1;

    /* "chaplotype.pyx":161
 *         else:
 *             self.minVarPos = self.startPos
 *             self.maxVarPos = self.endPos             # <<<<<<<<<<<<<<
 *             self.shortHaplotypeSequence = self.shortReferenceSequence
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence, self.shortReferenceSequence, 0, 1)
 */
    __pyx_t_1 = __pyx_v_self->endPos;
    __pyx_v_self->maxVarPos = __pyx_t_1;

    /* "chaplotype.pyx":162
 *             self.minVarPos = self.startPos
 *             self.maxVarPos = self.endPos
 *             self.shortHaplotypeSequence = self.shortReferenceSequence             # <<<<<<<<<<<<<<
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence, self.shortReferenceSequence, 0, 1)
 * 
 */
    __pyx_t_4 = __pyx_v_self->shortReferenceSequence;
    __Pyx_INCREF(__pyx_t_4);
    __Pyx_GIVEREF(__pyx_t_4);
    __Pyx_GOTREF(__pyx_v_self->shortHaplotypeSequence);
    __Pyx_DECREF(__pyx_v_self->shortHaplotypeSequence);
    __pyx_v_self->shortHaplotypeSequence = ((PyObject*)__pyx_t_4);
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":163
 *             self.maxVarPos = self.endPos
 *             self.shortHaplotypeSequence = self.shortReferenceSequence
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence, self.shortReferenceSequence, 0, 1)             # <<<<<<<<<<<<<<
 * 
 *         self.referenceSequence = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.endPos + self.endBufferSize)
 */
    __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_startPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 163, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 163, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_INCREF(__pyx_v_refName);
    __Pyx_GIVEREF(__pyx_v_refName);
    PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_refName);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_4);
    __Pyx_INCREF(__pyx_v_self->shortReferenceSequence);
    __Pyx_GIVEREF(__pyx_v_self->shortReferenceSequence);
    PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_self->shortReferenceSequence);
    __Pyx_INCREF(__pyx_v_self->shortReferenceSequence);
    __Pyx_GIVEREF(__pyx_v_self->shortReferenceSequence);
    PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_v_self->shortReferenceSequence);
    __Pyx_INCREF(__pyx_int_0);
    __Pyx_GIVEREF(__pyx_int_0);
    PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_0);
    __Pyx_INCREF(__pyx_int_1);
    __Pyx_GIVEREF(__pyx_int_1);
    PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_1);
    __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_7variant_Variant), __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 163, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_GIVEREF(__pyx_t_4);
    __Pyx_GOTREF(__pyx_v_self->longVar);
    __Pyx_DECREF(((PyObject *)__pyx_v_self->longVar));
    __pyx_v_self->longVar = ((struct __pyx_obj_7variant_Variant *)__pyx_t_4);
    __pyx_t_4 = 0;
  }
  __pyx_L3:;

  /* "chaplotype.pyx":165
 *             self.longVar = Variant(refName, startPos, self.shortReferenceSequence, self.shortReferenceSequence, 0, 1)
 * 
 *         self.referenceSequence = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.endPos + self.endBufferSize)             # <<<<<<<<<<<<<<
 * 
 *         if len(self.variants) == 0:
 */
  __pyx_t_4 = __pyx_v_self->refName;
  __Pyx_INCREF(__pyx_t_4);
  __pyx_t_7 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_4), (__pyx_v_self->startPos - __pyx_v_self->endBufferSize), (__pyx_v_self->endPos + __pyx_v_self->endBufferSize)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 165, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __Pyx_GIVEREF(__pyx_t_7);
  __Pyx_GOTREF(__pyx_v_self->referenceSequence);
  __Pyx_DECREF(__pyx_v_self->referenceSequence);
  __pyx_v_self->referenceSequence = ((PyObject*)__pyx_t_7);
  __pyx_t_7 = 0;

  /* "chaplotype.pyx":167
 *         self.referenceSequence = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.endPos + self.endBufferSize)
 * 
 *         if len(self.variants) == 0:             # <<<<<<<<<<<<<<
 *             self.haplotypeSequence = self.referenceSequence
 *         else:
 */
  __pyx_t_7 = __pyx_v_self->variants;
  __Pyx_INCREF(__pyx_t_7);
  if (unlikely(__pyx_t_7 == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(0, 167, __pyx_L1_error)
  }
  __pyx_t_10 = PyTuple_GET_SIZE(__pyx_t_7); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 167, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  __pyx_t_8 = ((__pyx_t_10 == 0) != 0);
  if (__pyx_t_8) {

    /* "chaplotype.pyx":168
 * 
 *         if len(self.variants) == 0:
 *             self.haplotypeSequence = self.referenceSequence             # <<<<<<<<<<<<<<
 *         else:
 *             leftBuffer  = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.startPos)
 */
    __pyx_t_7 = __pyx_v_self->referenceSequence;
    __Pyx_INCREF(__pyx_t_7);
    __Pyx_GIVEREF(__pyx_t_7);
    __Pyx_GOTREF(__pyx_v_self->haplotypeSequence);
    __Pyx_DECREF(__pyx_v_self->haplotypeSequence);
    __pyx_v_self->haplotypeSequence = ((PyObject*)__pyx_t_7);
    __pyx_t_7 = 0;

    /* "chaplotype.pyx":167
 *         self.referenceSequence = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.endPos + self.endBufferSize)
 * 
 *         if len(self.variants) == 0:             # <<<<<<<<<<<<<<
 *             self.haplotypeSequence = self.referenceSequence
 *         else:
 */
    goto __pyx_L9;
  }

  /* "chaplotype.pyx":170
 *             self.haplotypeSequence = self.referenceSequence
 *         else:
 *             leftBuffer  = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.startPos)             # <<<<<<<<<<<<<<
 *             rightBuffer = self.refFile.getSequence(self.refName, self.endPos, self.endPos + self.endBufferSize)
 *             self.haplotypeSequence = leftBuffer + self.getMutatedSequence() + rightBuffer
 */
  /*else*/ {
    __pyx_t_7 = __pyx_v_self->refName;
    __Pyx_INCREF(__pyx_t_7);
    __pyx_t_4 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_7), (__pyx_v_self->startPos - __pyx_v_self->endBufferSize), __pyx_v_self->startPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 170, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __pyx_v_leftBuffer = ((PyObject*)__pyx_t_4);
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":171
 *         else:
 *             leftBuffer  = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.startPos)
 *             rightBuffer = self.refFile.getSequence(self.refName, self.endPos, self.endPos + self.endBufferSize)             # <<<<<<<<<<<<<<
 *             self.haplotypeSequence = leftBuffer + self.getMutatedSequence() + rightBuffer
 * 
 */
    __pyx_t_4 = __pyx_v_self->refName;
    __Pyx_INCREF(__pyx_t_4);
    __pyx_t_7 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_4), __pyx_v_self->endPos, (__pyx_v_self->endPos + __pyx_v_self->endBufferSize)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 171, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_v_rightBuffer = ((PyObject*)__pyx_t_7);
    __pyx_t_7 = 0;

    /* "chaplotype.pyx":172
 *             leftBuffer  = self.refFile.getSequence(self.refName, self.startPos - self.endBufferSize, self.startPos)
 *             rightBuffer = self.refFile.getSequence(self.refName, self.endPos, self.endPos + self.endBufferSize)
 *             self.haplotypeSequence = leftBuffer + self.getMutatedSequence() + rightBuffer             # <<<<<<<<<<<<<<
 * 
 *         self.cHaplotypeSequence = self.haplotypeSequence
 */
    __pyx_t_7 = __Pyx_PyBytes_FromString(__pyx_f_10chaplotype_9Haplotype_getMutatedSequence(__pyx_v_self)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 172, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_4 = PyNumber_Add(__pyx_v_leftBuffer, __pyx_t_7); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 172, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __pyx_t_7 = PyNumber_Add(__pyx_t_4, __pyx_v_rightBuffer); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 172, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __Pyx_GIVEREF(__pyx_t_7);
    __Pyx_GOTREF(__pyx_v_self->haplotypeSequence);
    __Pyx_DECREF(__pyx_v_self->haplotypeSequence);
    __pyx_v_self->haplotypeSequence = ((PyObject*)__pyx_t_7);
    __pyx_t_7 = 0;
  }
  __pyx_L9:;

  /* "chaplotype.pyx":174
 *             self.haplotypeSequence = leftBuffer + self.getMutatedSequence() + rightBuffer
 * 
 *         self.cHaplotypeSequence = self.haplotypeSequence             # <<<<<<<<<<<<<<
 *         self.hapLen             = len(self.cHaplotypeSequence)
 * 
 */
  if (unlikely(__pyx_v_self->haplotypeSequence == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
    __PYX_ERR(0, 174, __pyx_L1_error)
  }
  __pyx_t_11 = __Pyx_PyBytes_AsWritableString(__pyx_v_self->haplotypeSequence); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) __PYX_ERR(0, 174, __pyx_L1_error)
  __pyx_v_self->cHaplotypeSequence = __pyx_t_11;

  /* "chaplotype.pyx":175
 * 
 *         self.cHaplotypeSequence = self.haplotypeSequence
 *         self.hapLen             = len(self.cHaplotypeSequence)             # <<<<<<<<<<<<<<
 * 
 *         #if self.referenceSequence == self.haplotypeSequence and len(self.variants) != 0:
 */
  __pyx_t_12 = strlen(__pyx_v_self->cHaplotypeSequence); 
  __pyx_v_self->hapLen = __pyx_t_12;

  /* "chaplotype.pyx":180
 *         #    logger.error("Haplotype is broken. Var seq and ref seq are the same, and variants are %s" %(list(self.variants)))
 * 
 *         if self.hapLen > hash_size:             # <<<<<<<<<<<<<<
 *             logger.error("Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s" %(self.variants, self.hapLen, self.startPos, self.endPos, maxReadLength))
 *             logger.debug(self.haplotypeSequence)
 */
  __pyx_t_8 = ((__pyx_v_self->hapLen > __pyx_v_6calign_hash_size) != 0);
  if (unlikely(__pyx_t_8)) {

    /* "chaplotype.pyx":181
 * 
 *         if self.hapLen > hash_size:
 *             logger.error("Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s" %(self.variants, self.hapLen, self.startPos, self.endPos, maxReadLength))             # <<<<<<<<<<<<<<
 *             logger.debug(self.haplotypeSequence)
 *             raise StandardError, "Haplotype is too long. Max allowed length is %s" %(hash_size)
 */
    __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_logger); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_error); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->hapLen); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __pyx_t_13 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_13);
    __pyx_t_14 = __Pyx_PyInt_From_int(__pyx_v_maxReadLength); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __pyx_t_15 = PyTuple_New(5); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_15);
    __Pyx_INCREF(__pyx_v_self->variants);
    __Pyx_GIVEREF(__pyx_v_self->variants);
    PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_self->variants);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_15, 1, __pyx_t_4);
    __Pyx_GIVEREF(__pyx_t_6);
    PyTuple_SET_ITEM(__pyx_t_15, 2, __pyx_t_6);
    __Pyx_GIVEREF(__pyx_t_13);
    PyTuple_SET_ITEM(__pyx_t_15, 3, __pyx_t_13);
    __Pyx_GIVEREF(__pyx_t_14);
    PyTuple_SET_ITEM(__pyx_t_15, 4, __pyx_t_14);
    __pyx_t_4 = 0;
    __pyx_t_6 = 0;
    __pyx_t_13 = 0;
    __pyx_t_14 = 0;
    __pyx_t_14 = __Pyx_PyString_Format(__pyx_kp_s_Haplotype_with_vars_s_has_len_s, __pyx_t_15); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 181, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
    __pyx_t_15 = NULL;
    if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_5))) {
      __pyx_t_15 = PyMethod_GET_SELF(__pyx_t_5);
      if (likely(__pyx_t_15)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
        __Pyx_INCREF(__pyx_t_15);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_5, function);
      }
    }
    __pyx_t_7 = (__pyx_t_15) ? __Pyx_PyObject_Call2Args(__pyx_t_5, __pyx_t_15, __pyx_t_14) : __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_14);
    __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
    __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 181, __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;

    /* "chaplotype.pyx":182
 *         if self.hapLen > hash_size:
 *             logger.error("Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s" %(self.variants, self.hapLen, self.startPos, self.endPos, maxReadLength))
 *             logger.debug(self.haplotypeSequence)             # <<<<<<<<<<<<<<
 *             raise StandardError, "Haplotype is too long. Max allowed length is %s" %(hash_size)
 * 
 */
    __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_logger); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 182, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_14 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_debug); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 182, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = NULL;
    if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_14))) {
      __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_14);
      if (likely(__pyx_t_5)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_14);
        __Pyx_INCREF(__pyx_t_5);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_14, function);
      }
    }
    __pyx_t_7 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_14, __pyx_t_5, __pyx_v_self->haplotypeSequence) : __Pyx_PyObject_CallOneArg(__pyx_t_14, __pyx_v_self->haplotypeSequence);
    __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 182, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

    /* "chaplotype.pyx":183
 *             logger.error("Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s" %(self.variants, self.hapLen, self.startPos, self.endPos, maxReadLength))
 *             logger.debug(self.haplotypeSequence)
 *             raise StandardError, "Haplotype is too long. Max allowed length is %s" %(hash_size)             # <<<<<<<<<<<<<<
 * 
 *         self.cHomopolQ            = homopolq
 */
    __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_6calign_hash_size); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 183, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_14 = __Pyx_PyString_Format(__pyx_kp_s_Haplotype_is_too_long_Max_allowe, __pyx_t_7); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 183, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_14, 0, 0);
    __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    __PYX_ERR(0, 183, __pyx_L1_error)

    /* "chaplotype.pyx":180
 *         #    logger.error("Haplotype is broken. Var seq and ref seq are the same, and variants are %s" %(list(self.variants)))
 * 
 *         if self.hapLen > hash_size:             # <<<<<<<<<<<<<<
 *             logger.error("Haplotype with vars %s has len %s. Start is %s. End is %s. maxReadLen = %s" %(self.variants, self.hapLen, self.startPos, self.endPos, maxReadLength))
 *             logger.debug(self.haplotypeSequence)
 */
  }

  /* "chaplotype.pyx":185
 *             raise StandardError, "Haplotype is too long. Max allowed length is %s" %(hash_size)
 * 
 *         self.cHomopolQ            = homopolq             # <<<<<<<<<<<<<<
 *         self.hapSequenceHash      = NULL
 *         self.hapSequenceNextArray = NULL
 */
  if (unlikely(__pyx_v_10chaplotype_homopolq == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
    __PYX_ERR(0, 185, __pyx_L1_error)
  }
  __pyx_t_11 = __Pyx_PyBytes_AsWritableString(__pyx_v_10chaplotype_homopolq); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) __PYX_ERR(0, 185, __pyx_L1_error)
  __pyx_v_self->cHomopolQ = __pyx_t_11;

  /* "chaplotype.pyx":186
 * 
 *         self.cHomopolQ            = homopolq
 *         self.hapSequenceHash      = NULL             # <<<<<<<<<<<<<<
 *         self.hapSequenceNextArray = NULL
 *         self.likelihoodCache      = NULL
 */
  __pyx_v_self->hapSequenceHash = NULL;

  /* "chaplotype.pyx":187
 *         self.cHomopolQ            = homopolq
 *         self.hapSequenceHash      = NULL
 *         self.hapSequenceNextArray = NULL             # <<<<<<<<<<<<<<
 *         self.likelihoodCache      = NULL
 *         self.lenCache             = 0
 */
  __pyx_v_self->hapSequenceNextArray = NULL;

  /* "chaplotype.pyx":188
 *         self.hapSequenceHash      = NULL
 *         self.hapSequenceNextArray = NULL
 *         self.likelihoodCache      = NULL             # <<<<<<<<<<<<<<
 *         self.lenCache             = 0
 *         self.mapCounts            = <int*>malloc( (2*(self.hapLen+maxReadLength))*sizeof(int) )
 */
  __pyx_v_self->likelihoodCache = NULL;

  /* "chaplotype.pyx":189
 *         self.hapSequenceNextArray = NULL
 *         self.likelihoodCache      = NULL
 *         self.lenCache             = 0             # <<<<<<<<<<<<<<
 *         self.mapCounts            = <int*>malloc( (2*(self.hapLen+maxReadLength))*sizeof(int) )
 *         self.mapCountsLen         = 2 * (self.hapLen + maxReadLength)
 */
  __pyx_v_self->lenCache = 0;

  /* "chaplotype.pyx":190
 *         self.likelihoodCache      = NULL
 *         self.lenCache             = 0
 *         self.mapCounts            = <int*>malloc( (2*(self.hapLen+maxReadLength))*sizeof(int) )             # <<<<<<<<<<<<<<
 *         self.mapCountsLen         = 2 * (self.hapLen + maxReadLength)
 * 
 */
  __pyx_v_self->mapCounts = ((int *)malloc(((2 * (__pyx_v_self->hapLen + __pyx_v_maxReadLength)) * (sizeof(int)))));

  /* "chaplotype.pyx":191
 *         self.lenCache             = 0
 *         self.mapCounts            = <int*>malloc( (2*(self.hapLen+maxReadLength))*sizeof(int) )
 *         self.mapCountsLen         = 2 * (self.hapLen + maxReadLength)             # <<<<<<<<<<<<<<
 * 
 *     def __dealloc__(self):
 */
  __pyx_v_self->mapCountsLen = (2 * (__pyx_v_self->hapLen + __pyx_v_maxReadLength));

  /* "chaplotype.pyx":127
 *     this haplotype in the reference.
 *     """
 *     def __init__(self, bytes refName, int startPos, int endPos, tuple variants, FastaFile refFile, int maxReadLength, options):             # <<<<<<<<<<<<<<
 *         """
 *         Constructor. Takes a tuple of variants and a
 */

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_13);
  __Pyx_XDECREF(__pyx_t_14);
  __Pyx_XDECREF(__pyx_t_15);
  __Pyx_AddTraceback("chaplotype.Haplotype.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_XDECREF((PyObject *)__pyx_v_v);
  __Pyx_XDECREF(__pyx_v_leftBuffer);
  __Pyx_XDECREF(__pyx_v_rightBuffer);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":193
 *         self.mapCountsLen         = 2 * (self.hapLen + maxReadLength)
 * 
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Clean up cache.
 */

/* Python wrapper */
static void __pyx_pw_10chaplotype_9Haplotype_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_10chaplotype_9Haplotype_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_10chaplotype_9Haplotype_2__dealloc__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static void __pyx_pf_10chaplotype_9Haplotype_2__dealloc__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "chaplotype.pyx":197
 *         Clean up cache.
 *         """
 *         if self.likelihoodCache != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.likelihoodCache)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->likelihoodCache != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":198
 *         """
 *         if self.likelihoodCache != NULL:
 *             my_free(self.likelihoodCache)             # <<<<<<<<<<<<<<
 * 
 *         if self.hapSequenceHash != NULL:
 */
    __pyx_f_10chaplotype_my_free(__pyx_v_self->likelihoodCache);

    /* "chaplotype.pyx":197
 *         Clean up cache.
 *         """
 *         if self.likelihoodCache != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.likelihoodCache)
 * 
 */
  }

  /* "chaplotype.pyx":200
 *             my_free(self.likelihoodCache)
 * 
 *         if self.hapSequenceHash != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.hapSequenceHash)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->hapSequenceHash != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":201
 * 
 *         if self.hapSequenceHash != NULL:
 *             my_free(self.hapSequenceHash)             # <<<<<<<<<<<<<<
 * 
 *         if self.hapSequenceNextArray != NULL:
 */
    __pyx_f_10chaplotype_my_free(__pyx_v_self->hapSequenceHash);

    /* "chaplotype.pyx":200
 *             my_free(self.likelihoodCache)
 * 
 *         if self.hapSequenceHash != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.hapSequenceHash)
 * 
 */
  }

  /* "chaplotype.pyx":203
 *             my_free(self.hapSequenceHash)
 * 
 *         if self.hapSequenceNextArray != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.hapSequenceNextArray)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->hapSequenceNextArray != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":204
 * 
 *         if self.hapSequenceNextArray != NULL:
 *             my_free(self.hapSequenceNextArray)             # <<<<<<<<<<<<<<
 * 
 *         if self.localGapOpen != NULL:
 */
    __pyx_f_10chaplotype_my_free(__pyx_v_self->hapSequenceNextArray);

    /* "chaplotype.pyx":203
 *             my_free(self.hapSequenceHash)
 * 
 *         if self.hapSequenceNextArray != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.hapSequenceNextArray)
 * 
 */
  }

  /* "chaplotype.pyx":206
 *             my_free(self.hapSequenceNextArray)
 * 
 *         if self.localGapOpen != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.localGapOpen)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->localGapOpen != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":207
 * 
 *         if self.localGapOpen != NULL:
 *             my_free(self.localGapOpen)             # <<<<<<<<<<<<<<
 * 
 *         if self.mapCounts != NULL:
 */
    __pyx_f_10chaplotype_my_free(__pyx_v_self->localGapOpen);

    /* "chaplotype.pyx":206
 *             my_free(self.hapSequenceNextArray)
 * 
 *         if self.localGapOpen != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.localGapOpen)
 * 
 */
  }

  /* "chaplotype.pyx":209
 *             my_free(self.localGapOpen)
 * 
 *         if self.mapCounts != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.mapCounts)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->mapCounts != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":210
 * 
 *         if self.mapCounts != NULL:
 *             my_free(self.mapCounts)             # <<<<<<<<<<<<<<
 * 
 *     def __copy__(self):
 */
    __pyx_f_10chaplotype_my_free(__pyx_v_self->mapCounts);

    /* "chaplotype.pyx":209
 *             my_free(self.localGapOpen)
 * 
 *         if self.mapCounts != NULL:             # <<<<<<<<<<<<<<
 *             my_free(self.mapCounts)
 * 
 */
  }

  /* "chaplotype.pyx":193
 *         self.mapCountsLen         = 2 * (self.hapLen + maxReadLength)
 * 
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Clean up cache.
 */

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

/* "chaplotype.pyx":212
 *             my_free(self.mapCounts)
 * 
 *     def __copy__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Make sure this never gets called for haplotypes.
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_5__copy__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_10chaplotype_9Haplotype_4__copy__[] = "\n        Make sure this never gets called for haplotypes.\n        ";
static PyObject *__pyx_pw_10chaplotype_9Haplotype_5__copy__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__copy__ (wrapper)", 0);
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype_4__copy__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_4__copy__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__copy__", 0);

  /* "chaplotype.pyx":216
 *         Make sure this never gets called for haplotypes.
 *         """
 *         raise StandardError, "Oh no! The bridge is gone!"             # <<<<<<<<<<<<<<
 * 
 *     def __richcmp__(Haplotype self, Haplotype other, int opCode):
 */
  __Pyx_Raise(__pyx_builtin_StandardError, __pyx_kp_s_Oh_no_The_bridge_is_gone, 0, 0);
  __PYX_ERR(0, 216, __pyx_L1_error)

  /* "chaplotype.pyx":212
 *             my_free(self.mapCounts)
 * 
 *     def __copy__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Make sure this never gets called for haplotypes.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_AddTraceback("chaplotype.Haplotype.__copy__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":218
 *         raise StandardError, "Oh no! The bridge is gone!"
 * 
 *     def __richcmp__(Haplotype self, Haplotype other, int opCode):             # <<<<<<<<<<<<<<
 *         """
 *         Comparison function:
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_7__richcmp__(PyObject *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_opCode); /*proto*/
static PyObject *__pyx_pw_10chaplotype_9Haplotype_7__richcmp__(PyObject *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_opCode) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__richcmp__ (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_10chaplotype_Haplotype, 1, "other", 0))) __PYX_ERR(0, 218, __pyx_L1_error)
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype_6__richcmp__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self), ((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_other), ((int)__pyx_v_opCode));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_6__richcmp__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_other, int __pyx_v_opCode) {
  PyObject *__pyx_v_thisSeq = NULL;
  PyObject *__pyx_v_otherSeq = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  __Pyx_RefNannySetupContext("__richcmp__", 0);

  /* "chaplotype.pyx":226
 *         """
 *         # <
 *         if opCode == 0:             # <<<<<<<<<<<<<<
 *             if self.refName < other.refName:
 *                 return True
 */
  switch (__pyx_v_opCode) {
    case 0:

    /* "chaplotype.pyx":227
 *         # <
 *         if opCode == 0:
 *             if self.refName < other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->refName, __pyx_v_other->refName, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 227, __pyx_L1_error)
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 227, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":228
 *         if opCode == 0:
 *             if self.refName < other.refName:
 *                 return True             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":227
 *         # <
 *         if opCode == 0:
 *             if self.refName < other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 */
    }

    /* "chaplotype.pyx":229
 *             if self.refName < other.refName:
 *                 return True
 *             elif self.refName == other.refName and self.startPos < other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 */
    __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 229, __pyx_L1_error)
    __pyx_t_4 = (__pyx_t_3 != 0);
    if (__pyx_t_4) {
    } else {
      __pyx_t_2 = __pyx_t_4;
      goto __pyx_L4_bool_binop_done;
    }
    __pyx_t_4 = ((__pyx_v_self->startPos < __pyx_v_other->startPos) != 0);
    __pyx_t_2 = __pyx_t_4;
    __pyx_L4_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":230
 *                 return True
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return True             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":229
 *             if self.refName < other.refName:
 *                 return True
 *             elif self.refName == other.refName and self.startPos < other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 */
    }

    /* "chaplotype.pyx":231
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    __pyx_t_4 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 231, __pyx_L1_error)
    __pyx_t_3 = (__pyx_t_4 != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L6_bool_binop_done;
    }
    __pyx_t_3 = ((__pyx_v_self->startPos == __pyx_v_other->startPos) != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L6_bool_binop_done;
    }
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->haplotypeSequence, __pyx_v_other->haplotypeSequence, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 231, __pyx_L1_error)
    __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 231, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_2 = __pyx_t_3;
    __pyx_L6_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":232
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 *                 return True             # <<<<<<<<<<<<<<
 *             else:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":231
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    }

    /* "chaplotype.pyx":234
 *                 return True
 *             else:
 *                 return False             # <<<<<<<<<<<<<<
 *         # <=
 *         elif opCode == 1:
 */
    /*else*/ {
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":226
 *         """
 *         # <
 *         if opCode == 0:             # <<<<<<<<<<<<<<
 *             if self.refName < other.refName:
 *                 return True
 */
    break;
    case 1:

    /* "chaplotype.pyx":237
 *         # <=
 *         elif opCode == 1:
 *             if self.refName > other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->refName, __pyx_v_other->refName, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 237, __pyx_L1_error)
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 237, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":238
 *         elif opCode == 1:
 *             if self.refName > other.refName:
 *                 return False             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":237
 *         # <=
 *         elif opCode == 1:
 *             if self.refName > other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 */
    }

    /* "chaplotype.pyx":239
 *             if self.refName > other.refName:
 *                 return False
 *             elif self.refName == other.refName and self.startPos > other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 */
    __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 239, __pyx_L1_error)
    __pyx_t_4 = (__pyx_t_3 != 0);
    if (__pyx_t_4) {
    } else {
      __pyx_t_2 = __pyx_t_4;
      goto __pyx_L10_bool_binop_done;
    }
    __pyx_t_4 = ((__pyx_v_self->startPos > __pyx_v_other->startPos) != 0);
    __pyx_t_2 = __pyx_t_4;
    __pyx_L10_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":240
 *                 return False
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return False             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":239
 *             if self.refName > other.refName:
 *                 return False
 *             elif self.refName == other.refName and self.startPos > other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 */
    }

    /* "chaplotype.pyx":241
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    __pyx_t_4 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 241, __pyx_L1_error)
    __pyx_t_3 = (__pyx_t_4 != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L12_bool_binop_done;
    }
    __pyx_t_3 = ((__pyx_v_self->startPos == __pyx_v_other->startPos) != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L12_bool_binop_done;
    }
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->haplotypeSequence, __pyx_v_other->haplotypeSequence, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 241, __pyx_L1_error)
    __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 241, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_2 = __pyx_t_3;
    __pyx_L12_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":242
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 *                 return False             # <<<<<<<<<<<<<<
 *             else:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":241
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    }

    /* "chaplotype.pyx":244
 *                 return False
 *             else:
 *                 return True             # <<<<<<<<<<<<<<
 *         # >
 *         elif opCode == 4:
 */
    /*else*/ {
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":236
 *                 return False
 *         # <=
 *         elif opCode == 1:             # <<<<<<<<<<<<<<
 *             if self.refName > other.refName:
 *                 return False
 */
    break;
    case 4:

    /* "chaplotype.pyx":247
 *         # >
 *         elif opCode == 4:
 *             if self.refName > other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->refName, __pyx_v_other->refName, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 247, __pyx_L1_error)
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 247, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":248
 *         elif opCode == 4:
 *             if self.refName > other.refName:
 *                 return True             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":247
 *         # >
 *         elif opCode == 4:
 *             if self.refName > other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 */
    }

    /* "chaplotype.pyx":249
 *             if self.refName > other.refName:
 *                 return True
 *             elif self.refName == other.refName and self.startPos > other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 */
    __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 249, __pyx_L1_error)
    __pyx_t_4 = (__pyx_t_3 != 0);
    if (__pyx_t_4) {
    } else {
      __pyx_t_2 = __pyx_t_4;
      goto __pyx_L16_bool_binop_done;
    }
    __pyx_t_4 = ((__pyx_v_self->startPos > __pyx_v_other->startPos) != 0);
    __pyx_t_2 = __pyx_t_4;
    __pyx_L16_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":250
 *                 return True
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return True             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":249
 *             if self.refName > other.refName:
 *                 return True
 *             elif self.refName == other.refName and self.startPos > other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 */
    }

    /* "chaplotype.pyx":251
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    __pyx_t_4 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 251, __pyx_L1_error)
    __pyx_t_3 = (__pyx_t_4 != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L18_bool_binop_done;
    }
    __pyx_t_3 = ((__pyx_v_self->startPos == __pyx_v_other->startPos) != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L18_bool_binop_done;
    }
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->haplotypeSequence, __pyx_v_other->haplotypeSequence, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 251, __pyx_L1_error)
    __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 251, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_2 = __pyx_t_3;
    __pyx_L18_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":252
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:
 *                 return True             # <<<<<<<<<<<<<<
 *             else:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":251
 *             elif self.refName == other.refName and self.startPos > other.startPos:
 *                 return True
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence > other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    }

    /* "chaplotype.pyx":254
 *                 return True
 *             else:
 *                 return False             # <<<<<<<<<<<<<<
 *         # >=
 *         elif opCode == 5:
 */
    /*else*/ {
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":246
 *                 return True
 *         # >
 *         elif opCode == 4:             # <<<<<<<<<<<<<<
 *             if self.refName > other.refName:
 *                 return True
 */
    break;
    case 5:

    /* "chaplotype.pyx":257
 *         # >=
 *         elif opCode == 5:
 *             if self.refName < other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->refName, __pyx_v_other->refName, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 257, __pyx_L1_error)
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 257, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":258
 *         elif opCode == 5:
 *             if self.refName < other.refName:
 *                 return False             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":257
 *         # >=
 *         elif opCode == 5:
 *             if self.refName < other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 */
    }

    /* "chaplotype.pyx":259
 *             if self.refName < other.refName:
 *                 return False
 *             elif self.refName == other.refName and self.startPos < other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 */
    __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 259, __pyx_L1_error)
    __pyx_t_4 = (__pyx_t_3 != 0);
    if (__pyx_t_4) {
    } else {
      __pyx_t_2 = __pyx_t_4;
      goto __pyx_L22_bool_binop_done;
    }
    __pyx_t_4 = ((__pyx_v_self->startPos < __pyx_v_other->startPos) != 0);
    __pyx_t_2 = __pyx_t_4;
    __pyx_L22_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":260
 *                 return False
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return False             # <<<<<<<<<<<<<<
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":259
 *             if self.refName < other.refName:
 *                 return False
 *             elif self.refName == other.refName and self.startPos < other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 */
    }

    /* "chaplotype.pyx":261
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    __pyx_t_4 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 261, __pyx_L1_error)
    __pyx_t_3 = (__pyx_t_4 != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L24_bool_binop_done;
    }
    __pyx_t_3 = ((__pyx_v_self->startPos == __pyx_v_other->startPos) != 0);
    if (__pyx_t_3) {
    } else {
      __pyx_t_2 = __pyx_t_3;
      goto __pyx_L24_bool_binop_done;
    }
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_self->haplotypeSequence, __pyx_v_other->haplotypeSequence, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 261, __pyx_L1_error)
    __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 261, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_2 = __pyx_t_3;
    __pyx_L24_bool_binop_done:;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":262
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:
 *                 return False             # <<<<<<<<<<<<<<
 *             else:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":261
 *             elif self.refName == other.refName and self.startPos < other.startPos:
 *                 return False
 *             elif self.refName == other.refName and self.startPos == other.startPos and self.haplotypeSequence < other.haplotypeSequence:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    }

    /* "chaplotype.pyx":264
 *                 return False
 *             else:
 *                 return True             # <<<<<<<<<<<<<<
 *         # ==
 *         if opCode == 2:
 */
    /*else*/ {
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":256
 *                 return False
 *         # >=
 *         elif opCode == 5:             # <<<<<<<<<<<<<<
 *             if self.refName < other.refName:
 *                 return False
 */
    break;
    default: break;
  }

  /* "chaplotype.pyx":266
 *                 return True
 *         # ==
 *         if opCode == 2:             # <<<<<<<<<<<<<<
 *             if self.refName != other.refName:
 *                 return False
 */
  switch (__pyx_v_opCode) {
    case 2:

    /* "chaplotype.pyx":267
 *         # ==
 *         if opCode == 2:
 *             if self.refName != other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.startPos != other.startPos:
 */
    __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 267, __pyx_L1_error)
    __pyx_t_3 = (__pyx_t_2 != 0);
    if (__pyx_t_3) {

      /* "chaplotype.pyx":268
 *         if opCode == 2:
 *             if self.refName != other.refName:
 *                 return False             # <<<<<<<<<<<<<<
 *             elif self.startPos != other.startPos:
 *                 return False
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":267
 *         # ==
 *         if opCode == 2:
 *             if self.refName != other.refName:             # <<<<<<<<<<<<<<
 *                 return False
 *             elif self.startPos != other.startPos:
 */
    }

    /* "chaplotype.pyx":269
 *             if self.refName != other.refName:
 *                 return False
 *             elif self.startPos != other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    __pyx_t_3 = ((__pyx_v_self->startPos != __pyx_v_other->startPos) != 0);
    if (__pyx_t_3) {

      /* "chaplotype.pyx":270
 *                 return False
 *             elif self.startPos != other.startPos:
 *                 return False             # <<<<<<<<<<<<<<
 *             else:
 *                 thisSeq  = self.haplotypeSequence
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_False);
      __pyx_r = Py_False;
      goto __pyx_L0;

      /* "chaplotype.pyx":269
 *             if self.refName != other.refName:
 *                 return False
 *             elif self.startPos != other.startPos:             # <<<<<<<<<<<<<<
 *                 return False
 *             else:
 */
    }

    /* "chaplotype.pyx":272
 *                 return False
 *             else:
 *                 thisSeq  = self.haplotypeSequence             # <<<<<<<<<<<<<<
 *                 otherSeq = other.haplotypeSequence
 *                 return thisSeq == otherSeq
 */
    /*else*/ {
      __pyx_t_1 = __pyx_v_self->haplotypeSequence;
      __Pyx_INCREF(__pyx_t_1);
      __pyx_v_thisSeq = ((PyObject*)__pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":273
 *             else:
 *                 thisSeq  = self.haplotypeSequence
 *                 otherSeq = other.haplotypeSequence             # <<<<<<<<<<<<<<
 *                 return thisSeq == otherSeq
 * 
 */
      __pyx_t_1 = __pyx_v_other->haplotypeSequence;
      __Pyx_INCREF(__pyx_t_1);
      __pyx_v_otherSeq = ((PyObject*)__pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":274
 *                 thisSeq  = self.haplotypeSequence
 *                 otherSeq = other.haplotypeSequence
 *                 return thisSeq == otherSeq             # <<<<<<<<<<<<<<
 * 
 *         # !=
 */
      __Pyx_XDECREF(__pyx_r);
      __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_thisSeq, __pyx_v_otherSeq, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 274, __pyx_L1_error)
      __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 274, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_r = __pyx_t_1;
      __pyx_t_1 = 0;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":266
 *                 return True
 *         # ==
 *         if opCode == 2:             # <<<<<<<<<<<<<<
 *             if self.refName != other.refName:
 *                 return False
 */
    break;
    case 3:

    /* "chaplotype.pyx":278
 *         # !=
 *         elif opCode == 3:
 *             if self.refName != other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.startPos != other.startPos:
 */
    __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->refName, __pyx_v_other->refName, Py_NE)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 278, __pyx_L1_error)
    __pyx_t_2 = (__pyx_t_3 != 0);
    if (__pyx_t_2) {

      /* "chaplotype.pyx":279
 *         elif opCode == 3:
 *             if self.refName != other.refName:
 *                 return True             # <<<<<<<<<<<<<<
 *             elif self.startPos != other.startPos:
 *                 return True
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":278
 *         # !=
 *         elif opCode == 3:
 *             if self.refName != other.refName:             # <<<<<<<<<<<<<<
 *                 return True
 *             elif self.startPos != other.startPos:
 */
    }

    /* "chaplotype.pyx":280
 *             if self.refName != other.refName:
 *                 return True
 *             elif self.startPos != other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    __pyx_t_2 = ((__pyx_v_self->startPos != __pyx_v_other->startPos) != 0);
    if (__pyx_t_2) {

      /* "chaplotype.pyx":281
 *                 return True
 *             elif self.startPos != other.startPos:
 *                 return True             # <<<<<<<<<<<<<<
 *             else:
 *                 thisSeq = self.haplotypeSequence
 */
      __Pyx_XDECREF(__pyx_r);
      __Pyx_INCREF(Py_True);
      __pyx_r = Py_True;
      goto __pyx_L0;

      /* "chaplotype.pyx":280
 *             if self.refName != other.refName:
 *                 return True
 *             elif self.startPos != other.startPos:             # <<<<<<<<<<<<<<
 *                 return True
 *             else:
 */
    }

    /* "chaplotype.pyx":283
 *                 return True
 *             else:
 *                 thisSeq = self.haplotypeSequence             # <<<<<<<<<<<<<<
 *                 otherSeq = other.haplotypeSequence
 *                 return thisSeq != otherSeq
 */
    /*else*/ {
      __pyx_t_1 = __pyx_v_self->haplotypeSequence;
      __Pyx_INCREF(__pyx_t_1);
      __pyx_v_thisSeq = ((PyObject*)__pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":284
 *             else:
 *                 thisSeq = self.haplotypeSequence
 *                 otherSeq = other.haplotypeSequence             # <<<<<<<<<<<<<<
 *                 return thisSeq != otherSeq
 *         else:
 */
      __pyx_t_1 = __pyx_v_other->haplotypeSequence;
      __Pyx_INCREF(__pyx_t_1);
      __pyx_v_otherSeq = ((PyObject*)__pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":285
 *                 thisSeq = self.haplotypeSequence
 *                 otherSeq = other.haplotypeSequence
 *                 return thisSeq != otherSeq             # <<<<<<<<<<<<<<
 *         else:
 *             raise StandardError, "Op code %s not implemented in haplotype__richcmp__()" %(opCode)
 */
      __Pyx_XDECREF(__pyx_r);
      __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_thisSeq, __pyx_v_otherSeq, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 285, __pyx_L1_error)
      __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 285, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_r = __pyx_t_1;
      __pyx_t_1 = 0;
      goto __pyx_L0;
    }

    /* "chaplotype.pyx":277
 * 
 *         # !=
 *         elif opCode == 3:             # <<<<<<<<<<<<<<
 *             if self.refName != other.refName:
 *                 return True
 */
    break;
    default:

    /* "chaplotype.pyx":287
 *                 return thisSeq != otherSeq
 *         else:
 *             raise StandardError, "Op code %s not implemented in haplotype__richcmp__()" %(opCode)             # <<<<<<<<<<<<<<
 * 
 *     def __hash__(self):
 */
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_opCode); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 287, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_Op_code_s_not_implemented_in_hap, __pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 287, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_5, 0, 0);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __PYX_ERR(0, 287, __pyx_L1_error)
    break;
  }

  /* "chaplotype.pyx":218
 *         raise StandardError, "Oh no! The bridge is gone!"
 * 
 *     def __richcmp__(Haplotype self, Haplotype other, int opCode):             # <<<<<<<<<<<<<<
 *         """
 *         Comparison function:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("chaplotype.Haplotype.__richcmp__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_thisSeq);
  __Pyx_XDECREF(__pyx_v_otherSeq);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":289
 *             raise StandardError, "Op code %s not implemented in haplotype__richcmp__()" %(opCode)
 * 
 *     def __hash__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Implementing this function allows haplotypes to be hashed, and so stored in
 */

/* Python wrapper */
static Py_hash_t __pyx_pw_10chaplotype_9Haplotype_9__hash__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_10chaplotype_9Haplotype_8__hash__[] = "\n        Implementing this function allows haplotypes to be hashed, and so stored in\n        a set or dictionary. The supporting reads are not included in the hashing, as\n        we want two haplotypes to give the same hash id if they have the same positions\n        and sequences.\n        ";
#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_10chaplotype_9Haplotype_8__hash__;
#endif
static Py_hash_t __pyx_pw_10chaplotype_9Haplotype_9__hash__(PyObject *__pyx_v_self) {
  Py_hash_t __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype_8__hash__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static Py_hash_t __pyx_pf_10chaplotype_9Haplotype_8__hash__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  Py_hash_t __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  Py_hash_t __pyx_t_5;
  __Pyx_RefNannySetupContext("__hash__", 0);

  /* "chaplotype.pyx":296
 *         and sequences.
 *         """
 *         if self.hash == -1:             # <<<<<<<<<<<<<<
 *             self.hash = hash((self.refName, self.startPos, self.endPos, self.haplotypeSequence))
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->hash == -1L) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":297
 *         """
 *         if self.hash == -1:
 *             self.hash = hash((self.refName, self.startPos, self.endPos, self.haplotypeSequence))             # <<<<<<<<<<<<<<
 * 
 *         return self.hash
 */
    __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 297, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 297, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 297, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_INCREF(__pyx_v_self->refName);
    __Pyx_GIVEREF(__pyx_v_self->refName);
    PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_self->refName);
    __Pyx_GIVEREF(__pyx_t_2);
    PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_2);
    __Pyx_GIVEREF(__pyx_t_3);
    PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_3);
    __Pyx_INCREF(__pyx_v_self->haplotypeSequence);
    __Pyx_GIVEREF(__pyx_v_self->haplotypeSequence);
    PyTuple_SET_ITEM(__pyx_t_4, 3, __pyx_v_self->haplotypeSequence);
    __pyx_t_2 = 0;
    __pyx_t_3 = 0;
    __pyx_t_5 = PyObject_Hash(__pyx_t_4); if (unlikely(__pyx_t_5 == ((Py_hash_t)-1))) __PYX_ERR(0, 297, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_v_self->hash = __pyx_t_5;

    /* "chaplotype.pyx":296
 *         and sequences.
 *         """
 *         if self.hash == -1:             # <<<<<<<<<<<<<<
 *             self.hash = hash((self.refName, self.startPos, self.endPos, self.haplotypeSequence))
 * 
 */
  }

  /* "chaplotype.pyx":299
 *             self.hash = hash((self.refName, self.startPos, self.endPos, self.haplotypeSequence))
 * 
 *         return self.hash             # <<<<<<<<<<<<<<
 * 
 *     cdef char* getShortHaplotypeSequence(self):
 */
  __pyx_r = __pyx_v_self->hash;
  goto __pyx_L0;

  /* "chaplotype.pyx":289
 *             raise StandardError, "Op code %s not implemented in haplotype__richcmp__()" %(opCode)
 * 
 *     def __hash__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Implementing this function allows haplotypes to be hashed, and so stored in
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_AddTraceback("chaplotype.Haplotype.__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;
}

/* "chaplotype.pyx":301
 *         return self.hash
 * 
 *     cdef char* getShortHaplotypeSequence(self):             # <<<<<<<<<<<<<<
 *         if self.shortHaplotypeSequence == None:
 *             return self.getMutatedSequence()
 */

static char *__pyx_f_10chaplotype_9Haplotype_getShortHaplotypeSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  char *__pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  char *__pyx_t_2;
  __Pyx_RefNannySetupContext("getShortHaplotypeSequence", 0);

  /* "chaplotype.pyx":302
 * 
 *     cdef char* getShortHaplotypeSequence(self):
 *         if self.shortHaplotypeSequence == None:             # <<<<<<<<<<<<<<
 *             return self.getMutatedSequence()
 *         return self.shortHaplotypeSequence
 */
  __pyx_t_1 = (__Pyx_PyBytes_Equals(__pyx_v_self->shortHaplotypeSequence, Py_None, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 302, __pyx_L1_error)
  if (__pyx_t_1) {

    /* "chaplotype.pyx":303
 *     cdef char* getShortHaplotypeSequence(self):
 *         if self.shortHaplotypeSequence == None:
 *             return self.getMutatedSequence()             # <<<<<<<<<<<<<<
 *         return self.shortHaplotypeSequence
 * 
 */
    __pyx_r = __pyx_f_10chaplotype_9Haplotype_getMutatedSequence(__pyx_v_self);
    goto __pyx_L0;

    /* "chaplotype.pyx":302
 * 
 *     cdef char* getShortHaplotypeSequence(self):
 *         if self.shortHaplotypeSequence == None:             # <<<<<<<<<<<<<<
 *             return self.getMutatedSequence()
 *         return self.shortHaplotypeSequence
 */
  }

  /* "chaplotype.pyx":304
 *         if self.shortHaplotypeSequence == None:
 *             return self.getMutatedSequence()
 *         return self.shortHaplotypeSequence             # <<<<<<<<<<<<<<
 * 
 *     cdef double* alignReads(self, int individualIndex, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadsStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenReadsStart, cAlignedRead** brokenReadsEnd, int useMapQualCap):
 */
  if (unlikely(__pyx_v_self->shortHaplotypeSequence == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
    __PYX_ERR(0, 304, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyBytes_AsWritableString(__pyx_v_self->shortHaplotypeSequence); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) __PYX_ERR(0, 304, __pyx_L1_error)
  __pyx_r = __pyx_t_2;
  goto __pyx_L0;

  /* "chaplotype.pyx":301
 *         return self.hash
 * 
 *     cdef char* getShortHaplotypeSequence(self):             # <<<<<<<<<<<<<<
 *         if self.shortHaplotypeSequence == None:
 *             return self.getMutatedSequence()
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("chaplotype.Haplotype.getShortHaplotypeSequence", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":306
 *         return self.shortHaplotypeSequence
 * 
 *     cdef double* alignReads(self, int individualIndex, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadsStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenReadsStart, cAlignedRead** brokenReadsEnd, int useMapQualCap):             # <<<<<<<<<<<<<<
 *         """
 *         """
 */

static double *__pyx_f_10chaplotype_9Haplotype_alignReads(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, int __pyx_v_individualIndex, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_start, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_end, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_badReadsStart, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_badReadsEnd, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_brokenReadsStart, __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_brokenReadsEnd, int __pyx_v_useMapQualCap) {
  int __pyx_v_readIndex;
  double __pyx_v_score;
  int __pyx_v_nReads;
  int __pyx_v_nBadReads;
  int __pyx_v_nBrokenReads;
  int __pyx_v_totalReads;
  int __pyx_v_readOverlap;
  CYTHON_UNUSED int __pyx_v_readLen;
  double *__pyx_v_temp;
  double *__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;
  __Pyx_RefNannySetupContext("alignReads", 0);

  /* "chaplotype.pyx":309
 *         """
 *         """
 *         cdef int readIndex = 0             # <<<<<<<<<<<<<<
 *         cdef double score = 0.0
 *         cdef int nReads = end - start
 */
  __pyx_v_readIndex = 0;

  /* "chaplotype.pyx":310
 *         """
 *         cdef int readIndex = 0
 *         cdef double score = 0.0             # <<<<<<<<<<<<<<
 *         cdef int nReads = end - start
 *         cdef int nBadReads = badReadsEnd - badReadsStart
 */
  __pyx_v_score = 0.0;

  /* "chaplotype.pyx":311
 *         cdef int readIndex = 0
 *         cdef double score = 0.0
 *         cdef int nReads = end - start             # <<<<<<<<<<<<<<
 *         cdef int nBadReads = badReadsEnd - badReadsStart
 *         cdef int nBrokenReads = brokenReadsEnd - brokenReadsStart
 */
  __pyx_v_nReads = (__pyx_v_end - __pyx_v_start);

  /* "chaplotype.pyx":312
 *         cdef double score = 0.0
 *         cdef int nReads = end - start
 *         cdef int nBadReads = badReadsEnd - badReadsStart             # <<<<<<<<<<<<<<
 *         cdef int nBrokenReads = brokenReadsEnd - brokenReadsStart
 *         cdef int totalReads = nReads + nBadReads + nBrokenReads
 */
  __pyx_v_nBadReads = (__pyx_v_badReadsEnd - __pyx_v_badReadsStart);

  /* "chaplotype.pyx":313
 *         cdef int nReads = end - start
 *         cdef int nBadReads = badReadsEnd - badReadsStart
 *         cdef int nBrokenReads = brokenReadsEnd - brokenReadsStart             # <<<<<<<<<<<<<<
 *         cdef int totalReads = nReads + nBadReads + nBrokenReads
 *         cdef int readOverlap = 0
 */
  __pyx_v_nBrokenReads = (__pyx_v_brokenReadsEnd - __pyx_v_brokenReadsStart);

  /* "chaplotype.pyx":314
 *         cdef int nBadReads = badReadsEnd - badReadsStart
 *         cdef int nBrokenReads = brokenReadsEnd - brokenReadsStart
 *         cdef int totalReads = nReads + nBadReads + nBrokenReads             # <<<<<<<<<<<<<<
 *         cdef int readOverlap = 0
 *         cdef int readLen = 0
 */
  __pyx_v_totalReads = ((__pyx_v_nReads + __pyx_v_nBadReads) + __pyx_v_nBrokenReads);

  /* "chaplotype.pyx":315
 *         cdef int nBrokenReads = brokenReadsEnd - brokenReadsStart
 *         cdef int totalReads = nReads + nBadReads + nBrokenReads
 *         cdef int readOverlap = 0             # <<<<<<<<<<<<<<
 *         cdef int readLen = 0
 *         cdef double* temp = NULL
 */
  __pyx_v_readOverlap = 0;

  /* "chaplotype.pyx":316
 *         cdef int totalReads = nReads + nBadReads + nBrokenReads
 *         cdef int readOverlap = 0
 *         cdef int readLen = 0             # <<<<<<<<<<<<<<
 *         cdef double* temp = NULL
 * 
 */
  __pyx_v_readLen = 0;

  /* "chaplotype.pyx":317
 *         cdef int readOverlap = 0
 *         cdef int readLen = 0
 *         cdef double* temp = NULL             # <<<<<<<<<<<<<<
 * 
 *         # Either first time, or new individual
 */
  __pyx_v_temp = NULL;

  /* "chaplotype.pyx":320
 * 
 *         # Either first time, or new individual
 *         if individualIndex != self.lastIndividualIndex:             # <<<<<<<<<<<<<<
 *             if self.likelihoodCache == NULL:
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))
 */
  __pyx_t_1 = ((__pyx_v_individualIndex != __pyx_v_self->lastIndividualIndex) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":321
 *         # Either first time, or new individual
 *         if individualIndex != self.lastIndividualIndex:
 *             if self.likelihoodCache == NULL:             # <<<<<<<<<<<<<<
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))
 *                 self.lenCache = totalReads
 */
    __pyx_t_1 = ((__pyx_v_self->likelihoodCache == NULL) != 0);
    if (__pyx_t_1) {

      /* "chaplotype.pyx":322
 *         if individualIndex != self.lastIndividualIndex:
 *             if self.likelihoodCache == NULL:
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))             # <<<<<<<<<<<<<<
 *                 self.lenCache = totalReads
 * 
 */
      __pyx_v_self->likelihoodCache = ((double *)__pyx_f_10chaplotype_my_malloc(((__pyx_v_totalReads + 1) * (sizeof(double)))));

      /* "chaplotype.pyx":323
 *             if self.likelihoodCache == NULL:
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))
 *                 self.lenCache = totalReads             # <<<<<<<<<<<<<<
 * 
 *                 if self.likelihoodCache == NULL:
 */
      __pyx_v_self->lenCache = __pyx_v_totalReads;

      /* "chaplotype.pyx":325
 *                 self.lenCache = totalReads
 * 
 *                 if self.likelihoodCache == NULL:             # <<<<<<<<<<<<<<
 *                     logger.error("Could not allocate haplotype cache")
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"
 */
      __pyx_t_1 = ((__pyx_v_self->likelihoodCache == NULL) != 0);
      if (unlikely(__pyx_t_1)) {

        /* "chaplotype.pyx":326
 * 
 *                 if self.likelihoodCache == NULL:
 *                     logger.error("Could not allocate haplotype cache")             # <<<<<<<<<<<<<<
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"
 *             else:
 */
        __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_logger); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 326, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_error); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 326, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __pyx_t_3 = NULL;
        if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) {
          __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4);
          if (likely(__pyx_t_3)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
            __Pyx_INCREF(__pyx_t_3);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_4, function);
          }
        }
        __pyx_t_2 = (__pyx_t_3) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_3, __pyx_kp_s_Could_not_allocate_haplotype_cac) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_kp_s_Could_not_allocate_haplotype_cac);
        __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
        if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 326, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

        /* "chaplotype.pyx":327
 *                 if self.likelihoodCache == NULL:
 *                     logger.error("Could not allocate haplotype cache")
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"             # <<<<<<<<<<<<<<
 *             else:
 *                 if totalReads >= self.lenCache:
 */
        __Pyx_Raise(__pyx_builtin_StandardError, __pyx_kp_s_Out_of_memory_in_cHaplotype_alig, 0, 0);
        __PYX_ERR(0, 327, __pyx_L1_error)

        /* "chaplotype.pyx":325
 *                 self.lenCache = totalReads
 * 
 *                 if self.likelihoodCache == NULL:             # <<<<<<<<<<<<<<
 *                     logger.error("Could not allocate haplotype cache")
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"
 */
      }

      /* "chaplotype.pyx":321
 *         # Either first time, or new individual
 *         if individualIndex != self.lastIndividualIndex:
 *             if self.likelihoodCache == NULL:             # <<<<<<<<<<<<<<
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))
 *                 self.lenCache = totalReads
 */
      goto __pyx_L4;
    }

    /* "chaplotype.pyx":329
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"
 *             else:
 *                 if totalReads >= self.lenCache:             # <<<<<<<<<<<<<<
 *                     temp = <double*>realloc(self.likelihoodCache, 2*totalReads*sizeof(double))
 * 
 */
    /*else*/ {
      __pyx_t_1 = ((__pyx_v_totalReads >= __pyx_v_self->lenCache) != 0);
      if (__pyx_t_1) {

        /* "chaplotype.pyx":330
 *             else:
 *                 if totalReads >= self.lenCache:
 *                     temp = <double*>realloc(self.likelihoodCache, 2*totalReads*sizeof(double))             # <<<<<<<<<<<<<<
 * 
 *                     if temp == NULL:
 */
        __pyx_v_temp = ((double *)realloc(__pyx_v_self->likelihoodCache, ((2 * __pyx_v_totalReads) * (sizeof(double)))));

        /* "chaplotype.pyx":332
 *                     temp = <double*>realloc(self.likelihoodCache, 2*totalReads*sizeof(double))
 * 
 *                     if temp == NULL:             # <<<<<<<<<<<<<<
 *                         logger.error("Could not reallocate haplotype cache")
 *                         raise StandardError, "Out of memory in cHaplotype.alignReads"
 */
        __pyx_t_1 = ((__pyx_v_temp == NULL) != 0);
        if (unlikely(__pyx_t_1)) {

          /* "chaplotype.pyx":333
 * 
 *                     if temp == NULL:
 *                         logger.error("Could not reallocate haplotype cache")             # <<<<<<<<<<<<<<
 *                         raise StandardError, "Out of memory in cHaplotype.alignReads"
 * 
 */
          __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_logger); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 333, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 333, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_3);
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
          __pyx_t_4 = NULL;
          if (CYTHON_UNPACK_METHODS && unlikely(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_Call2Args(__pyx_t_3, __pyx_t_4, __pyx_kp_s_Could_not_reallocate_haplotype_c) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_kp_s_Could_not_reallocate_haplotype_c);
          __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
          if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 333, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

          /* "chaplotype.pyx":334
 *                     if temp == NULL:
 *                         logger.error("Could not reallocate haplotype cache")
 *                         raise StandardError, "Out of memory in cHaplotype.alignReads"             # <<<<<<<<<<<<<<
 * 
 *                     self.likelihoodCache = temp
 */
          __Pyx_Raise(__pyx_builtin_StandardError, __pyx_kp_s_Out_of_memory_in_cHaplotype_alig, 0, 0);
          __PYX_ERR(0, 334, __pyx_L1_error)

          /* "chaplotype.pyx":332
 *                     temp = <double*>realloc(self.likelihoodCache, 2*totalReads*sizeof(double))
 * 
 *                     if temp == NULL:             # <<<<<<<<<<<<<<
 *                         logger.error("Could not reallocate haplotype cache")
 *                         raise StandardError, "Out of memory in cHaplotype.alignReads"
 */
        }

        /* "chaplotype.pyx":336
 *                         raise StandardError, "Out of memory in cHaplotype.alignReads"
 * 
 *                     self.likelihoodCache = temp             # <<<<<<<<<<<<<<
 *                     self.lenCache = 2*totalReads
 * 
 */
        __pyx_v_self->likelihoodCache = __pyx_v_temp;

        /* "chaplotype.pyx":337
 * 
 *                     self.likelihoodCache = temp
 *                     self.lenCache = 2*totalReads             # <<<<<<<<<<<<<<
 * 
 *             self.lastIndividualIndex = individualIndex
 */
        __pyx_v_self->lenCache = (2 * __pyx_v_totalReads);

        /* "chaplotype.pyx":329
 *                     raise StandardError, "Out of memory in cHaplotype.alignReads"
 *             else:
 *                 if totalReads >= self.lenCache:             # <<<<<<<<<<<<<<
 *                     temp = <double*>realloc(self.likelihoodCache, 2*totalReads*sizeof(double))
 * 
 */
      }
    }
    __pyx_L4:;

    /* "chaplotype.pyx":339
 *                     self.lenCache = 2*totalReads
 * 
 *             self.lastIndividualIndex = individualIndex             # <<<<<<<<<<<<<<
 * 
 *             while start != end:
 */
    __pyx_v_self->lastIndividualIndex = __pyx_v_individualIndex;

    /* "chaplotype.pyx":341
 *             self.lastIndividualIndex = individualIndex
 * 
 *             while start != end:             # <<<<<<<<<<<<<<
 * 
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, start[0])
 */
    while (1) {
      __pyx_t_1 = ((__pyx_v_start != __pyx_v_end) != 0);
      if (!__pyx_t_1) break;

      /* "chaplotype.pyx":343
 *             while start != end:
 * 
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, start[0])             # <<<<<<<<<<<<<<
 * 
 *                 if Read_IsQCFail(start[0]) or readOverlap < hash_nucs:
 */
      __pyx_v_readOverlap = __pyx_f_10chaplotype_computeOverlapOfReadAndHaplotype(__pyx_v_self->startPos, __pyx_v_self->endPos, (__pyx_v_start[0]));

      /* "chaplotype.pyx":345
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, start[0])
 * 
 *                 if Read_IsQCFail(start[0]) or readOverlap < hash_nucs:             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 */
      __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsQCFail((__pyx_v_start[0])) != 0);
      if (!__pyx_t_5) {
      } else {
        __pyx_t_1 = __pyx_t_5;
        goto __pyx_L11_bool_binop_done;
      }
      __pyx_t_5 = ((__pyx_v_readOverlap < __pyx_v_6calign_hash_nucs) != 0);
      __pyx_t_1 = __pyx_t_5;
      __pyx_L11_bool_binop_done:;
      if (__pyx_t_1) {

        /* "chaplotype.pyx":346
 * 
 *                 if Read_IsQCFail(start[0]) or readOverlap < hash_nucs:
 *                     self.likelihoodCache[readIndex] = 0             # <<<<<<<<<<<<<<
 *                 else:
 *                     score = alignReadToHaplotype(start[0], self, useMapQualCap, self.options.calculateFlankScore)
 */
        (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = 0.0;

        /* "chaplotype.pyx":345
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, start[0])
 * 
 *                 if Read_IsQCFail(start[0]) or readOverlap < hash_nucs:             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 */
        goto __pyx_L10;
      }

      /* "chaplotype.pyx":348
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 *                     score = alignReadToHaplotype(start[0], self, useMapQualCap, self.options.calculateFlankScore)             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = score
 * 
 */
      /*else*/ {
        __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->options, __pyx_n_s_calculateFlankScore); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 348, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 348, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __pyx_v_score = __pyx_f_10chaplotype_alignReadToHaplotype((__pyx_v_start[0]), __pyx_v_self, __pyx_v_useMapQualCap, __pyx_t_6);

        /* "chaplotype.pyx":349
 *                 else:
 *                     score = alignReadToHaplotype(start[0], self, useMapQualCap, self.options.calculateFlankScore)
 *                     self.likelihoodCache[readIndex] = score             # <<<<<<<<<<<<<<
 * 
 *                 start += 1
 */
        (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = __pyx_v_score;
      }
      __pyx_L10:;

      /* "chaplotype.pyx":351
 *                     self.likelihoodCache[readIndex] = score
 * 
 *                 start += 1             # <<<<<<<<<<<<<<
 *                 readIndex += 1
 * 
 */
      __pyx_v_start = (__pyx_v_start + 1);

      /* "chaplotype.pyx":352
 * 
 *                 start += 1
 *                 readIndex += 1             # <<<<<<<<<<<<<<
 * 
 *             while badReadsStart != badReadsEnd:
 */
      __pyx_v_readIndex = (__pyx_v_readIndex + 1);
    }

    /* "chaplotype.pyx":354
 *                 readIndex += 1
 * 
 *             while badReadsStart != badReadsEnd:             # <<<<<<<<<<<<<<
 * 
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, badReadsStart[0])
 */
    while (1) {
      __pyx_t_1 = ((__pyx_v_badReadsStart != __pyx_v_badReadsEnd) != 0);
      if (!__pyx_t_1) break;

      /* "chaplotype.pyx":356
 *             while badReadsStart != badReadsEnd:
 * 
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, badReadsStart[0])             # <<<<<<<<<<<<<<
 * 
 *                 if Read_IsQCFail(badReadsStart[0]) or readOverlap < hash_nucs:
 */
      __pyx_v_readOverlap = __pyx_f_10chaplotype_computeOverlapOfReadAndHaplotype(__pyx_v_self->startPos, __pyx_v_self->endPos, (__pyx_v_badReadsStart[0]));

      /* "chaplotype.pyx":358
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, badReadsStart[0])
 * 
 *                 if Read_IsQCFail(badReadsStart[0]) or readOverlap < hash_nucs:             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 */
      __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsQCFail((__pyx_v_badReadsStart[0])) != 0);
      if (!__pyx_t_5) {
      } else {
        __pyx_t_1 = __pyx_t_5;
        goto __pyx_L16_bool_binop_done;
      }
      __pyx_t_5 = ((__pyx_v_readOverlap < __pyx_v_6calign_hash_nucs) != 0);
      __pyx_t_1 = __pyx_t_5;
      __pyx_L16_bool_binop_done:;
      if (__pyx_t_1) {

        /* "chaplotype.pyx":359
 * 
 *                 if Read_IsQCFail(badReadsStart[0]) or readOverlap < hash_nucs:
 *                     self.likelihoodCache[readIndex] = 0             # <<<<<<<<<<<<<<
 *                 else:
 *                     score = alignReadToHaplotype(badReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)
 */
        (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = 0.0;

        /* "chaplotype.pyx":358
 *                 readOverlap = computeOverlapOfReadAndHaplotype(self.startPos, self.endPos, badReadsStart[0])
 * 
 *                 if Read_IsQCFail(badReadsStart[0]) or readOverlap < hash_nucs:             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 */
        goto __pyx_L15;
      }

      /* "chaplotype.pyx":361
 *                     self.likelihoodCache[readIndex] = 0
 *                 else:
 *                     score = alignReadToHaplotype(badReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)             # <<<<<<<<<<<<<<
 *                     self.likelihoodCache[readIndex] = score
 * 
 */
      /*else*/ {
        __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->options, __pyx_n_s_calculateFlankScore); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 361, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __pyx_v_score = __pyx_f_10chaplotype_alignReadToHaplotype((__pyx_v_badReadsStart[0]), __pyx_v_self, __pyx_v_useMapQualCap, __pyx_t_6);

        /* "chaplotype.pyx":362
 *                 else:
 *                     score = alignReadToHaplotype(badReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)
 *                     self.likelihoodCache[readIndex] = score             # <<<<<<<<<<<<<<
 * 
 *                 badReadsStart += 1
 */
        (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = __pyx_v_score;
      }
      __pyx_L15:;

      /* "chaplotype.pyx":364
 *                     self.likelihoodCache[readIndex] = score
 * 
 *                 badReadsStart += 1             # <<<<<<<<<<<<<<
 *                 readIndex += 1
 * 
 */
      __pyx_v_badReadsStart = (__pyx_v_badReadsStart + 1);

      /* "chaplotype.pyx":365
 * 
 *                 badReadsStart += 1
 *                 readIndex += 1             # <<<<<<<<<<<<<<
 * 
 *             # It doesn't make sense to check overlap for the broken mates, as their mapping positions don't make
 */
      __pyx_v_readIndex = (__pyx_v_readIndex + 1);
    }

    /* "chaplotype.pyx":369
 *             # It doesn't make sense to check overlap for the broken mates, as their mapping positions don't make
 *             # sense in this context.
 *             while brokenReadsStart != brokenReadsEnd:             # <<<<<<<<<<<<<<
 *                 score = alignReadToHaplotype(brokenReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)
 *                 self.likelihoodCache[readIndex] = score
 */
    while (1) {
      __pyx_t_1 = ((__pyx_v_brokenReadsStart != __pyx_v_brokenReadsEnd) != 0);
      if (!__pyx_t_1) break;

      /* "chaplotype.pyx":370
 *             # sense in this context.
 *             while brokenReadsStart != brokenReadsEnd:
 *                 score = alignReadToHaplotype(brokenReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)             # <<<<<<<<<<<<<<
 *                 self.likelihoodCache[readIndex] = score
 *                 brokenReadsStart += 1
 */
      __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->options, __pyx_n_s_calculateFlankScore); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 370, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 370, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_v_score = __pyx_f_10chaplotype_alignReadToHaplotype((__pyx_v_brokenReadsStart[0]), __pyx_v_self, __pyx_v_useMapQualCap, __pyx_t_6);

      /* "chaplotype.pyx":371
 *             while brokenReadsStart != brokenReadsEnd:
 *                 score = alignReadToHaplotype(brokenReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)
 *                 self.likelihoodCache[readIndex] = score             # <<<<<<<<<<<<<<
 *                 brokenReadsStart += 1
 *                 readIndex += 1
 */
      (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = __pyx_v_score;

      /* "chaplotype.pyx":372
 *                 score = alignReadToHaplotype(brokenReadsStart[0], self, useMapQualCap, self.options.calculateFlankScore)
 *                 self.likelihoodCache[readIndex] = score
 *                 brokenReadsStart += 1             # <<<<<<<<<<<<<<
 *                 readIndex += 1
 * 
 */
      __pyx_v_brokenReadsStart = (__pyx_v_brokenReadsStart + 1);

      /* "chaplotype.pyx":373
 *                 self.likelihoodCache[readIndex] = score
 *                 brokenReadsStart += 1
 *                 readIndex += 1             # <<<<<<<<<<<<<<
 * 
 *             self.likelihoodCache[readIndex] = 999 # End marker
 */
      __pyx_v_readIndex = (__pyx_v_readIndex + 1);
    }

    /* "chaplotype.pyx":375
 *                 readIndex += 1
 * 
 *             self.likelihoodCache[readIndex] = 999 # End marker             # <<<<<<<<<<<<<<
 * 
 *         return self.likelihoodCache
 */
    (__pyx_v_self->likelihoodCache[__pyx_v_readIndex]) = 999.0;

    /* "chaplotype.pyx":320
 * 
 *         # Either first time, or new individual
 *         if individualIndex != self.lastIndividualIndex:             # <<<<<<<<<<<<<<
 *             if self.likelihoodCache == NULL:
 *                 self.likelihoodCache = <double*>(my_malloc((totalReads+1)*sizeof(double)))
 */
  }

  /* "chaplotype.pyx":377
 *             self.likelihoodCache[readIndex] = 999 # End marker
 * 
 *         return self.likelihoodCache             # <<<<<<<<<<<<<<
 * 
 *     cdef inline double alignSingleRead(self, cAlignedRead* theRead, int useMapQualCap):
 */
  __pyx_r = __pyx_v_self->likelihoodCache;
  goto __pyx_L0;

  /* "chaplotype.pyx":306
 *         return self.shortHaplotypeSequence
 * 
 *     cdef double* alignReads(self, int individualIndex, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadsStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenReadsStart, cAlignedRead** brokenReadsEnd, int useMapQualCap):             # <<<<<<<<<<<<<<
 *         """
 *         """
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.alignReads", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":379
 *         return self.likelihoodCache
 * 
 *     cdef inline double alignSingleRead(self, cAlignedRead* theRead, int useMapQualCap):             # <<<<<<<<<<<<<<
 *         """
 *         Returns the alignment score for a single read. If 'useMapQualCap' is True, then read likelihood
 */

static double __pyx_f_10chaplotype_9Haplotype_alignSingleRead(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, __pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead, int __pyx_v_useMapQualCap) {
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_t_2;
  __Pyx_RefNannySetupContext("alignSingleRead", 0);

  /* "chaplotype.pyx":384
 *         is capped using the mapping quality of the read. Otherwise it is capped at 1e-300.
 *         """
 *         return alignReadToHaplotype(theRead, self, useMapQualCap, self.options.calculateFlankScore)             # <<<<<<<<<<<<<<
 * 
 *     cdef char* getReferenceSequence(self, prefix = 0):
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->options, __pyx_n_s_calculateFlankScore); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 384, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 384, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_r = __pyx_f_10chaplotype_alignReadToHaplotype(__pyx_v_theRead, __pyx_v_self, __pyx_v_useMapQualCap, __pyx_t_2);
  goto __pyx_L0;

  /* "chaplotype.pyx":379
 *         return self.likelihoodCache
 * 
 *     cdef inline double alignSingleRead(self, cAlignedRead* theRead, int useMapQualCap):             # <<<<<<<<<<<<<<
 *         """
 *         Returns the alignment score for a single read. If 'useMapQualCap' is True, then read likelihood
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.alignSingleRead", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":386
 *         return alignReadToHaplotype(theRead, self, useMapQualCap, self.options.calculateFlankScore)
 * 
 *     cdef char* getReferenceSequence(self, prefix = 0):             # <<<<<<<<<<<<<<
 *         """
 *         Return the refernece sequence for the region covered by this haplotype. pretty shows where the variants are.
 */

static char *__pyx_f_10chaplotype_9Haplotype_getReferenceSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args) {
  PyObject *__pyx_v_prefix = ((PyObject *)__pyx_int_0);
  PyObject *__pyx_v_seqMax = NULL;
  char *__pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_t_3;
  char *__pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  long __pyx_t_7;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  PY_LONG_LONG __pyx_t_10;
  PY_LONG_LONG __pyx_t_11;
  __Pyx_RefNannySetupContext("getReferenceSequence", 0);
  if (__pyx_optional_args) {
    if (__pyx_optional_args->__pyx_n > 0) {
      __pyx_v_prefix = __pyx_optional_args->prefix;
    }
  }

  /* "chaplotype.pyx":390
 *         Return the refernece sequence for the region covered by this haplotype. pretty shows where the variants are.
 *         """
 *         if prefix == 0 and self.referenceSequence != None:             # <<<<<<<<<<<<<<
 *             return self.referenceSequence
 * 
 */
  __pyx_t_2 = __Pyx_PyInt_EqObjC(__pyx_v_prefix, __pyx_int_0, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 390, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 390, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (__pyx_t_3) {
  } else {
    __pyx_t_1 = __pyx_t_3;
    goto __pyx_L4_bool_binop_done;
  }
  __pyx_t_3 = (__Pyx_PyBytes_Equals(__pyx_v_self->referenceSequence, Py_None, Py_NE)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 390, __pyx_L1_error)
  __pyx_t_1 = __pyx_t_3;
  __pyx_L4_bool_binop_done:;
  if (__pyx_t_1) {

    /* "chaplotype.pyx":391
 *         """
 *         if prefix == 0 and self.referenceSequence != None:
 *             return self.referenceSequence             # <<<<<<<<<<<<<<
 * 
 *         seqMax = self.refFile.refs[self.refName].SeqLength - 1
 */
    if (unlikely(__pyx_v_self->referenceSequence == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
      __PYX_ERR(0, 391, __pyx_L1_error)
    }
    __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_self->referenceSequence); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 391, __pyx_L1_error)
    __pyx_r = __pyx_t_4;
    goto __pyx_L0;

    /* "chaplotype.pyx":390
 *         Return the refernece sequence for the region covered by this haplotype. pretty shows where the variants are.
 *         """
 *         if prefix == 0 and self.referenceSequence != None:             # <<<<<<<<<<<<<<
 *             return self.referenceSequence
 * 
 */
  }

  /* "chaplotype.pyx":393
 *             return self.referenceSequence
 * 
 *         seqMax = self.refFile.refs[self.refName].SeqLength - 1             # <<<<<<<<<<<<<<
 *         self.referenceSequence = self.refFile.getSequence(self.refName, max(0, self.startPos - prefix), min(self.endPos + prefix, seqMax))
 *         return self.referenceSequence
 */
  if (unlikely(__pyx_v_self->refFile->refs == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
    __PYX_ERR(0, 393, __pyx_L1_error)
  }
  __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->refFile->refs, __pyx_v_self->refName); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 393, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_SeqLength); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 393, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_t_5, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 393, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_v_seqMax = __pyx_t_2;
  __pyx_t_2 = 0;

  /* "chaplotype.pyx":394
 * 
 *         seqMax = self.refFile.refs[self.refName].SeqLength - 1
 *         self.referenceSequence = self.refFile.getSequence(self.refName, max(0, self.startPos - prefix), min(self.endPos + prefix, seqMax))             # <<<<<<<<<<<<<<
 *         return self.referenceSequence
 * 
 */
  __pyx_t_2 = __pyx_v_self->refName;
  __Pyx_INCREF(__pyx_t_2);
  __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __pyx_t_6 = PyNumber_Subtract(__pyx_t_5, __pyx_v_prefix); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_t_7 = 0;
  __pyx_t_8 = __Pyx_PyInt_From_long(__pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_8);
  __pyx_t_9 = PyObject_RichCompare(__pyx_t_6, __pyx_t_8, Py_GT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
  if (__pyx_t_1) {
    __Pyx_INCREF(__pyx_t_6);
    __pyx_t_5 = __pyx_t_6;
  } else {
    __pyx_t_9 = __Pyx_PyInt_From_long(__pyx_t_7); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 394, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_9);
    __pyx_t_5 = __pyx_t_9;
    __pyx_t_9 = 0;
  }
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_10 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_5); if (unlikely((__pyx_t_10 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __Pyx_INCREF(__pyx_v_seqMax);
  __pyx_t_5 = __pyx_v_seqMax;
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_t_9 = PyNumber_Add(__pyx_t_6, __pyx_v_prefix); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_9);
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, __pyx_t_9, Py_LT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 394, __pyx_L1_error)
  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
  if (__pyx_t_1) {
    __Pyx_INCREF(__pyx_t_5);
    __pyx_t_6 = __pyx_t_5;
  } else {
    __Pyx_INCREF(__pyx_t_9);
    __pyx_t_6 = __pyx_t_9;
  }
  __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_t_11 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_6); if (unlikely((__pyx_t_11 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_6 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_2), __pyx_t_10, __pyx_t_11); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 394, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_GIVEREF(__pyx_t_6);
  __Pyx_GOTREF(__pyx_v_self->referenceSequence);
  __Pyx_DECREF(__pyx_v_self->referenceSequence);
  __pyx_v_self->referenceSequence = ((PyObject*)__pyx_t_6);
  __pyx_t_6 = 0;

  /* "chaplotype.pyx":395
 *         seqMax = self.refFile.refs[self.refName].SeqLength - 1
 *         self.referenceSequence = self.refFile.getSequence(self.refName, max(0, self.startPos - prefix), min(self.endPos + prefix, seqMax))
 *         return self.referenceSequence             # <<<<<<<<<<<<<<
 * 
 *     cdef char* getMutatedSequence(self):
 */
  if (unlikely(__pyx_v_self->referenceSequence == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
    __PYX_ERR(0, 395, __pyx_L1_error)
  }
  __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_self->referenceSequence); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 395, __pyx_L1_error)
  __pyx_r = __pyx_t_4;
  goto __pyx_L0;

  /* "chaplotype.pyx":386
 *         return alignReadToHaplotype(theRead, self, useMapQualCap, self.options.calculateFlankScore)
 * 
 *     cdef char* getReferenceSequence(self, prefix = 0):             # <<<<<<<<<<<<<<
 *         """
 *         Return the refernece sequence for the region covered by this haplotype. pretty shows where the variants are.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.getReferenceSequence", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_seqMax);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":397
 *         return self.referenceSequence
 * 
 *     cdef char* getMutatedSequence(self):             # <<<<<<<<<<<<<<
 *         """
 *         Return the reference sequence mutated with all the variants being
 */

static char *__pyx_f_10chaplotype_9Haplotype_getMutatedSequence(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  struct __pyx_obj_7variant_Variant *__pyx_v_v = 0;
  struct __pyx_obj_7variant_Variant *__pyx_v_firstVar = 0;
  PyObject *__pyx_v_currentPos = NULL;
  PyObject *__pyx_v_bitsOfMutatedSeq = NULL;
  char *__pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  PY_LONG_LONG __pyx_t_5;
  Py_ssize_t __pyx_t_6;
  PyObject *__pyx_t_7 = NULL;
  int __pyx_t_8;
  Py_ssize_t __pyx_t_9;
  PyObject *__pyx_t_10 = NULL;
  char *__pyx_t_11;
  __Pyx_RefNannySetupContext("getMutatedSequence", 0);

  /* "chaplotype.pyx":410
 *         cdef Variant firstVar
 * 
 *         if self.haplotypeSequence is None:             # <<<<<<<<<<<<<<
 * 
 *             currentPos = self.startPos
 */
  __pyx_t_1 = (__pyx_v_self->haplotypeSequence == ((PyObject*)Py_None));
  __pyx_t_2 = (__pyx_t_1 != 0);
  if (__pyx_t_2) {

    /* "chaplotype.pyx":412
 *         if self.haplotypeSequence is None:
 * 
 *             currentPos = self.startPos             # <<<<<<<<<<<<<<
 *             # Get sequence up to one base before the first variant
 *             firstVar = self.variants[0]
 */
    __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 412, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_v_currentPos = __pyx_t_3;
    __pyx_t_3 = 0;

    /* "chaplotype.pyx":414
 *             currentPos = self.startPos
 *             # Get sequence up to one base before the first variant
 *             firstVar = self.variants[0]             # <<<<<<<<<<<<<<
 *             #if firstVar.refPos == currentPos, no need to get the sequence before the variant
 *             bitsOfMutatedSeq = []
 */
    if (unlikely(__pyx_v_self->variants == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
      __PYX_ERR(0, 414, __pyx_L1_error)
    }
    if (!(likely(((PyTuple_GET_ITEM(__pyx_v_self->variants, 0)) == Py_None) || likely(__Pyx_TypeTest(PyTuple_GET_ITEM(__pyx_v_self->variants, 0), __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 414, __pyx_L1_error)
    __pyx_t_3 = PyTuple_GET_ITEM(__pyx_v_self->variants, 0);
    __Pyx_INCREF(__pyx_t_3);
    __pyx_v_firstVar = ((struct __pyx_obj_7variant_Variant *)__pyx_t_3);
    __pyx_t_3 = 0;

    /* "chaplotype.pyx":416
 *             firstVar = self.variants[0]
 *             #if firstVar.refPos == currentPos, no need to get the sequence before the variant
 *             bitsOfMutatedSeq = []             # <<<<<<<<<<<<<<
 *             if firstVar.refPos != currentPos:
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 */
    __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 416, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_v_bitsOfMutatedSeq = ((PyObject*)__pyx_t_3);
    __pyx_t_3 = 0;

    /* "chaplotype.pyx":417
 *             #if firstVar.refPos == currentPos, no need to get the sequence before the variant
 *             bitsOfMutatedSeq = []
 *             if firstVar.refPos != currentPos:             # <<<<<<<<<<<<<<
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 *                 currentPos = firstVar.refPos
 */
    __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_firstVar->refPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 417, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_currentPos, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 417, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 417, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":418
 *             bitsOfMutatedSeq = []
 *             if firstVar.refPos != currentPos:
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]             # <<<<<<<<<<<<<<
 *                 currentPos = firstVar.refPos
 *             for v in self.variants:
 */
      __pyx_t_4 = __pyx_v_self->refName;
      __Pyx_INCREF(__pyx_t_4);
      __pyx_t_5 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_v_currentPos); if (unlikely((__pyx_t_5 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 418, __pyx_L1_error)
      __pyx_t_3 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_4), __pyx_t_5, __pyx_v_firstVar->refPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 418, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 418, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_GIVEREF(__pyx_t_3);
      PyList_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
      __pyx_t_3 = 0;
      __Pyx_DECREF_SET(__pyx_v_bitsOfMutatedSeq, ((PyObject*)__pyx_t_4));
      __pyx_t_4 = 0;

      /* "chaplotype.pyx":419
 *             if firstVar.refPos != currentPos:
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 *                 currentPos = firstVar.refPos             # <<<<<<<<<<<<<<
 *             for v in self.variants:
 *                 # Move up to one base before the next variant, if we're not already there.
 */
      __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_firstVar->refPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 419, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_DECREF_SET(__pyx_v_currentPos, __pyx_t_4);
      __pyx_t_4 = 0;

      /* "chaplotype.pyx":417
 *             #if firstVar.refPos == currentPos, no need to get the sequence before the variant
 *             bitsOfMutatedSeq = []
 *             if firstVar.refPos != currentPos:             # <<<<<<<<<<<<<<
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 *                 currentPos = firstVar.refPos
 */
    }

    /* "chaplotype.pyx":420
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 *                 currentPos = firstVar.refPos
 *             for v in self.variants:             # <<<<<<<<<<<<<<
 *                 # Move up to one base before the next variant, if we're not already there.
 *                 if v.refPos > currentPos:
 */
    if (unlikely(__pyx_v_self->variants == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
      __PYX_ERR(0, 420, __pyx_L1_error)
    }
    __pyx_t_4 = __pyx_v_self->variants; __Pyx_INCREF(__pyx_t_4); __pyx_t_6 = 0;
    for (;;) {
      if (__pyx_t_6 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_6); __Pyx_INCREF(__pyx_t_3); __pyx_t_6++; if (unlikely(0 < 0)) __PYX_ERR(0, 420, __pyx_L1_error)
      #else
      __pyx_t_3 = PySequence_ITEM(__pyx_t_4, __pyx_t_6); __pyx_t_6++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 420, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      #endif
      if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 420, __pyx_L1_error)
      __Pyx_XDECREF_SET(__pyx_v_v, ((struct __pyx_obj_7variant_Variant *)__pyx_t_3));
      __pyx_t_3 = 0;

      /* "chaplotype.pyx":422
 *             for v in self.variants:
 *                 # Move up to one base before the next variant, if we're not already there.
 *                 if v.refPos > currentPos:             # <<<<<<<<<<<<<<
 *                     bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, v.refPos))
 *                     currentPos = v.refPos
 */
      __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_v->refPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 422, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_7 = PyObject_RichCompare(__pyx_t_3, __pyx_v_currentPos, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 422, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 422, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      if (__pyx_t_2) {

        /* "chaplotype.pyx":423
 *                 # Move up to one base before the next variant, if we're not already there.
 *                 if v.refPos > currentPos:
 *                     bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, v.refPos))             # <<<<<<<<<<<<<<
 *                     currentPos = v.refPos
 *                 # SNP/Mult-SNP/Complex
 */
        __pyx_t_7 = __pyx_v_self->refName;
        __Pyx_INCREF(__pyx_t_7);
        __pyx_t_5 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_v_currentPos); if (unlikely((__pyx_t_5 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 423, __pyx_L1_error)
        __pyx_t_3 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_7), __pyx_t_5, __pyx_v_v->refPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 423, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_bitsOfMutatedSeq, __pyx_t_3); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 423, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

        /* "chaplotype.pyx":424
 *                 if v.refPos > currentPos:
 *                     bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, v.refPos))
 *                     currentPos = v.refPos             # <<<<<<<<<<<<<<
 *                 # SNP/Mult-SNP/Complex
 *                 if v.nAdded == v.nRemoved:
 */
        __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_v->refPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 424, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF_SET(__pyx_v_currentPos, __pyx_t_3);
        __pyx_t_3 = 0;

        /* "chaplotype.pyx":422
 *             for v in self.variants:
 *                 # Move up to one base before the next variant, if we're not already there.
 *                 if v.refPos > currentPos:             # <<<<<<<<<<<<<<
 *                     bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, v.refPos))
 *                     currentPos = v.refPos
 */
      }

      /* "chaplotype.pyx":426
 *                     currentPos = v.refPos
 *                 # SNP/Mult-SNP/Complex
 *                 if v.nAdded == v.nRemoved:             # <<<<<<<<<<<<<<
 *                     bitsOfMutatedSeq.append(v.added)
 *                     currentPos += v.nRemoved
 */
      __pyx_t_2 = ((__pyx_v_v->nAdded == __pyx_v_v->nRemoved) != 0);
      if (__pyx_t_2) {

        /* "chaplotype.pyx":427
 *                 # SNP/Mult-SNP/Complex
 *                 if v.nAdded == v.nRemoved:
 *                     bitsOfMutatedSeq.append(v.added)             # <<<<<<<<<<<<<<
 *                     currentPos += v.nRemoved
 * 
 */
        __pyx_t_3 = __pyx_v_v->added;
        __Pyx_INCREF(__pyx_t_3);
        __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_bitsOfMutatedSeq, __pyx_t_3); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 427, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

        /* "chaplotype.pyx":428
 *                 if v.nAdded == v.nRemoved:
 *                     bitsOfMutatedSeq.append(v.added)
 *                     currentPos += v.nRemoved             # <<<<<<<<<<<<<<
 * 
 *                 # Arbitrary length-changing sequence replacement
 */
        __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_v->nRemoved); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 428, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_currentPos, __pyx_t_3); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 428, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __Pyx_DECREF_SET(__pyx_v_currentPos, __pyx_t_7);
        __pyx_t_7 = 0;

        /* "chaplotype.pyx":426
 *                     currentPos = v.refPos
 *                 # SNP/Mult-SNP/Complex
 *                 if v.nAdded == v.nRemoved:             # <<<<<<<<<<<<<<
 *                     bitsOfMutatedSeq.append(v.added)
 *                     currentPos += v.nRemoved
 */
        goto __pyx_L8;
      }

      /* "chaplotype.pyx":433
 *                 else:
 *                     #HP : Need to be careful here, this seem to deal with indels only, not sequence replacement ABC -> CGA
 *                     if len(v.added) ==0 or len(v.removed) ==0:             # <<<<<<<<<<<<<<
 *                         if v.refPos == currentPos:
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 */
      /*else*/ {
        __pyx_t_7 = __pyx_v_v->added;
        __Pyx_INCREF(__pyx_t_7);
        if (unlikely(__pyx_t_7 == Py_None)) {
          PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
          __PYX_ERR(0, 433, __pyx_L1_error)
        }
        __pyx_t_9 = PyBytes_GET_SIZE(__pyx_t_7); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 433, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __pyx_t_1 = ((__pyx_t_9 == 0) != 0);
        if (!__pyx_t_1) {
        } else {
          __pyx_t_2 = __pyx_t_1;
          goto __pyx_L10_bool_binop_done;
        }
        __pyx_t_7 = __pyx_v_v->removed;
        __Pyx_INCREF(__pyx_t_7);
        if (unlikely(__pyx_t_7 == Py_None)) {
          PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
          __PYX_ERR(0, 433, __pyx_L1_error)
        }
        __pyx_t_9 = PyBytes_GET_SIZE(__pyx_t_7); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 433, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __pyx_t_1 = ((__pyx_t_9 == 0) != 0);
        __pyx_t_2 = __pyx_t_1;
        __pyx_L10_bool_binop_done:;
        if (__pyx_t_2) {

          /* "chaplotype.pyx":434
 *                     #HP : Need to be careful here, this seem to deal with indels only, not sequence replacement ABC -> CGA
 *                     if len(v.added) ==0 or len(v.removed) ==0:
 *                         if v.refPos == currentPos:             # <<<<<<<<<<<<<<
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 *                             currentPos += 1
 */
          __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_v->refPos); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 434, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          __pyx_t_3 = PyObject_RichCompare(__pyx_t_7, __pyx_v_currentPos, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 434, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
          __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 434, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          if (__pyx_t_2) {

            /* "chaplotype.pyx":435
 *                     if len(v.added) ==0 or len(v.removed) ==0:
 *                         if v.refPos == currentPos:
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))             # <<<<<<<<<<<<<<
 *                             currentPos += 1
 *                     currentPos += v.nRemoved
 */
            __pyx_t_3 = __pyx_v_self->refName;
            __Pyx_INCREF(__pyx_t_3);
            __pyx_t_7 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getCharacter(__pyx_v_self->refFile, ((PyObject*)__pyx_t_3), __pyx_v_v->refPos); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 435, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_7);
            __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
            __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_bitsOfMutatedSeq, __pyx_t_7); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 435, __pyx_L1_error)
            __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

            /* "chaplotype.pyx":436
 *                         if v.refPos == currentPos:
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 *                             currentPos += 1             # <<<<<<<<<<<<<<
 *                     currentPos += v.nRemoved
 *                     bitsOfMutatedSeq.append(v.added)
 */
            __pyx_t_7 = __Pyx_PyInt_AddObjC(__pyx_v_currentPos, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 436, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_7);
            __Pyx_DECREF_SET(__pyx_v_currentPos, __pyx_t_7);
            __pyx_t_7 = 0;

            /* "chaplotype.pyx":434
 *                     #HP : Need to be careful here, this seem to deal with indels only, not sequence replacement ABC -> CGA
 *                     if len(v.added) ==0 or len(v.removed) ==0:
 *                         if v.refPos == currentPos:             # <<<<<<<<<<<<<<
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 *                             currentPos += 1
 */
          }

          /* "chaplotype.pyx":433
 *                 else:
 *                     #HP : Need to be careful here, this seem to deal with indels only, not sequence replacement ABC -> CGA
 *                     if len(v.added) ==0 or len(v.removed) ==0:             # <<<<<<<<<<<<<<
 *                         if v.refPos == currentPos:
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 */
        }

        /* "chaplotype.pyx":437
 *                             bitsOfMutatedSeq.append(self.refFile.getCharacter(self.refName, v.refPos))
 *                             currentPos += 1
 *                     currentPos += v.nRemoved             # <<<<<<<<<<<<<<
 *                     bitsOfMutatedSeq.append(v.added)
 * 
 */
        __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_v->nRemoved); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 437, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_currentPos, __pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 437, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __Pyx_DECREF_SET(__pyx_v_currentPos, __pyx_t_3);
        __pyx_t_3 = 0;

        /* "chaplotype.pyx":438
 *                             currentPos += 1
 *                     currentPos += v.nRemoved
 *                     bitsOfMutatedSeq.append(v.added)             # <<<<<<<<<<<<<<
 * 
 *             # Is this ok when currentPos == endPos?
 */
        __pyx_t_3 = __pyx_v_v->added;
        __Pyx_INCREF(__pyx_t_3);
        __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_bitsOfMutatedSeq, __pyx_t_3); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 438, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      }
      __pyx_L8:;

      /* "chaplotype.pyx":420
 *                 bitsOfMutatedSeq = [self.refFile.getSequence(self.refName, currentPos, firstVar.refPos)]
 *                 currentPos = firstVar.refPos
 *             for v in self.variants:             # <<<<<<<<<<<<<<
 *                 # Move up to one base before the next variant, if we're not already there.
 *                 if v.refPos > currentPos:
 */
    }
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

    /* "chaplotype.pyx":441
 * 
 *             # Is this ok when currentPos == endPos?
 *             if currentPos > self.endPos + 1:             # <<<<<<<<<<<<<<
 *                 logger.error("cpos = %s end pos = %s. Variants are %s" %(currentPos, self.endPos, self.variants))
 * 
 */
    __pyx_t_4 = __Pyx_PyInt_From_long((__pyx_v_self->endPos + 1)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 441, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_3 = PyObject_RichCompare(__pyx_v_currentPos, __pyx_t_4, Py_GT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 441, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 441, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":442
 *             # Is this ok when currentPos == endPos?
 *             if currentPos > self.endPos + 1:
 *                 logger.error("cpos = %s end pos = %s. Variants are %s" %(currentPos, self.endPos, self.variants))             # <<<<<<<<<<<<<<
 * 
 *             if currentPos < self.endPos:
 */
      __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_logger); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_error); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_10);
      __Pyx_INCREF(__pyx_v_currentPos);
      __Pyx_GIVEREF(__pyx_v_currentPos);
      PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_currentPos);
      __Pyx_GIVEREF(__pyx_t_4);
      PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_4);
      __Pyx_INCREF(__pyx_v_self->variants);
      __Pyx_GIVEREF(__pyx_v_self->variants);
      PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_self->variants);
      __pyx_t_4 = 0;
      __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_cpos_s_end_pos_s_Variants_are_s, __pyx_t_10); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
      __pyx_t_10 = NULL;
      if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_7))) {
        __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_7);
        if (likely(__pyx_t_10)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
          __Pyx_INCREF(__pyx_t_10);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_7, function);
        }
      }
      __pyx_t_3 = (__pyx_t_10) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_10, __pyx_t_4) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_t_4);
      __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 442, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

      /* "chaplotype.pyx":441
 * 
 *             # Is this ok when currentPos == endPos?
 *             if currentPos > self.endPos + 1:             # <<<<<<<<<<<<<<
 *                 logger.error("cpos = %s end pos = %s. Variants are %s" %(currentPos, self.endPos, self.variants))
 * 
 */
    }

    /* "chaplotype.pyx":444
 *                 logger.error("cpos = %s end pos = %s. Variants are %s" %(currentPos, self.endPos, self.variants))
 * 
 *             if currentPos < self.endPos:             # <<<<<<<<<<<<<<
 *                 bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, self.endPos))
 * 
 */
    __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 444, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_7 = PyObject_RichCompare(__pyx_v_currentPos, __pyx_t_3, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 444, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 444, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    if (__pyx_t_2) {

      /* "chaplotype.pyx":445
 * 
 *             if currentPos < self.endPos:
 *                 bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, self.endPos))             # <<<<<<<<<<<<<<
 * 
 *             self.haplotypeSequence = bytes(''.join(bitsOfMutatedSeq))
 */
      __pyx_t_7 = __pyx_v_self->refName;
      __Pyx_INCREF(__pyx_t_7);
      __pyx_t_5 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_v_currentPos); if (unlikely((__pyx_t_5 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 445, __pyx_L1_error)
      __pyx_t_3 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, ((PyObject*)__pyx_t_7), __pyx_t_5, __pyx_v_self->endPos); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 445, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_8 = __Pyx_PyList_Append(__pyx_v_bitsOfMutatedSeq, __pyx_t_3); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 445, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

      /* "chaplotype.pyx":444
 *                 logger.error("cpos = %s end pos = %s. Variants are %s" %(currentPos, self.endPos, self.variants))
 * 
 *             if currentPos < self.endPos:             # <<<<<<<<<<<<<<
 *                 bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, self.endPos))
 * 
 */
    }

    /* "chaplotype.pyx":447
 *                 bitsOfMutatedSeq.append(self.refFile.getSequence(self.refName, currentPos, self.endPos))
 * 
 *             self.haplotypeSequence = bytes(''.join(bitsOfMutatedSeq))             # <<<<<<<<<<<<<<
 * 
 *         return self.haplotypeSequence
 */
    __pyx_t_3 = __Pyx_PyString_Join(__pyx_kp_s_, __pyx_v_bitsOfMutatedSeq); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 447, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_7 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyBytes_Type)), __pyx_t_3); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 447, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_GIVEREF(__pyx_t_7);
    __Pyx_GOTREF(__pyx_v_self->haplotypeSequence);
    __Pyx_DECREF(__pyx_v_self->haplotypeSequence);
    __pyx_v_self->haplotypeSequence = ((PyObject*)__pyx_t_7);
    __pyx_t_7 = 0;

    /* "chaplotype.pyx":410
 *         cdef Variant firstVar
 * 
 *         if self.haplotypeSequence is None:             # <<<<<<<<<<<<<<
 * 
 *             currentPos = self.startPos
 */
  }

  /* "chaplotype.pyx":449
 *             self.haplotypeSequence = bytes(''.join(bitsOfMutatedSeq))
 * 
 *         return self.haplotypeSequence             # <<<<<<<<<<<<<<
 * 
 *     cdef list homopolymerLengths( self ):
 */
  if (unlikely(__pyx_v_self->haplotypeSequence == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
    __PYX_ERR(0, 449, __pyx_L1_error)
  }
  __pyx_t_11 = __Pyx_PyBytes_AsWritableString(__pyx_v_self->haplotypeSequence); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) __PYX_ERR(0, 449, __pyx_L1_error)
  __pyx_r = __pyx_t_11;
  goto __pyx_L0;

  /* "chaplotype.pyx":397
 *         return self.referenceSequence
 * 
 *     cdef char* getMutatedSequence(self):             # <<<<<<<<<<<<<<
 *         """
 *         Return the reference sequence mutated with all the variants being
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.getMutatedSequence", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF((PyObject *)__pyx_v_v);
  __Pyx_XDECREF((PyObject *)__pyx_v_firstVar);
  __Pyx_XDECREF(__pyx_v_currentPos);
  __Pyx_XDECREF(__pyx_v_bitsOfMutatedSeq);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":451
 *         return self.haplotypeSequence
 * 
 *     cdef list homopolymerLengths( self ):             # <<<<<<<<<<<<<<
 *         """
 *         Return a list of homopolymer lengths for the sequence surrounding
 */

static PyObject *__pyx_f_10chaplotype_9Haplotype_homopolymerLengths(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  PyObject *__pyx_v_vsf = 0;
  PyObject *__pyx_v_v = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  __Pyx_RefNannySetupContext("homopolymerLengths", 0);

  /* "chaplotype.pyx":456
 *         each variant in this haplotype.
 *         """
 *         cdef tuple vsf = self.variants             # <<<<<<<<<<<<<<
 *         if len( vsf ) == 0:
 *             return []
 */
  __pyx_t_1 = __pyx_v_self->variants;
  __Pyx_INCREF(__pyx_t_1);
  __pyx_v_vsf = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":457
 *         """
 *         cdef tuple vsf = self.variants
 *         if len( vsf ) == 0:             # <<<<<<<<<<<<<<
 *             return []
 *         else:
 */
  if (unlikely(__pyx_v_vsf == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(0, 457, __pyx_L1_error)
  }
  __pyx_t_2 = PyTuple_GET_SIZE(__pyx_v_vsf); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(0, 457, __pyx_L1_error)
  __pyx_t_3 = ((__pyx_t_2 == 0) != 0);
  if (__pyx_t_3) {

    /* "chaplotype.pyx":458
 *         cdef tuple vsf = self.variants
 *         if len( vsf ) == 0:
 *             return []             # <<<<<<<<<<<<<<
 *         else:
 *             return [ self.homopolymerLengthForOneVariant( v ) for v in vsf ]
 */
    __Pyx_XDECREF(__pyx_r);
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 458, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_r = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
    goto __pyx_L0;

    /* "chaplotype.pyx":457
 *         """
 *         cdef tuple vsf = self.variants
 *         if len( vsf ) == 0:             # <<<<<<<<<<<<<<
 *             return []
 *         else:
 */
  }

  /* "chaplotype.pyx":460
 *             return []
 *         else:
 *             return [ self.homopolymerLengthForOneVariant( v ) for v in vsf ]             # <<<<<<<<<<<<<<
 * 
 *     cdef int homopolymerLengthForOneVariant(self, Variant variant):
 */
  /*else*/ {
    __Pyx_XDECREF(__pyx_r);
    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 460, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    if (unlikely(__pyx_v_vsf == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
      __PYX_ERR(0, 460, __pyx_L1_error)
    }
    __pyx_t_4 = __pyx_v_vsf; __Pyx_INCREF(__pyx_t_4); __pyx_t_2 = 0;
    for (;;) {
      if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 460, __pyx_L1_error)
      #else
      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      #endif
      __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_5);
      __pyx_t_5 = 0;
      if (!(likely(((__pyx_v_v) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_v, __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 460, __pyx_L1_error)
      __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_f_10chaplotype_9Haplotype_homopolymerLengthForOneVariant(__pyx_v_self, ((struct __pyx_obj_7variant_Variant *)__pyx_v_v))); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    }
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_r = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
    goto __pyx_L0;
  }

  /* "chaplotype.pyx":451
 *         return self.haplotypeSequence
 * 
 *     cdef list homopolymerLengths( self ):             # <<<<<<<<<<<<<<
 *         """
 *         Return a list of homopolymer lengths for the sequence surrounding
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("chaplotype.Haplotype.homopolymerLengths", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_vsf);
  __Pyx_XDECREF(__pyx_v_v);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":462
 *             return [ self.homopolymerLengthForOneVariant( v ) for v in vsf ]
 * 
 *     cdef int homopolymerLengthForOneVariant(self, Variant variant):             # <<<<<<<<<<<<<<
 *         """
 *         Calculate and return the length of the largest homopolymer
 */

static int __pyx_f_10chaplotype_9Haplotype_homopolymerLengthForOneVariant(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_7variant_Variant *__pyx_v_variant) {
  PyObject *__pyx_v_varChrom = NULL;
  PyObject *__pyx_v_varPos = NULL;
  PyObject *__pyx_v_leftRefSeq = NULL;
  PyObject *__pyx_v_rightRefSeq = NULL;
  PyObject *__pyx_v_leftHpSize = NULL;
  PyObject *__pyx_v_rightHpSize = NULL;
  PyObject *__pyx_v_firstLeftChar = NULL;
  PyObject *__pyx_v_firstRightChar = NULL;
  PyObject *__pyx_v_char = NULL;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PY_LONG_LONG __pyx_t_2;
  PY_LONG_LONG __pyx_t_3;
  int __pyx_t_4;
  Py_ssize_t __pyx_t_5;
  int __pyx_t_6;
  PyObject *__pyx_t_7 = NULL;
  PyObject *(*__pyx_t_8)(PyObject *);
  PyObject *__pyx_t_9 = NULL;
  PyObject *__pyx_t_10 = NULL;
  int __pyx_t_11;
  __Pyx_RefNannySetupContext("homopolymerLengthForOneVariant", 0);

  /* "chaplotype.pyx":468
 *         left and right, and return the largest.
 *         """
 *         varChrom = variant.refName             # <<<<<<<<<<<<<<
 *         varPos = variant.refPos
 * 
 */
  __pyx_t_1 = __pyx_v_variant->refName;
  __Pyx_INCREF(__pyx_t_1);
  __pyx_v_varChrom = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":469
 *         """
 *         varChrom = variant.refName
 *         varPos = variant.refPos             # <<<<<<<<<<<<<<
 * 
 *         leftRefSeq = self.refFile.getSequence(varChrom, varPos-20, varPos)
 */
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_variant->refPos); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 469, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_varPos = __pyx_t_1;
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":471
 *         varPos = variant.refPos
 * 
 *         leftRefSeq = self.refFile.getSequence(varChrom, varPos-20, varPos)             # <<<<<<<<<<<<<<
 *         rightRefSeq = self.refFile.getSequence(varChrom, varPos+1, varPos + 21)
 * 
 */
  __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_v_varPos, __pyx_int_20, 20, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 471, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_1); if (unlikely((__pyx_t_2 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 471, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_3 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_v_varPos); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 471, __pyx_L1_error)
  __pyx_t_1 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, __pyx_v_varChrom, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 471, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_leftRefSeq = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":472
 * 
 *         leftRefSeq = self.refFile.getSequence(varChrom, varPos-20, varPos)
 *         rightRefSeq = self.refFile.getSequence(varChrom, varPos+1, varPos + 21)             # <<<<<<<<<<<<<<
 * 
 *         if len(leftRefSeq) == 0 or len(rightRefSeq) == 0:
 */
  __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_varPos, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 472, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_1); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 472, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_varPos, __pyx_int_21, 21, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 472, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_1); if (unlikely((__pyx_t_2 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 472, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, __pyx_v_varChrom, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 472, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_rightRefSeq = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":474
 *         rightRefSeq = self.refFile.getSequence(varChrom, varPos+1, varPos + 21)
 * 
 *         if len(leftRefSeq) == 0 or len(rightRefSeq) == 0:             # <<<<<<<<<<<<<<
 *             return 0
 * 
 */
  if (unlikely(__pyx_v_leftRefSeq == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(0, 474, __pyx_L1_error)
  }
  __pyx_t_5 = PyBytes_GET_SIZE(__pyx_v_leftRefSeq); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 474, __pyx_L1_error)
  __pyx_t_6 = ((__pyx_t_5 == 0) != 0);
  if (!__pyx_t_6) {
  } else {
    __pyx_t_4 = __pyx_t_6;
    goto __pyx_L4_bool_binop_done;
  }
  if (unlikely(__pyx_v_rightRefSeq == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    __PYX_ERR(0, 474, __pyx_L1_error)
  }
  __pyx_t_5 = PyBytes_GET_SIZE(__pyx_v_rightRefSeq); if (unlikely(__pyx_t_5 == ((Py_ssize_t)-1))) __PYX_ERR(0, 474, __pyx_L1_error)
  __pyx_t_6 = ((__pyx_t_5 == 0) != 0);
  __pyx_t_4 = __pyx_t_6;
  __pyx_L4_bool_binop_done:;
  if (__pyx_t_4) {

    /* "chaplotype.pyx":475
 * 
 *         if len(leftRefSeq) == 0 or len(rightRefSeq) == 0:
 *             return 0             # <<<<<<<<<<<<<<
 * 
 *         leftHpSize = 0
 */
    __pyx_r = 0;
    goto __pyx_L0;

    /* "chaplotype.pyx":474
 *         rightRefSeq = self.refFile.getSequence(varChrom, varPos+1, varPos + 21)
 * 
 *         if len(leftRefSeq) == 0 or len(rightRefSeq) == 0:             # <<<<<<<<<<<<<<
 *             return 0
 * 
 */
  }

  /* "chaplotype.pyx":477
 *             return 0
 * 
 *         leftHpSize = 0             # <<<<<<<<<<<<<<
 *         rightHpSize = 0
 * 
 */
  __Pyx_INCREF(__pyx_int_0);
  __pyx_v_leftHpSize = __pyx_int_0;

  /* "chaplotype.pyx":478
 * 
 *         leftHpSize = 0
 *         rightHpSize = 0             # <<<<<<<<<<<<<<
 * 
 *         firstLeftChar = leftRefSeq[-1]
 */
  __Pyx_INCREF(__pyx_int_0);
  __pyx_v_rightHpSize = __pyx_int_0;

  /* "chaplotype.pyx":480
 *         rightHpSize = 0
 * 
 *         firstLeftChar = leftRefSeq[-1]             # <<<<<<<<<<<<<<
 *         firstRightChar = rightRefSeq[0]
 * 
 */
  __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_leftRefSeq, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 480, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_firstLeftChar = __pyx_t_1;
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":481
 * 
 *         firstLeftChar = leftRefSeq[-1]
 *         firstRightChar = rightRefSeq[0]             # <<<<<<<<<<<<<<
 * 
 *         for char in reversed(leftRefSeq):
 */
  __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_rightRefSeq, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 481, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_firstRightChar = __pyx_t_1;
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":483
 *         firstRightChar = rightRefSeq[0]
 * 
 *         for char in reversed(leftRefSeq):             # <<<<<<<<<<<<<<
 *             if char == firstLeftChar:
 *                 leftHpSize += 1
 */
  __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_reversed, __pyx_v_leftRefSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 483, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
    __pyx_t_7 = __pyx_t_1; __Pyx_INCREF(__pyx_t_7); __pyx_t_5 = 0;
    __pyx_t_8 = NULL;
  } else {
    __pyx_t_5 = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 483, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 483, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  for (;;) {
    if (likely(!__pyx_t_8)) {
      if (likely(PyList_CheckExact(__pyx_t_7))) {
        if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_7)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_1 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 483, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_7, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 483, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      } else {
        if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_7)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 483, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_7, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 483, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      }
    } else {
      __pyx_t_1 = __pyx_t_8(__pyx_t_7);
      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(0, 483, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_1);
    }
    __Pyx_XDECREF_SET(__pyx_v_char, __pyx_t_1);
    __pyx_t_1 = 0;

    /* "chaplotype.pyx":484
 * 
 *         for char in reversed(leftRefSeq):
 *             if char == firstLeftChar:             # <<<<<<<<<<<<<<
 *                 leftHpSize += 1
 *             else:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_char, __pyx_v_firstLeftChar, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 484, __pyx_L1_error)
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 484, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_4) {

      /* "chaplotype.pyx":485
 *         for char in reversed(leftRefSeq):
 *             if char == firstLeftChar:
 *                 leftHpSize += 1             # <<<<<<<<<<<<<<
 *             else:
 *                 break
 */
      __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_leftHpSize, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 485, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF_SET(__pyx_v_leftHpSize, __pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":484
 * 
 *         for char in reversed(leftRefSeq):
 *             if char == firstLeftChar:             # <<<<<<<<<<<<<<
 *                 leftHpSize += 1
 *             else:
 */
      goto __pyx_L8;
    }

    /* "chaplotype.pyx":487
 *                 leftHpSize += 1
 *             else:
 *                 break             # <<<<<<<<<<<<<<
 * 
 *         for char in rightRefSeq:
 */
    /*else*/ {
      goto __pyx_L7_break;
    }
    __pyx_L8:;

    /* "chaplotype.pyx":483
 *         firstRightChar = rightRefSeq[0]
 * 
 *         for char in reversed(leftRefSeq):             # <<<<<<<<<<<<<<
 *             if char == firstLeftChar:
 *                 leftHpSize += 1
 */
  }
  __pyx_L7_break:;
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

  /* "chaplotype.pyx":489
 *                 break
 * 
 *         for char in rightRefSeq:             # <<<<<<<<<<<<<<
 *             if char == firstRightChar:
 *                 rightHpSize += 1
 */
  __pyx_t_7 = PyObject_GetIter(__pyx_v_rightRefSeq); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 489, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 489, __pyx_L1_error)
  for (;;) {
    {
      __pyx_t_1 = __pyx_t_8(__pyx_t_7);
      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(0, 489, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_1);
    }
    __Pyx_XDECREF_SET(__pyx_v_char, __pyx_t_1);
    __pyx_t_1 = 0;

    /* "chaplotype.pyx":490
 * 
 *         for char in rightRefSeq:
 *             if char == firstRightChar:             # <<<<<<<<<<<<<<
 *                 rightHpSize += 1
 *             else:
 */
    __pyx_t_1 = PyObject_RichCompare(__pyx_v_char, __pyx_v_firstRightChar, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 490, __pyx_L1_error)
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 490, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (__pyx_t_4) {

      /* "chaplotype.pyx":491
 *         for char in rightRefSeq:
 *             if char == firstRightChar:
 *                 rightHpSize += 1             # <<<<<<<<<<<<<<
 *             else:
 *                 break
 */
      __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_rightHpSize, __pyx_int_1, 1, 1, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 491, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF_SET(__pyx_v_rightHpSize, __pyx_t_1);
      __pyx_t_1 = 0;

      /* "chaplotype.pyx":490
 * 
 *         for char in rightRefSeq:
 *             if char == firstRightChar:             # <<<<<<<<<<<<<<
 *                 rightHpSize += 1
 *             else:
 */
      goto __pyx_L11;
    }

    /* "chaplotype.pyx":493
 *                 rightHpSize += 1
 *             else:
 *                 break             # <<<<<<<<<<<<<<
 * 
 *         if firstLeftChar != firstRightChar:
 */
    /*else*/ {
      goto __pyx_L10_break;
    }
    __pyx_L11:;

    /* "chaplotype.pyx":489
 *                 break
 * 
 *         for char in rightRefSeq:             # <<<<<<<<<<<<<<
 *             if char == firstRightChar:
 *                 rightHpSize += 1
 */
  }
  __pyx_L10_break:;
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;

  /* "chaplotype.pyx":495
 *                 break
 * 
 *         if firstLeftChar != firstRightChar:             # <<<<<<<<<<<<<<
 *             return max(leftHpSize, rightHpSize)
 *         else:
 */
  __pyx_t_7 = PyObject_RichCompare(__pyx_v_firstLeftChar, __pyx_v_firstRightChar, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 495, __pyx_L1_error)
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 495, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  if (__pyx_t_4) {

    /* "chaplotype.pyx":496
 * 
 *         if firstLeftChar != firstRightChar:
 *             return max(leftHpSize, rightHpSize)             # <<<<<<<<<<<<<<
 *         else:
 *             return leftHpSize + rightHpSize
 */
    __Pyx_INCREF(__pyx_v_rightHpSize);
    __pyx_t_7 = __pyx_v_rightHpSize;
    __Pyx_INCREF(__pyx_v_leftHpSize);
    __pyx_t_1 = __pyx_v_leftHpSize;
    __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_t_1, Py_GT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 496, __pyx_L1_error)
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 496, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
    if (__pyx_t_4) {
      __Pyx_INCREF(__pyx_t_7);
      __pyx_t_9 = __pyx_t_7;
    } else {
      __Pyx_INCREF(__pyx_t_1);
      __pyx_t_9 = __pyx_t_1;
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __pyx_t_11 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 496, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    __pyx_r = __pyx_t_11;
    goto __pyx_L0;

    /* "chaplotype.pyx":495
 *                 break
 * 
 *         if firstLeftChar != firstRightChar:             # <<<<<<<<<<<<<<
 *             return max(leftHpSize, rightHpSize)
 *         else:
 */
  }

  /* "chaplotype.pyx":498
 *             return max(leftHpSize, rightHpSize)
 *         else:
 *             return leftHpSize + rightHpSize             # <<<<<<<<<<<<<<
 * 
 *     cdef bytes getSequenceContext(self, Variant variant):
 */
  /*else*/ {
    __pyx_t_9 = PyNumber_Add(__pyx_v_leftHpSize, __pyx_v_rightHpSize); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 498, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_9);
    __pyx_t_11 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 498, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    __pyx_r = __pyx_t_11;
    goto __pyx_L0;
  }

  /* "chaplotype.pyx":462
 *             return [ self.homopolymerLengthForOneVariant( v ) for v in vsf ]
 * 
 *     cdef int homopolymerLengthForOneVariant(self, Variant variant):             # <<<<<<<<<<<<<<
 *         """
 *         Calculate and return the length of the largest homopolymer
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.homopolymerLengthForOneVariant", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_varChrom);
  __Pyx_XDECREF(__pyx_v_varPos);
  __Pyx_XDECREF(__pyx_v_leftRefSeq);
  __Pyx_XDECREF(__pyx_v_rightRefSeq);
  __Pyx_XDECREF(__pyx_v_leftHpSize);
  __Pyx_XDECREF(__pyx_v_rightHpSize);
  __Pyx_XDECREF(__pyx_v_firstLeftChar);
  __Pyx_XDECREF(__pyx_v_firstRightChar);
  __Pyx_XDECREF(__pyx_v_char);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":500
 *             return leftHpSize + rightHpSize
 * 
 *     cdef bytes getSequenceContext(self, Variant variant):             # <<<<<<<<<<<<<<
 *         """
 *         Return the sequence surrounding this variant's position.
 */

static PyObject *__pyx_f_10chaplotype_9Haplotype_getSequenceContext(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, struct __pyx_obj_7variant_Variant *__pyx_v_variant) {
  PyObject *__pyx_v_varChrom = NULL;
  PyObject *__pyx_v_varPos = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PY_LONG_LONG __pyx_t_2;
  PY_LONG_LONG __pyx_t_3;
  __Pyx_RefNannySetupContext("getSequenceContext", 0);

  /* "chaplotype.pyx":504
 *         Return the sequence surrounding this variant's position.
 *         """
 *         varChrom = variant.refName             # <<<<<<<<<<<<<<
 *         varPos = variant.refPos
 *         return self.refFile.getSequence(varChrom, varPos-10, varPos + 11)
 */
  __pyx_t_1 = __pyx_v_variant->refName;
  __Pyx_INCREF(__pyx_t_1);
  __pyx_v_varChrom = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":505
 *         """
 *         varChrom = variant.refName
 *         varPos = variant.refPos             # <<<<<<<<<<<<<<
 *         return self.refFile.getSequence(varChrom, varPos-10, varPos + 11)
 * 
 */
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_variant->refPos); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 505, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_varPos = __pyx_t_1;
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":506
 *         varChrom = variant.refName
 *         varPos = variant.refPos
 *         return self.refFile.getSequence(varChrom, varPos-10, varPos + 11)             # <<<<<<<<<<<<<<
 * 
 *     cdef dict vcfINFO(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_v_varPos, __pyx_int_10, 10, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 506, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_1); if (unlikely((__pyx_t_2 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 506, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_varPos, __pyx_int_11, 11, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 506, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_PY_LONG_LONG(__pyx_t_1); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) __PYX_ERR(0, 506, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = ((struct __pyx_vtabstruct_9fastafile_FastaFile *)__pyx_v_self->refFile->__pyx_vtab)->getSequence(__pyx_v_self->refFile, __pyx_v_varChrom, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 506, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "chaplotype.pyx":500
 *             return leftHpSize + rightHpSize
 * 
 *     cdef bytes getSequenceContext(self, Variant variant):             # <<<<<<<<<<<<<<
 *         """
 *         Return the sequence surrounding this variant's position.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("chaplotype.Haplotype.getSequenceContext", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_varChrom);
  __Pyx_XDECREF(__pyx_v_varPos);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":508
 *         return self.refFile.getSequence(varChrom, varPos-10, varPos + 11)
 * 
 *     cdef dict vcfINFO(self):             # <<<<<<<<<<<<<<
 *         """
 *         Information to go in the vcf file INFO field - a two level dictionary of variant - field - value
 */

static PyObject *__pyx_f_10chaplotype_9Haplotype_vcfINFO(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  struct __pyx_obj_7variant_Variant *__pyx_v_variant = 0;
  PyObject *__pyx_v_INFO = 0;
  PyObject *__pyx_v_homopolymerLengths = NULL;
  PyObject *__pyx_v_vsf = NULL;
  PyObject *__pyx_v_varIndex = NULL;
  PyObject *__pyx_v_HP = NULL;
  PyObject *__pyx_v_SC = 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 = NULL;
  PyObject *__pyx_t_5 = NULL;
  __Pyx_RefNannySetupContext("vcfINFO", 0);

  /* "chaplotype.pyx":520
 *         """
 *         cdef Variant variant
 *         cdef dict INFO = {}             # <<<<<<<<<<<<<<
 * 
 *         homopolymerLengths = self.homopolymerLengths()
 */
  __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 520, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_INFO = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":522
 *         cdef dict INFO = {}
 * 
 *         homopolymerLengths = self.homopolymerLengths()             # <<<<<<<<<<<<<<
 *         vsf = self.variants
 * 
 */
  __pyx_t_1 = __pyx_f_10chaplotype_9Haplotype_homopolymerLengths(__pyx_v_self); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 522, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_homopolymerLengths = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":523
 * 
 *         homopolymerLengths = self.homopolymerLengths()
 *         vsf = self.variants             # <<<<<<<<<<<<<<
 * 
 *         for varIndex, variant in enumerate( self.variants ):
 */
  __pyx_t_1 = __pyx_v_self->variants;
  __Pyx_INCREF(__pyx_t_1);
  __pyx_v_vsf = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":525
 *         vsf = self.variants
 * 
 *         for varIndex, variant in enumerate( self.variants ):             # <<<<<<<<<<<<<<
 *             HP = homopolymerLengths[varIndex]
 *             SC = self.getSequenceContext(variant)
 */
  __Pyx_INCREF(__pyx_int_0);
  __pyx_t_1 = __pyx_int_0;
  __pyx_t_2 = __pyx_v_self->variants; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
  for (;;) {
    if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
    #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 525, __pyx_L1_error)
    #else
    __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 525, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    #endif
    if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_7variant_Variant))))) __PYX_ERR(0, 525, __pyx_L1_error)
    __Pyx_XDECREF_SET(__pyx_v_variant, ((struct __pyx_obj_7variant_Variant *)__pyx_t_4));
    __pyx_t_4 = 0;
    __Pyx_INCREF(__pyx_t_1);
    __Pyx_XDECREF_SET(__pyx_v_varIndex, __pyx_t_1);
    __pyx_t_4 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 525, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_1);
    __pyx_t_1 = __pyx_t_4;
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":526
 * 
 *         for varIndex, variant in enumerate( self.variants ):
 *             HP = homopolymerLengths[varIndex]             # <<<<<<<<<<<<<<
 *             SC = self.getSequenceContext(variant)
 * 
 */
    if (unlikely(__pyx_v_homopolymerLengths == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
      __PYX_ERR(0, 526, __pyx_L1_error)
    }
    __pyx_t_4 = __Pyx_PyObject_GetItem(__pyx_v_homopolymerLengths, __pyx_v_varIndex); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 526, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_XDECREF_SET(__pyx_v_HP, __pyx_t_4);
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":527
 *         for varIndex, variant in enumerate( self.variants ):
 *             HP = homopolymerLengths[varIndex]
 *             SC = self.getSequenceContext(variant)             # <<<<<<<<<<<<<<
 * 
 *             INFO[vsf[varIndex]] = {'HP':[HP], 'SC':[SC]}
 */
    __pyx_t_4 = __pyx_f_10chaplotype_9Haplotype_getSequenceContext(__pyx_v_self, __pyx_v_variant); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 527, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_XDECREF_SET(__pyx_v_SC, ((PyObject*)__pyx_t_4));
    __pyx_t_4 = 0;

    /* "chaplotype.pyx":529
 *             SC = self.getSequenceContext(variant)
 * 
 *             INFO[vsf[varIndex]] = {'HP':[HP], 'SC':[SC]}             # <<<<<<<<<<<<<<
 * 
 *         return INFO
 */
    __pyx_t_4 = __Pyx_PyDict_NewPresized(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_INCREF(__pyx_v_HP);
    __Pyx_GIVEREF(__pyx_v_HP);
    PyList_SET_ITEM(__pyx_t_5, 0, __pyx_v_HP);
    if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_HP, __pyx_t_5) < 0) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_INCREF(__pyx_v_SC);
    __Pyx_GIVEREF(__pyx_v_SC);
    PyList_SET_ITEM(__pyx_t_5, 0, __pyx_v_SC);
    if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_SC, __pyx_t_5) < 0) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (unlikely(__pyx_v_vsf == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
      __PYX_ERR(0, 529, __pyx_L1_error)
    }
    __pyx_t_5 = __Pyx_PyObject_GetItem(__pyx_v_vsf, __pyx_v_varIndex); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (unlikely(PyDict_SetItem(__pyx_v_INFO, __pyx_t_5, __pyx_t_4) < 0)) __PYX_ERR(0, 529, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

    /* "chaplotype.pyx":525
 *         vsf = self.variants
 * 
 *         for varIndex, variant in enumerate( self.variants ):             # <<<<<<<<<<<<<<
 *             HP = homopolymerLengths[varIndex]
 *             SC = self.getSequenceContext(variant)
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":531
 *             INFO[vsf[varIndex]] = {'HP':[HP], 'SC':[SC]}
 * 
 *         return INFO             # <<<<<<<<<<<<<<
 * 
 *     def __str__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_INFO);
  __pyx_r = __pyx_v_INFO;
  goto __pyx_L0;

  /* "chaplotype.pyx":508
 *         return self.refFile.getSequence(varChrom, varPos-10, varPos + 11)
 * 
 *     cdef dict vcfINFO(self):             # <<<<<<<<<<<<<<
 *         """
 *         Information to go in the vcf file INFO field - a two level dictionary of variant - field - value
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_AddTraceback("chaplotype.Haplotype.vcfINFO", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF((PyObject *)__pyx_v_variant);
  __Pyx_XDECREF(__pyx_v_INFO);
  __Pyx_XDECREF(__pyx_v_homopolymerLengths);
  __Pyx_XDECREF(__pyx_v_vsf);
  __Pyx_XDECREF(__pyx_v_varIndex);
  __Pyx_XDECREF(__pyx_v_HP);
  __Pyx_XDECREF(__pyx_v_SC);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":533
 *         return INFO
 * 
 *     def __str__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Generate a string representation of the haplotype. This is useful for
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_11__str__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_10chaplotype_9Haplotype_10__str__[] = "\n        Generate a string representation of the haplotype. This is useful for\n        debugging.\n        ";
#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_10chaplotype_9Haplotype_10__str__;
#endif
static PyObject *__pyx_pw_10chaplotype_9Haplotype_11__str__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype_10__str__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_10__str__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  PyObject *__pyx_v_vars = NULL;
  PyObject *__pyx_v_string = NULL;
  PyObject *__pyx_v_v = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  Py_ssize_t __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  __Pyx_RefNannySetupContext("__str__", 0);

  /* "chaplotype.pyx":538
 *         debugging.
 *         """
 *         if len(self.variants) == 0:             # <<<<<<<<<<<<<<
 *             return '  Haplotype(*Reference*) %s:%s-%s' %(self.refName, self.startPos, self.endPos)
 * 
 */
  __pyx_t_1 = __pyx_v_self->variants;
  __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(0, 538, __pyx_L1_error)
  }
  __pyx_t_2 = PyTuple_GET_SIZE(__pyx_t_1); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(0, 538, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_3 = ((__pyx_t_2 == 0) != 0);
  if (__pyx_t_3) {

    /* "chaplotype.pyx":539
 *         """
 *         if len(self.variants) == 0:
 *             return '  Haplotype(*Reference*) %s:%s-%s' %(self.refName, self.startPos, self.endPos)             # <<<<<<<<<<<<<<
 * 
 *         vars = [str(v) for v in self.variants]
 */
    __Pyx_XDECREF(__pyx_r);
    __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 539, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 539, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 539, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_INCREF(__pyx_v_self->refName);
    __Pyx_GIVEREF(__pyx_v_self->refName);
    PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_self->refName);
    __Pyx_GIVEREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_4);
    __pyx_t_1 = 0;
    __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Haplotype_Reference_s_s_s, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 539, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_r = __pyx_t_4;
    __pyx_t_4 = 0;
    goto __pyx_L0;

    /* "chaplotype.pyx":538
 *         debugging.
 *         """
 *         if len(self.variants) == 0:             # <<<<<<<<<<<<<<
 *             return '  Haplotype(*Reference*) %s:%s-%s' %(self.refName, self.startPos, self.endPos)
 * 
 */
  }

  /* "chaplotype.pyx":541
 *             return '  Haplotype(*Reference*) %s:%s-%s' %(self.refName, self.startPos, self.endPos)
 * 
 *         vars = [str(v) for v in self.variants]             # <<<<<<<<<<<<<<
 *         string = "  Haplotype(" + ",".join(vars) + ") %s:%s-%s" %(self.refName, self.startPos, self.endPos)
 * 
 */
  __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 541, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  if (unlikely(__pyx_v_self->variants == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
    __PYX_ERR(0, 541, __pyx_L1_error)
  }
  __pyx_t_5 = __pyx_v_self->variants; __Pyx_INCREF(__pyx_t_5); __pyx_t_2 = 0;
  for (;;) {
    if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
    #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(0, 541, __pyx_L1_error)
    #else
    __pyx_t_1 = PySequence_ITEM(__pyx_t_5, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 541, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    #endif
    __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_1);
    __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_v); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 541, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_1))) __PYX_ERR(0, 541, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __pyx_v_vars = ((PyObject*)__pyx_t_4);
  __pyx_t_4 = 0;

  /* "chaplotype.pyx":542
 * 
 *         vars = [str(v) for v in self.variants]
 *         string = "  Haplotype(" + ",".join(vars) + ") %s:%s-%s" %(self.refName, self.startPos, self.endPos)             # <<<<<<<<<<<<<<
 * 
 *         return string
 */
  __pyx_t_4 = __Pyx_PyString_Join(__pyx_kp_s__2, __pyx_v_vars); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_t_5 = PyNumber_Add(__pyx_kp_s_Haplotype, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->startPos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->endPos); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_INCREF(__pyx_v_self->refName);
  __Pyx_GIVEREF(__pyx_v_self->refName);
  PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self->refName);
  __Pyx_GIVEREF(__pyx_t_4);
  PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
  __Pyx_GIVEREF(__pyx_t_1);
  PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_1);
  __pyx_t_4 = 0;
  __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_s_s_s, __pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_6 = PyNumber_Add(__pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 542, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_string = ((PyObject*)__pyx_t_6);
  __pyx_t_6 = 0;

  /* "chaplotype.pyx":544
 *         string = "  Haplotype(" + ",".join(vars) + ") %s:%s-%s" %(self.refName, self.startPos, self.endPos)
 * 
 *         return string             # <<<<<<<<<<<<<<
 * 
 *     def __repr__(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_string);
  __pyx_r = __pyx_v_string;
  goto __pyx_L0;

  /* "chaplotype.pyx":533
 *         return INFO
 * 
 *     def __str__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Generate a string representation of the haplotype. This is useful for
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_AddTraceback("chaplotype.Haplotype.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_vars);
  __Pyx_XDECREF(__pyx_v_string);
  __Pyx_XDECREF(__pyx_v_v);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":546
 *         return string
 * 
 *     def __repr__(self):             # <<<<<<<<<<<<<<
 *         """
 *         The representation function. Called when printing the screen.
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_13__repr__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_10chaplotype_9Haplotype_12__repr__[] = "\n        The representation function. Called when printing the screen.\n        ";
#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_10chaplotype_9Haplotype_12__repr__;
#endif
static PyObject *__pyx_pw_10chaplotype_9Haplotype_13__repr__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__repr__ (wrapper)", 0);
  __pyx_r = __pyx_pf_10chaplotype_9Haplotype_12__repr__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_12__repr__(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  __Pyx_RefNannySetupContext("__repr__", 0);

  /* "chaplotype.pyx":550
 *         The representation function. Called when printing the screen.
 *         """
 *         return self.__str__()             # <<<<<<<<<<<<<<
 * 
 *     cdef void annotateWithGapOpen(self):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_str); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 550, __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(0, 550, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "chaplotype.pyx":546
 *         return string
 * 
 *     def __repr__(self):             # <<<<<<<<<<<<<<
 *         """
 *         The representation function. Called when printing the screen.
 */

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

/* "chaplotype.pyx":552
 *         return self.__str__()
 * 
 *     cdef void annotateWithGapOpen(self):             # <<<<<<<<<<<<<<
 *         """
 *         Annotate this haplotype with a context-specific gap open penalty, using the
 */

static void __pyx_f_10chaplotype_9Haplotype_annotateWithGapOpen(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  int __pyx_v_index;
  char *__pyx_v_seq;
  char *__pyx_v_errorModel;
  int __pyx_v_homopol;
  int __pyx_v_homopollen;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  char *__pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  __Pyx_RefNannySetupContext("annotateWithGapOpen", 0);

  /* "chaplotype.pyx":558
 *         """
 *         # Only do this one per haplotype
 *         if self.localGapOpen != NULL:             # <<<<<<<<<<<<<<
 *             return
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->localGapOpen != NULL) != 0);
  if (__pyx_t_1) {

    /* "chaplotype.pyx":559
 *         # Only do this one per haplotype
 *         if self.localGapOpen != NULL:
 *             return             # <<<<<<<<<<<<<<
 * 
 *         cdef int index = self.hapLen
 */
    goto __pyx_L0;

    /* "chaplotype.pyx":558
 *         """
 *         # Only do this one per haplotype
 *         if self.localGapOpen != NULL:             # <<<<<<<<<<<<<<
 *             return
 * 
 */
  }

  /* "chaplotype.pyx":561
 *             return
 * 
 *         cdef int index = self.hapLen             # <<<<<<<<<<<<<<
 *         cdef char* seq = self.cHaplotypeSequence
 *         cdef char* errorModel = self.cHomopolQ
 */
  __pyx_t_2 = __pyx_v_self->hapLen;
  __pyx_v_index = __pyx_t_2;

  /* "chaplotype.pyx":562
 * 
 *         cdef int index = self.hapLen
 *         cdef char* seq = self.cHaplotypeSequence             # <<<<<<<<<<<<<<
 *         cdef char* errorModel = self.cHomopolQ
 *         cdef int homopol = -1
 */
  __pyx_t_3 = __pyx_v_self->cHaplotypeSequence;
  __pyx_v_seq = __pyx_t_3;

  /* "chaplotype.pyx":563
 *         cdef int index = self.hapLen
 *         cdef char* seq = self.cHaplotypeSequence
 *         cdef char* errorModel = self.cHomopolQ             # <<<<<<<<<<<<<<
 *         cdef int homopol = -1
 *         cdef int homopollen = 0
 */
  __pyx_t_3 = __pyx_v_self->cHomopolQ;
  __pyx_v_errorModel = __pyx_t_3;

  /* "chaplotype.pyx":564
 *         cdef char* seq = self.cHaplotypeSequence
 *         cdef char* errorModel = self.cHomopolQ
 *         cdef int homopol = -1             # <<<<<<<<<<<<<<
 *         cdef int homopollen = 0
 * 
 */
  __pyx_v_homopol = -1;

  /* "chaplotype.pyx":565
 *         cdef char* errorModel = self.cHomopolQ
 *         cdef int homopol = -1
 *         cdef int homopollen = 0             # <<<<<<<<<<<<<<
 * 
 *         self.localGapOpen = <char*>(malloc((self.hapLen+1)*sizeof(char)))
 */
  __pyx_v_homopollen = 0;

  /* "chaplotype.pyx":567
 *         cdef int homopollen = 0
 * 
 *         self.localGapOpen = <char*>(malloc((self.hapLen+1)*sizeof(char)))             # <<<<<<<<<<<<<<
 * 
 *         # compute local gap open penalties by applying a homopolymer model
 */
  __pyx_v_self->localGapOpen = ((char *)malloc(((__pyx_v_self->hapLen + 1) * (sizeof(char)))));

  /* "chaplotype.pyx":572
 *         # Fill in from the back to help left-justify indels (though this is prob. unnecessary)
 * 
 *         self.localGapOpen[index] = 0             # <<<<<<<<<<<<<<
 * 
 *         while index > 0:
 */
  (__pyx_v_self->localGapOpen[__pyx_v_index]) = 0;

  /* "chaplotype.pyx":574
 *         self.localGapOpen[index] = 0
 * 
 *         while index > 0:             # <<<<<<<<<<<<<<
 *             index -= 1
 * 
 */
  while (1) {
    __pyx_t_1 = ((__pyx_v_index > 0) != 0);
    if (!__pyx_t_1) break;

    /* "chaplotype.pyx":575
 * 
 *         while index > 0:
 *             index -= 1             # <<<<<<<<<<<<<<
 * 
 *             if seq[index] == homopol:
 */
    __pyx_v_index = (__pyx_v_index - 1);

    /* "chaplotype.pyx":577
 *             index -= 1
 * 
 *             if seq[index] == homopol:             # <<<<<<<<<<<<<<
 *                 if errorModel[homopollen+1] != 0:
 *                     homopollen += 1
 */
    __pyx_t_1 = (((__pyx_v_seq[__pyx_v_index]) == __pyx_v_homopol) != 0);
    if (__pyx_t_1) {

      /* "chaplotype.pyx":578
 * 
 *             if seq[index] == homopol:
 *                 if errorModel[homopollen+1] != 0:             # <<<<<<<<<<<<<<
 *                     homopollen += 1
 *             else:
 */
      __pyx_t_1 = (((__pyx_v_errorModel[(__pyx_v_homopollen + 1)]) != 0) != 0);
      if (__pyx_t_1) {

        /* "chaplotype.pyx":579
 *             if seq[index] == homopol:
 *                 if errorModel[homopollen+1] != 0:
 *                     homopollen += 1             # <<<<<<<<<<<<<<
 *             else:
 *                 homopollen = 0
 */
        __pyx_v_homopollen = (__pyx_v_homopollen + 1);

        /* "chaplotype.pyx":578
 * 
 *             if seq[index] == homopol:
 *                 if errorModel[homopollen+1] != 0:             # <<<<<<<<<<<<<<
 *                     homopollen += 1
 *             else:
 */
      }

      /* "chaplotype.pyx":577
 *             index -= 1
 * 
 *             if seq[index] == homopol:             # <<<<<<<<<<<<<<
 *                 if errorModel[homopollen+1] != 0:
 *                     homopollen += 1
 */
      goto __pyx_L6;
    }

    /* "chaplotype.pyx":581
 *                     homopollen += 1
 *             else:
 *                 homopollen = 0             # <<<<<<<<<<<<<<
 * 
 *             self.localGapOpen[index] = <char>( <int>(errorModel[homopollen]) - (<int>'!') )
 */
    /*else*/ {
      __pyx_v_homopollen = 0;
    }
    __pyx_L6:;

    /* "chaplotype.pyx":583
 *                 homopollen = 0
 * 
 *             self.localGapOpen[index] = <char>( <int>(errorModel[homopollen]) - (<int>'!') )             # <<<<<<<<<<<<<<
 * 
 *             if self.localGapOpen[index] < 0:
 */
    (__pyx_v_self->localGapOpen[__pyx_v_index]) = ((char)(((int)(__pyx_v_errorModel[__pyx_v_homopollen])) - ((int)'!')));

    /* "chaplotype.pyx":585
 *             self.localGapOpen[index] = <char>( <int>(errorModel[homopollen]) - (<int>'!') )
 * 
 *             if self.localGapOpen[index] < 0:             # <<<<<<<<<<<<<<
 *                 raise ValueError("Internal error: encountered negative gap open score (%s, at position %s)" % (self.localGapOpen[index], index))
 * 
 */
    __pyx_t_1 = (((__pyx_v_self->localGapOpen[__pyx_v_index]) < 0) != 0);
    if (unlikely(__pyx_t_1)) {

      /* "chaplotype.pyx":586
 * 
 *             if self.localGapOpen[index] < 0:
 *                 raise ValueError("Internal error: encountered negative gap open score (%s, at position %s)" % (self.localGapOpen[index], index))             # <<<<<<<<<<<<<<
 * 
 *             homopol = seq[index];
 */
      __pyx_t_4 = __Pyx_PyInt_From_char((__pyx_v_self->localGapOpen[__pyx_v_index])); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 586, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_index); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 586, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 586, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_GIVEREF(__pyx_t_4);
      PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
      __Pyx_GIVEREF(__pyx_t_5);
      PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
      __pyx_t_4 = 0;
      __pyx_t_5 = 0;
      __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_Internal_error_encountered_negat, __pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 586, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 586, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      __Pyx_Raise(__pyx_t_6, 0, 0, 0);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __PYX_ERR(0, 586, __pyx_L1_error)

      /* "chaplotype.pyx":585
 *             self.localGapOpen[index] = <char>( <int>(errorModel[homopollen]) - (<int>'!') )
 * 
 *             if self.localGapOpen[index] < 0:             # <<<<<<<<<<<<<<
 *                 raise ValueError("Internal error: encountered negative gap open score (%s, at position %s)" % (self.localGapOpen[index], index))
 * 
 */
    }

    /* "chaplotype.pyx":588
 *                 raise ValueError("Internal error: encountered negative gap open score (%s, at position %s)" % (self.localGapOpen[index], index))
 * 
 *             homopol = seq[index];             # <<<<<<<<<<<<<<
 *             if homopol == 'N':
 *                 homopol = 0
 */
    __pyx_v_homopol = (__pyx_v_seq[__pyx_v_index]);

    /* "chaplotype.pyx":589
 * 
 *             homopol = seq[index];
 *             if homopol == 'N':             # <<<<<<<<<<<<<<
 *                 homopol = 0
 * 
 */
    __pyx_t_1 = ((__pyx_v_homopol == 'N') != 0);
    if (__pyx_t_1) {

      /* "chaplotype.pyx":590
 *             homopol = seq[index];
 *             if homopol == 'N':
 *                 homopol = 0             # <<<<<<<<<<<<<<
 * 
 * ##################################################################################################
 */
      __pyx_v_homopol = 0;

      /* "chaplotype.pyx":589
 * 
 *             homopol = seq[index];
 *             if homopol == 'N':             # <<<<<<<<<<<<<<
 *                 homopol = 0
 * 
 */
    }
  }

  /* "chaplotype.pyx":552
 *         return self.__str__()
 * 
 *     cdef void annotateWithGapOpen(self):             # <<<<<<<<<<<<<<
 *         """
 *         Annotate this haplotype with a context-specific gap open penalty, using the
 */

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_WriteUnraisable("chaplotype.Haplotype.annotateWithGapOpen", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_15__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_10chaplotype_9Haplotype_15__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_10chaplotype_9Haplotype_14__reduce_cython__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_14__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 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(1, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("chaplotype.Haplotype.__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("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 */

/* Python wrapper */
static PyObject *__pyx_pw_10chaplotype_9Haplotype_17__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_10chaplotype_9Haplotype_17__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_10chaplotype_9Haplotype_16__setstate_cython__(((struct __pyx_obj_10chaplotype_Haplotype *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

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

static PyObject *__pyx_pf_10chaplotype_9Haplotype_16__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 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(1, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 */

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

/* "chaplotype.pyx":594
 * ##################################################################################################
 * 
 * cdef double alignReadToHaplotype(cAlignedRead* read, Haplotype hap, int useMapQualCap, int calculateFlankScore):             # <<<<<<<<<<<<<<
 *     """
 *     This is the basic, banded-alignment routine that forms the heart of Platypus. This function decides where to anchor the
 */

static double __pyx_f_10chaplotype_alignReadToHaplotype(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_hap, int __pyx_v_useMapQualCap, int __pyx_v_calculateFlankScore) {
  char *__pyx_v_hapSeq;
  CYTHON_UNUSED char *__pyx_v_aln1;
  CYTHON_UNUSED char *__pyx_v_aln2;
  CYTHON_UNUSED char *__pyx_v_errorModel;
  int __pyx_v_hapStart;
  int __pyx_v_gapExtend;
  int __pyx_v_nucprior;
  int __pyx_v_hapLen;
  int __pyx_v_hapFlank;
  char *__pyx_v_readSeq;
  char *__pyx_v_readQuals;
  int __pyx_v_readStart;
  int __pyx_v_readLen;
  CYTHON_UNUSED int __pyx_v_mapQual;
  int __pyx_v_alignScore;
  double __pyx_v_probMapWrong;
  double __pyx_v_probMapRight;
  int __pyx_v_offset1;
  int __pyx_v_offset2;
  double __pyx_v_likelihoodCap;
  double __pyx_v_alignScoreThreshold;
  double __pyx_v_shapeParameter;
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  int __pyx_t_2;
  short __pyx_t_3;
  unsigned char __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  PyObject *__pyx_t_10 = NULL;
  PyObject *__pyx_t_11 = NULL;
  PyObject *__pyx_t_12 = NULL;
  PyObject *__pyx_t_13 = NULL;
  PyObject *__pyx_t_14 = NULL;
  double __pyx_t_15;
  double __pyx_t_16;
  double __pyx_t_17;
  __Pyx_RefNannySetupContext("alignReadToHaplotype", 0);

  /* "chaplotype.pyx":602
 *     will be rubbish.
 *     """
 *     cdef char* hapSeq = hap.cHaplotypeSequence             # <<<<<<<<<<<<<<
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL
 */
  __pyx_t_1 = __pyx_v_hap->cHaplotypeSequence;
  __pyx_v_hapSeq = __pyx_t_1;

  /* "chaplotype.pyx":603
 *     """
 *     cdef char* hapSeq = hap.cHaplotypeSequence
 *     cdef char* aln1 = NULL             # <<<<<<<<<<<<<<
 *     cdef char* aln2 = NULL
 *     cdef char* errorModel = NULL
 */
  __pyx_v_aln1 = NULL;

  /* "chaplotype.pyx":604
 *     cdef char* hapSeq = hap.cHaplotypeSequence
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL             # <<<<<<<<<<<<<<
 *     cdef char* errorModel = NULL
 *     cdef int hapStart = hap.startPos - hap.endBufferSize
 */
  __pyx_v_aln2 = NULL;

  /* "chaplotype.pyx":605
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL
 *     cdef char* errorModel = NULL             # <<<<<<<<<<<<<<
 *     cdef int hapStart = hap.startPos - hap.endBufferSize
 *     cdef int gapExtend = 3
 */
  __pyx_v_errorModel = NULL;

  /* "chaplotype.pyx":606
 *     cdef char* aln2 = NULL
 *     cdef char* errorModel = NULL
 *     cdef int hapStart = hap.startPos - hap.endBufferSize             # <<<<<<<<<<<<<<
 *     cdef int gapExtend = 3
 *     cdef int nucprior = 2
 */
  __pyx_v_hapStart = (__pyx_v_hap->startPos - __pyx_v_hap->endBufferSize);

  /* "chaplotype.pyx":607
 *     cdef char* errorModel = NULL
 *     cdef int hapStart = hap.startPos - hap.endBufferSize
 *     cdef int gapExtend = 3             # <<<<<<<<<<<<<<
 *     cdef int nucprior = 2
 *     cdef int hapLen = hap.hapLen
 */
  __pyx_v_gapExtend = 3;

  /* "chaplotype.pyx":608
 *     cdef int hapStart = hap.startPos - hap.endBufferSize
 *     cdef int gapExtend = 3
 *     cdef int nucprior = 2             # <<<<<<<<<<<<<<
 *     cdef int hapLen = hap.hapLen
 *     cdef int hapFlank = hap.endBufferSize    # ignore contribution to score by mismatches in flank.  Set to 0 to include all mismatches
 */
  __pyx_v_nucprior = 2;

  /* "chaplotype.pyx":609
 *     cdef int gapExtend = 3
 *     cdef int nucprior = 2
 *     cdef int hapLen = hap.hapLen             # <<<<<<<<<<<<<<
 *     cdef int hapFlank = hap.endBufferSize    # ignore contribution to score by mismatches in flank.  Set to 0 to include all mismatches
 * 
 */
  __pyx_t_2 = __pyx_v_hap->hapLen;
  __pyx_v_hapLen = __pyx_t_2;

  /* "chaplotype.pyx":610
 *     cdef int nucprior = 2
 *     cdef int hapLen = hap.hapLen
 *     cdef int hapFlank = hap.endBufferSize    # ignore contribution to score by mismatches in flank.  Set to 0 to include all mismatches             # <<<<<<<<<<<<<<
 * 
 *     cdef char* readSeq = read.seq
 */
  __pyx_t_2 = __pyx_v_hap->endBufferSize;
  __pyx_v_hapFlank = __pyx_t_2;

  /* "chaplotype.pyx":612
 *     cdef int hapFlank = hap.endBufferSize    # ignore contribution to score by mismatches in flank.  Set to 0 to include all mismatches
 * 
 *     cdef char* readSeq = read.seq             # <<<<<<<<<<<<<<
 *     cdef char* readQuals = read.qual
 * 
 */
  __pyx_t_1 = __pyx_v_read->seq;
  __pyx_v_readSeq = __pyx_t_1;

  /* "chaplotype.pyx":613
 * 
 *     cdef char* readSeq = read.seq
 *     cdef char* readQuals = read.qual             # <<<<<<<<<<<<<<
 * 
 *     cdef int readStart = read.pos
 */
  __pyx_t_1 = __pyx_v_read->qual;
  __pyx_v_readQuals = __pyx_t_1;

  /* "chaplotype.pyx":615
 *     cdef char* readQuals = read.qual
 * 
 *     cdef int readStart = read.pos             # <<<<<<<<<<<<<<
 *     cdef int readLen = read.rlen
 *     cdef int mapQual = read.mapq
 */
  __pyx_t_2 = __pyx_v_read->pos;
  __pyx_v_readStart = __pyx_t_2;

  /* "chaplotype.pyx":616
 * 
 *     cdef int readStart = read.pos
 *     cdef int readLen = read.rlen             # <<<<<<<<<<<<<<
 *     cdef int mapQual = read.mapq
 * 
 */
  __pyx_t_3 = __pyx_v_read->rlen;
  __pyx_v_readLen = __pyx_t_3;

  /* "chaplotype.pyx":617
 *     cdef int readStart = read.pos
 *     cdef int readLen = read.rlen
 *     cdef int mapQual = read.mapq             # <<<<<<<<<<<<<<
 * 
 *     cdef int alignScore = 0
 */
  __pyx_t_4 = __pyx_v_read->mapq;
  __pyx_v_mapQual = __pyx_t_4;

  /* "chaplotype.pyx":619
 *     cdef int mapQual = read.mapq
 * 
 *     cdef int alignScore = 0             # <<<<<<<<<<<<<<
 * 
 *     cdef double probMapWrong = mLTOT*read.mapq  # A log value
 */
  __pyx_v_alignScore = 0;

  /* "chaplotype.pyx":621
 *     cdef int alignScore = 0
 * 
 *     cdef double probMapWrong = mLTOT*read.mapq  # A log value             # <<<<<<<<<<<<<<
 *     cdef double probMapRight = log(1.0 - exp(mLTOT*read.mapq)) # A log value
 * 
 */
  __pyx_v_probMapWrong = (__pyx_v_10chaplotype_mLTOT * __pyx_v_read->mapq);

  /* "chaplotype.pyx":622
 * 
 *     cdef double probMapWrong = mLTOT*read.mapq  # A log value
 *     cdef double probMapRight = log(1.0 - exp(mLTOT*read.mapq)) # A log value             # <<<<<<<<<<<<<<
 * 
 *     cdef int offset1 = 0
 */
  __pyx_v_probMapRight = log((1.0 - exp((__pyx_v_10chaplotype_mLTOT * __pyx_v_read->mapq))));

  /* "chaplotype.pyx":624
 *     cdef double probMapRight = log(1.0 - exp(mLTOT*read.mapq)) # A log value
 * 
 *     cdef int offset1 = 0             # <<<<<<<<<<<<<<
 *     cdef int offset2 = 0
 * 
 */
  __pyx_v_offset1 = 0;

  /* "chaplotype.pyx":625
 * 
 *     cdef int offset1 = 0
 *     cdef int offset2 = 0             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_v_offset2 = 0;

  /* "chaplotype.pyx":629
 * 
 *     # Arbitrary cap
 *     cdef double likelihoodCap = 0.0             # <<<<<<<<<<<<<<
 * 
 *     if useMapQualCap == True:
 */
  __pyx_v_likelihoodCap = 0.0;

  /* "chaplotype.pyx":631
 *     cdef double likelihoodCap = 0.0
 * 
 *     if useMapQualCap == True:             # <<<<<<<<<<<<<<
 *         likelihoodCap = probMapWrong
 *     else:
 */
  __pyx_t_5 = ((__pyx_v_useMapQualCap == 1) != 0);
  if (__pyx_t_5) {

    /* "chaplotype.pyx":632
 * 
 *     if useMapQualCap == True:
 *         likelihoodCap = probMapWrong             # <<<<<<<<<<<<<<
 *     else:
 *         likelihoodCap = -300 # Arbitrary cap close to min float value
 */
    __pyx_v_likelihoodCap = __pyx_v_probMapWrong;

    /* "chaplotype.pyx":631
 *     cdef double likelihoodCap = 0.0
 * 
 *     if useMapQualCap == True:             # <<<<<<<<<<<<<<
 *         likelihoodCap = probMapWrong
 *     else:
 */
    goto __pyx_L3;
  }

  /* "chaplotype.pyx":634
 *         likelihoodCap = probMapWrong
 *     else:
 *         likelihoodCap = -300 # Arbitrary cap close to min float value             # <<<<<<<<<<<<<<
 * 
 *     # Make sure read hash exists when needed
 */
  /*else*/ {
    __pyx_v_likelihoodCap = -300.0;
  }
  __pyx_L3:;

  /* "chaplotype.pyx":637
 * 
 *     # Make sure read hash exists when needed
 *     if read.hash == NULL:             # <<<<<<<<<<<<<<
 *         hashReadForMapping(read)
 * 
 */
  __pyx_t_5 = ((__pyx_v_read->hash == NULL) != 0);
  if (__pyx_t_5) {

    /* "chaplotype.pyx":638
 *     # Make sure read hash exists when needed
 *     if read.hash == NULL:
 *         hashReadForMapping(read)             # <<<<<<<<<<<<<<
 * 
 *     # Make sure haplotype hash exists when needed
 */
    __pyx_f_6calign_hashReadForMapping(__pyx_v_read);

    /* "chaplotype.pyx":637
 * 
 *     # Make sure read hash exists when needed
 *     if read.hash == NULL:             # <<<<<<<<<<<<<<
 *         hashReadForMapping(read)
 * 
 */
  }

  /* "chaplotype.pyx":641
 * 
 *     # Make sure haplotype hash exists when needed
 *     if hap.hapSequenceHash == NULL:             # <<<<<<<<<<<<<<
 *         hash_sequence_multihit(hap.cHaplotypeSequence, hap.hapLen, &hap.hapSequenceHash, &hap.hapSequenceNextArray)
 * 
 */
  __pyx_t_5 = ((__pyx_v_hap->hapSequenceHash == NULL) != 0);
  if (__pyx_t_5) {

    /* "chaplotype.pyx":642
 *     # Make sure haplotype hash exists when needed
 *     if hap.hapSequenceHash == NULL:
 *         hash_sequence_multihit(hap.cHaplotypeSequence, hap.hapLen, &hap.hapSequenceHash, &hap.hapSequenceNextArray)             # <<<<<<<<<<<<<<
 * 
 *     if hap.localGapOpen == NULL:
 */
    __pyx_f_6calign_hash_sequence_multihit(__pyx_v_hap->cHaplotypeSequence, __pyx_v_hap->hapLen, (&__pyx_v_hap->hapSequenceHash), (&__pyx_v_hap->hapSequenceNextArray));

    /* "chaplotype.pyx":641
 * 
 *     # Make sure haplotype hash exists when needed
 *     if hap.hapSequenceHash == NULL:             # <<<<<<<<<<<<<<
 *         hash_sequence_multihit(hap.cHaplotypeSequence, hap.hapLen, &hap.hapSequenceHash, &hap.hapSequenceNextArray)
 * 
 */
  }

  /* "chaplotype.pyx":644
 *         hash_sequence_multihit(hap.cHaplotypeSequence, hap.hapLen, &hap.hapSequenceHash, &hap.hapSequenceNextArray)
 * 
 *     if hap.localGapOpen == NULL:             # <<<<<<<<<<<<<<
 *         hap.annotateWithGapOpen()
 * 
 */
  __pyx_t_5 = ((__pyx_v_hap->localGapOpen == NULL) != 0);
  if (__pyx_t_5) {

    /* "chaplotype.pyx":645
 * 
 *     if hap.localGapOpen == NULL:
 *         hap.annotateWithGapOpen()             # <<<<<<<<<<<<<<
 * 
 *     if useMapQualCap:
 */
    __pyx_f_10chaplotype_9Haplotype_annotateWithGapOpen(__pyx_v_hap);

    /* "chaplotype.pyx":644
 *         hash_sequence_multihit(hap.cHaplotypeSequence, hap.hapLen, &hap.hapSequenceHash, &hap.hapSequenceNextArray)
 * 
 *     if hap.localGapOpen == NULL:             # <<<<<<<<<<<<<<
 *         hap.annotateWithGapOpen()
 * 
 */
  }

  /* "chaplotype.pyx":647
 *         hap.annotateWithGapOpen()
 * 
 *     if useMapQualCap:             # <<<<<<<<<<<<<<
 *         offset1 = hapStart - readStart
 *         offset2 = readStart + readLen - hap.startPos - hapLen
 */
  __pyx_t_5 = (__pyx_v_useMapQualCap != 0);
  if (__pyx_t_5) {

    /* "chaplotype.pyx":648
 * 
 *     if useMapQualCap:
 *         offset1 = hapStart - readStart             # <<<<<<<<<<<<<<
 *         offset2 = readStart + readLen - hap.startPos - hapLen
 *         if offset1 <0: offset1 = 0
 */
    __pyx_v_offset1 = (__pyx_v_hapStart - __pyx_v_readStart);

    /* "chaplotype.pyx":649
 *     if useMapQualCap:
 *         offset1 = hapStart - readStart
 *         offset2 = readStart + readLen - hap.startPos - hapLen             # <<<<<<<<<<<<<<
 *         if offset1 <0: offset1 = 0
 *         if offset2 <0: offset2 = 0
 */
    __pyx_v_offset2 = (((__pyx_v_readStart + __pyx_v_readLen) - __pyx_v_hap->startPos) - __pyx_v_hapLen);

    /* "chaplotype.pyx":650
 *         offset1 = hapStart - readStart
 *         offset2 = readStart + readLen - hap.startPos - hapLen
 *         if offset1 <0: offset1 = 0             # <<<<<<<<<<<<<<
 *         if offset2 <0: offset2 = 0
 *         readStart = readStart + offset1
 */
    __pyx_t_5 = ((__pyx_v_offset1 < 0) != 0);
    if (__pyx_t_5) {
      __pyx_v_offset1 = 0;
    }

    /* "chaplotype.pyx":651
 *         offset2 = readStart + readLen - hap.startPos - hapLen
 *         if offset1 <0: offset1 = 0
 *         if offset2 <0: offset2 = 0             # <<<<<<<<<<<<<<
 *         readStart = readStart + offset1
 *         readLen = readLen - offset1 - offset2
 */
    __pyx_t_5 = ((__pyx_v_offset2 < 0) != 0);
    if (__pyx_t_5) {
      __pyx_v_offset2 = 0;
    }

    /* "chaplotype.pyx":652
 *         if offset1 <0: offset1 = 0
 *         if offset2 <0: offset2 = 0
 *         readStart = readStart + offset1             # <<<<<<<<<<<<<<
 *         readLen = readLen - offset1 - offset2
 *         readSeq   += offset1
 */
    __pyx_v_readStart = (__pyx_v_readStart + __pyx_v_offset1);

    /* "chaplotype.pyx":653
 *         if offset2 <0: offset2 = 0
 *         readStart = readStart + offset1
 *         readLen = readLen - offset1 - offset2             # <<<<<<<<<<<<<<
 *         readSeq   += offset1
 *         readQuals += offset1
 */
    __pyx_v_readLen = ((__pyx_v_readLen - __pyx_v_offset1) - __pyx_v_offset2);

    /* "chaplotype.pyx":654
 *         readStart = readStart + offset1
 *         readLen = readLen - offset1 - offset2
 *         readSeq   += offset1             # <<<<<<<<<<<<<<
 *         readQuals += offset1
 *         #logger.debug("alignReads: i have updated readStart etc by offsets %s and %s" % (offset1, offset2))
 */
    __pyx_v_readSeq = (__pyx_v_readSeq + __pyx_v_offset1);

    /* "chaplotype.pyx":655
 *         readLen = readLen - offset1 - offset2
 *         readSeq   += offset1
 *         readQuals += offset1             # <<<<<<<<<<<<<<
 *         #logger.debug("alignReads: i have updated readStart etc by offsets %s and %s" % (offset1, offset2))
 * 
 */
    __pyx_v_readQuals = (__pyx_v_readQuals + __pyx_v_offset1);

    /* "chaplotype.pyx":647
 *         hap.annotateWithGapOpen()
 * 
 *     if useMapQualCap:             # <<<<<<<<<<<<<<
 *         offset1 = hapStart - readStart
 *         offset2 = readStart + readLen - hap.startPos - hapLen
 */
  }

  /* "chaplotype.pyx":660
 *     #logger.debug("alignReads: calling mapAndAlignReadToHaplotype with readseq start/len==%s %s hap start/len = %s %s  flank=%s" % (readStart,readLen,hapStart,hapLen,hapFlank))
 * 
 *     alignScore = mapAndAlignReadToHaplotype(readSeq, readQuals, readStart, hapStart, readLen, hapLen,             # <<<<<<<<<<<<<<
 *                                             hap.hapSequenceHash, hap.hapSequenceNextArray, read.hash, hapSeq,
 *                                             gapExtend, nucprior, hap.localGapOpen,
 */
  __pyx_v_alignScore = __pyx_f_6calign_mapAndAlignReadToHaplotype(__pyx_v_readSeq, __pyx_v_readQuals, __pyx_v_readStart, __pyx_v_hapStart, __pyx_v_readLen, __pyx_v_hapLen, __pyx_v_hap->hapSequenceHash, __pyx_v_hap->hapSequenceNextArray, __pyx_v_read->hash, __pyx_v_hapSeq, __pyx_v_gapExtend, __pyx_v_nucprior, __pyx_v_hap->localGapOpen, __pyx_v_hap->mapCounts, __pyx_v_hap->mapCountsLen, __pyx_v_hapFlank, __pyx_v_calculateFlankScore);

  /* "chaplotype.pyx":668
 *     # Hang added this to deal with HLA.  The idea is to cap the alignment score but in a smooth way.
 *     # (GL: modified to make the graph differentiable at the threshold, and to allow altering the shape with a single parameter)
 *     cdef double alignScoreThreshold = 100             # <<<<<<<<<<<<<<
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 */
  __pyx_v_alignScoreThreshold = 100.0;

  /* "chaplotype.pyx":669
 *     # (GL: modified to make the graph differentiable at the threshold, and to allow altering the shape with a single parameter)
 *     cdef double alignScoreThreshold = 100
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation             # <<<<<<<<<<<<<<
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,
 */
  __pyx_v_shapeParameter = 0.5;

  /* "chaplotype.pyx":670
 *     cdef double alignScoreThreshold = 100
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation
 *     if useMapQualCap and alignScore > alignScoreThreshold:             # <<<<<<<<<<<<<<
 *         return max( likelihoodCap,
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )
 */
  __pyx_t_6 = (__pyx_v_useMapQualCap != 0);
  if (__pyx_t_6) {
  } else {
    __pyx_t_5 = __pyx_t_6;
    goto __pyx_L11_bool_binop_done;
  }
  __pyx_t_6 = ((__pyx_v_alignScore > __pyx_v_alignScoreThreshold) != 0);
  __pyx_t_5 = __pyx_t_6;
  __pyx_L11_bool_binop_done:;
  if (__pyx_t_5) {

    /* "chaplotype.pyx":672
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )             # <<<<<<<<<<<<<<
 * 
 *     # standard case
 */
    __pyx_t_7 = PyFloat_FromDouble(__pyx_v_10chaplotype_mLTOT); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_8 = PyFloat_FromDouble((__pyx_v_alignScoreThreshold - 1.0)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_8);
    __Pyx_GetModuleGlobalName(__pyx_t_10, __pyx_n_s_math); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_10);
    __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_10, __pyx_n_s_pow); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_11);
    __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
    __pyx_t_10 = PyFloat_FromDouble(((__pyx_v_alignScore - __pyx_v_alignScoreThreshold) + 1.0)); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_10);
    __pyx_t_12 = PyFloat_FromDouble(__pyx_v_shapeParameter); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_12);
    __pyx_t_13 = NULL;
    __pyx_t_2 = 0;
    if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_11))) {
      __pyx_t_13 = PyMethod_GET_SELF(__pyx_t_11);
      if (likely(__pyx_t_13)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
        __Pyx_INCREF(__pyx_t_13);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_11, function);
        __pyx_t_2 = 1;
      }
    }
    #if CYTHON_FAST_PYCALL
    if (PyFunction_Check(__pyx_t_11)) {
      PyObject *__pyx_temp[3] = {__pyx_t_13, __pyx_t_10, __pyx_t_12};
      __pyx_t_9 = __Pyx_PyFunction_FastCall(__pyx_t_11, __pyx_temp+1-__pyx_t_2, 2+__pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 672, __pyx_L1_error)
      __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
      __Pyx_GOTREF(__pyx_t_9);
      __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
      __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
    } else
    #endif
    #if CYTHON_FAST_PYCCALL
    if (__Pyx_PyFastCFunction_Check(__pyx_t_11)) {
      PyObject *__pyx_temp[3] = {__pyx_t_13, __pyx_t_10, __pyx_t_12};
      __pyx_t_9 = __Pyx_PyCFunction_FastCall(__pyx_t_11, __pyx_temp+1-__pyx_t_2, 2+__pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 672, __pyx_L1_error)
      __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
      __Pyx_GOTREF(__pyx_t_9);
      __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
      __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
    } else
    #endif
    {
      __pyx_t_14 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 672, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_14);
      if (__pyx_t_13) {
        __Pyx_GIVEREF(__pyx_t_13); PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_13); __pyx_t_13 = NULL;
      }
      __Pyx_GIVEREF(__pyx_t_10);
      PyTuple_SET_ITEM(__pyx_t_14, 0+__pyx_t_2, __pyx_t_10);
      __Pyx_GIVEREF(__pyx_t_12);
      PyTuple_SET_ITEM(__pyx_t_14, 1+__pyx_t_2, __pyx_t_12);
      __pyx_t_10 = 0;
      __pyx_t_12 = 0;
      __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_14, NULL); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 672, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_9);
      __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    }
    __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
    __pyx_t_11 = PyFloat_FromDouble(__pyx_v_shapeParameter); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_11);
    __pyx_t_14 = __Pyx_PyNumber_Divide(__pyx_t_9, __pyx_t_11); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
    __pyx_t_11 = PyNumber_Add(__pyx_t_8, __pyx_t_14); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_11);
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
    __pyx_t_14 = PyNumber_Multiply(__pyx_t_7, __pyx_t_11); if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_14);
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;

    /* "chaplotype.pyx":671
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,             # <<<<<<<<<<<<<<
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )
 * 
 */
    __pyx_t_15 = __pyx_v_likelihoodCap;

    /* "chaplotype.pyx":672
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )             # <<<<<<<<<<<<<<
 * 
 *     # standard case
 */
    __pyx_t_7 = PyFloat_FromDouble(__pyx_t_15); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 671, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_7);
    __pyx_t_8 = PyObject_RichCompare(__pyx_t_14, __pyx_t_7, Py_GT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    if (__pyx_t_5) {
      __Pyx_INCREF(__pyx_t_14);
      __pyx_t_11 = __pyx_t_14;
    } else {

      /* "chaplotype.pyx":671
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,             # <<<<<<<<<<<<<<
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )
 * 
 */
      __pyx_t_8 = PyFloat_FromDouble(__pyx_t_15); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 671, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_8);
      __pyx_t_11 = __pyx_t_8;
      __pyx_t_8 = 0;
    }
    __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;

    /* "chaplotype.pyx":672
 *     if useMapQualCap and alignScore > alignScoreThreshold:
 *         return max( likelihoodCap,
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )             # <<<<<<<<<<<<<<
 * 
 *     # standard case
 */
    __pyx_t_15 = __pyx_PyFloat_AsDouble(__pyx_t_11); if (unlikely((__pyx_t_15 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 672, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
    __pyx_r = __pyx_t_15;
    goto __pyx_L0;

    /* "chaplotype.pyx":670
 *     cdef double alignScoreThreshold = 100
 *     cdef double shapeParameter = 0.5          # must be between 0 and 1; lower values give less abrupt truncation
 *     if useMapQualCap and alignScore > alignScoreThreshold:             # <<<<<<<<<<<<<<
 *         return max( likelihoodCap,
 *                     mLTOT * ( alignScoreThreshold - 1 + math.pow(alignScore - alignScoreThreshold + 1, shapeParameter) / shapeParameter ) )
 */
  }

  /* "chaplotype.pyx":676
 *     # standard case
 *     return max( likelihoodCap,
 *                 mLTOT*alignScore + probMapRight )             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_t_15 = ((__pyx_v_10chaplotype_mLTOT * __pyx_v_alignScore) + __pyx_v_probMapRight);

  /* "chaplotype.pyx":675
 * 
 *     # standard case
 *     return max( likelihoodCap,             # <<<<<<<<<<<<<<
 *                 mLTOT*alignScore + probMapRight )
 * 
 */
  __pyx_t_16 = __pyx_v_likelihoodCap;

  /* "chaplotype.pyx":676
 *     # standard case
 *     return max( likelihoodCap,
 *                 mLTOT*alignScore + probMapRight )             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  if (((__pyx_t_15 > __pyx_t_16) != 0)) {
    __pyx_t_17 = __pyx_t_15;
  } else {
    __pyx_t_17 = __pyx_t_16;
  }
  __pyx_r = __pyx_t_17;
  goto __pyx_L0;

  /* "chaplotype.pyx":594
 * ##################################################################################################
 * 
 * cdef double alignReadToHaplotype(cAlignedRead* read, Haplotype hap, int useMapQualCap, int calculateFlankScore):             # <<<<<<<<<<<<<<
 *     """
 *     This is the basic, banded-alignment routine that forms the heart of Platypus. This function decides where to anchor the
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_XDECREF(__pyx_t_11);
  __Pyx_XDECREF(__pyx_t_12);
  __Pyx_XDECREF(__pyx_t_13);
  __Pyx_XDECREF(__pyx_t_14);
  __Pyx_WriteUnraisable("chaplotype.alignReadToHaplotype", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "chaplotype.pyx":680
 * ###################################################################################################
 * 
 * cdef void logAlignmentOfReadToHaplotype(Haplotype hap, char* readSeq, char* readQuals, char* aln1, char* aln2, int mapPos, int alignScore, options):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin: uses the logger to output a string representation of
 */

static void __pyx_f_10chaplotype_logAlignmentOfReadToHaplotype(struct __pyx_obj_10chaplotype_Haplotype *__pyx_v_hap, CYTHON_UNUSED char *__pyx_v_readSeq, char *__pyx_v_readQuals, char *__pyx_v_aln1, char *__pyx_v_aln2, int __pyx_v_mapPos, int __pyx_v_alignScore, PyObject *__pyx_v_options) {
  PyObject *__pyx_v_alignmentChars = 0;
  PyObject *__pyx_v_hapSeq = 0;
  PyObject *__pyx_v_aln1Str = 0;
  PyObject *__pyx_v_aln2Str = 0;
  int __pyx_v_minQual;
  int __pyx_v_qualIndex;
  int __pyx_v_hapIndex;
  int __pyx_v_hadInsertion;
  PyObject *__pyx_v_theChar1 = NULL;
  PyObject *__pyx_v_theChar2 = NULL;
  PyObject *__pyx_v_newChar = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_t_3;
  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;
  PyObject *(*__pyx_t_9)(PyObject *);
  Py_ssize_t __pyx_t_10;
  int __pyx_t_11;
  int __pyx_t_12;
  __Pyx_RefNannySetupContext("logAlignmentOfReadToHaplotype", 0);

  /* "chaplotype.pyx":685
 *     the final alignment of this read to this haplotype.
 *     """
 *     cdef list alignmentChars = [" "] * mapPos             # <<<<<<<<<<<<<<
 *     cdef str hapSeq = str(hap.haplotypeSequence)
 *     cdef str aln1Str = str(aln1)
 */
  __pyx_t_1 = PyList_New(1 * ((__pyx_v_mapPos<0) ? 0:__pyx_v_mapPos)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 685, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  { Py_ssize_t __pyx_temp;
    for (__pyx_temp=0; __pyx_temp < __pyx_v_mapPos; __pyx_temp++) {
      __Pyx_INCREF(__pyx_kp_s__5);
      __Pyx_GIVEREF(__pyx_kp_s__5);
      PyList_SET_ITEM(__pyx_t_1, __pyx_temp, __pyx_kp_s__5);
    }
  }
  __pyx_v_alignmentChars = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":686
 *     """
 *     cdef list alignmentChars = [" "] * mapPos
 *     cdef str hapSeq = str(hap.haplotypeSequence)             # <<<<<<<<<<<<<<
 *     cdef str aln1Str = str(aln1)
 *     cdef str aln2Str = str(aln2)
 */
  __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_hap->haplotypeSequence); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 686, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) __PYX_ERR(0, 686, __pyx_L1_error)
  __pyx_v_hapSeq = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":687
 *     cdef list alignmentChars = [" "] * mapPos
 *     cdef str hapSeq = str(hap.haplotypeSequence)
 *     cdef str aln1Str = str(aln1)             # <<<<<<<<<<<<<<
 *     cdef str aln2Str = str(aln2)
 *     cdef int minQual = options.minBaseQual
 */
  __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_aln1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 687, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 687, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) __PYX_ERR(0, 687, __pyx_L1_error)
  __pyx_v_aln1Str = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "chaplotype.pyx":688
 *     cdef str hapSeq = str(hap.haplotypeSequence)
 *     cdef str aln1Str = str(aln1)
 *     cdef str aln2Str = str(aln2)             # <<<<<<<<<<<<<<
 *     cdef int minQual = options.minBaseQual
 *     cdef int qualIndex = 0
 */
  __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_aln2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 688, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 688, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) __PYX_ERR(0, 688, __pyx_L1_error)
  __pyx_v_aln2Str = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "chaplotype.pyx":689
 *     cdef str aln1Str = str(aln1)
 *     cdef str aln2Str = str(aln2)
 *     cdef int minQual = options.minBaseQual             # <<<<<<<<<<<<<<
 *     cdef int qualIndex = 0
 *     cdef int hapIndex = mapPos
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_options, __pyx_n_s_minBaseQual); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 689, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 689, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_minQual = __pyx_t_3;

  /* "chaplotype.pyx":690
 *     cdef str aln2Str = str(aln2)
 *     cdef int minQual = options.minBaseQual
 *     cdef int qualIndex = 0             # <<<<<<<<<<<<<<
 *     cdef int hapIndex = mapPos
 *     cdef int hadInsertion = False
 */
  __pyx_v_qualIndex = 0;

  /* "chaplotype.pyx":691
 *     cdef int minQual = options.minBaseQual
 *     cdef int qualIndex = 0
 *     cdef int hapIndex = mapPos             # <<<<<<<<<<<<<<
 *     cdef int hadInsertion = False
 * 
 */
  __pyx_v_hapIndex = __pyx_v_mapPos;

  /* "chaplotype.pyx":692
 *     cdef int qualIndex = 0
 *     cdef int hapIndex = mapPos
 *     cdef int hadInsertion = False             # <<<<<<<<<<<<<<
 * 
 *     for theChar1,theChar2 in zip(aln1Str,aln2Str):
 */
  __pyx_v_hadInsertion = 0;

  /* "chaplotype.pyx":694
 *     cdef int hadInsertion = False
 * 
 *     for theChar1,theChar2 in zip(aln1Str,aln2Str):             # <<<<<<<<<<<<<<
 * 
 *         if hapIndex >= len(hapSeq):
 */
  __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 694, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_INCREF(__pyx_v_aln1Str);
  __Pyx_GIVEREF(__pyx_v_aln1Str);
  PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_aln1Str);
  __Pyx_INCREF(__pyx_v_aln2Str);
  __Pyx_GIVEREF(__pyx_v_aln2Str);
  PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_aln2Str);
  __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_zip, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 694, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (likely(PyList_CheckExact(__pyx_t_2)) || PyTuple_CheckExact(__pyx_t_2)) {
    __pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
    __pyx_t_5 = NULL;
  } else {
    __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 694, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 694, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  for (;;) {
    if (likely(!__pyx_t_5)) {
      if (likely(PyList_CheckExact(__pyx_t_1))) {
        if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(0, 694, __pyx_L1_error)
        #else
        __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 694, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        #endif
      } else {
        if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
        __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(0, 694, __pyx_L1_error)
        #else
        __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 694, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        #endif
      }
    } else {
      __pyx_t_2 = __pyx_t_5(__pyx_t_1);
      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(0, 694, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_2);
    }
    if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
      PyObject* sequence = __pyx_t_2;
      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(0, 694, __pyx_L1_error)
      }
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      if (likely(PyTuple_CheckExact(sequence))) {
        __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0); 
        __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1); 
      } else {
        __pyx_t_6 = PyList_GET_ITEM(sequence, 0); 
        __pyx_t_7 = PyList_GET_ITEM(sequence, 1); 
      }
      __Pyx_INCREF(__pyx_t_6);
      __Pyx_INCREF(__pyx_t_7);
      #else
      __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 694, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 694, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      #endif
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    } else {
      Py_ssize_t index = -1;
      __pyx_t_8 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 694, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_8);
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
      index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L5_unpacking_failed;
      __Pyx_GOTREF(__pyx_t_6);
      index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L5_unpacking_failed;
      __Pyx_GOTREF(__pyx_t_7);
      if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) __PYX_ERR(0, 694, __pyx_L1_error)
      __pyx_t_9 = NULL;
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      goto __pyx_L6_unpacking_done;
      __pyx_L5_unpacking_failed:;
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      __pyx_t_9 = NULL;
      if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
      __PYX_ERR(0, 694, __pyx_L1_error)
      __pyx_L6_unpacking_done:;
    }
    __Pyx_XDECREF_SET(__pyx_v_theChar1, __pyx_t_6);
    __pyx_t_6 = 0;
    __Pyx_XDECREF_SET(__pyx_v_theChar2, __pyx_t_7);
    __pyx_t_7 = 0;

    /* "chaplotype.pyx":696
 *     for theChar1,theChar2 in zip(aln1Str,aln2Str):
 * 
 *         if hapIndex >= len(hapSeq):             # <<<<<<<<<<<<<<
 *             break
 * 
 */
    __pyx_t_10 = PyObject_Length(__pyx_v_hapSeq); if (unlikely(__pyx_t_10 == ((Py_ssize_t)-1))) __PYX_ERR(0, 696, __pyx_L1_error)
    __pyx_t_11 = ((__pyx_v_hapIndex >= __pyx_t_10) != 0);
    if (__pyx_t_11) {

      /* "chaplotype.pyx":697
 * 
 *         if hapIndex >= len(hapSeq):
 *             break             # <<<<<<<<<<<<<<
 * 
 *         # Gap in read: deletion of ref bases.
 */
      goto __pyx_L4_break;

      /* "chaplotype.pyx":696
 *     for theChar1,theChar2 in zip(aln1Str,aln2Str):
 * 
 *         if hapIndex >= len(hapSeq):             # <<<<<<<<<<<<<<
 *             break
 * 
 */
    }

    /* "chaplotype.pyx":700
 * 
 *         # Gap in read: deletion of ref bases.
 *         if theChar2 == "-":             # <<<<<<<<<<<<<<
 *             alignmentChars.append("-")
 *             hapIndex += 1
 */
    __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_v_theChar2, __pyx_kp_s__6, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 700, __pyx_L1_error)
    if (__pyx_t_11) {

      /* "chaplotype.pyx":701
 *         # Gap in read: deletion of ref bases.
 *         if theChar2 == "-":
 *             alignmentChars.append("-")             # <<<<<<<<<<<<<<
 *             hapIndex += 1
 * 
 */
      __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_alignmentChars, __pyx_kp_s__6); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 701, __pyx_L1_error)

      /* "chaplotype.pyx":702
 *         if theChar2 == "-":
 *             alignmentChars.append("-")
 *             hapIndex += 1             # <<<<<<<<<<<<<<
 * 
 *         # Gap in hap: deletion of ref bases.
 */
      __pyx_v_hapIndex = (__pyx_v_hapIndex + 1);

      /* "chaplotype.pyx":700
 * 
 *         # Gap in read: deletion of ref bases.
 *         if theChar2 == "-":             # <<<<<<<<<<<<<<
 *             alignmentChars.append("-")
 *             hapIndex += 1
 */
      goto __pyx_L8;
    }

    /* "chaplotype.pyx":705
 * 
 *         # Gap in hap: deletion of ref bases.
 *         elif theChar1 == "-":             # <<<<<<<<<<<<<<
 *             #alignmentChars.append("-")
 *             #hapOffset -= 1
 */
    __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_v_theChar1, __pyx_kp_s__6, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 705, __pyx_L1_error)
    if (__pyx_t_11) {

      /* "chaplotype.pyx":708
 *             #alignmentChars.append("-")
 *             #hapOffset -= 1
 *             qualIndex += 1             # <<<<<<<<<<<<<<
 *             hadInsertion = True
 * 
 */
      __pyx_v_qualIndex = (__pyx_v_qualIndex + 1);

      /* "chaplotype.pyx":709
 *             #hapOffset -= 1
 *             qualIndex += 1
 *             hadInsertion = True             # <<<<<<<<<<<<<<
 * 
 *         elif theChar2 == hapSeq[hapIndex]:
 */
      __pyx_v_hadInsertion = 1;

      /* "chaplotype.pyx":705
 * 
 *         # Gap in hap: deletion of ref bases.
 *         elif theChar1 == "-":             # <<<<<<<<<<<<<<
 *             #alignmentChars.append("-")
 *             #hapOffset -= 1
 */
      goto __pyx_L8;
    }

    /* "chaplotype.pyx":711
 *             hadInsertion = True
 * 
 *         elif theChar2 == hapSeq[hapIndex]:             # <<<<<<<<<<<<<<
 * 
 *             if hadInsertion:
 */
    __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_hapSeq, __pyx_v_hapIndex, int, 1, __Pyx_PyInt_From_int, 0, 1, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 711, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_7 = PyObject_RichCompare(__pyx_v_theChar2, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 711, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 711, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
    if (__pyx_t_11) {

      /* "chaplotype.pyx":713
 *         elif theChar2 == hapSeq[hapIndex]:
 * 
 *             if hadInsertion:             # <<<<<<<<<<<<<<
 *                 alignmentChars.append("!")
 *             else:
 */
      __pyx_t_11 = (__pyx_v_hadInsertion != 0);
      if (__pyx_t_11) {

        /* "chaplotype.pyx":714
 * 
 *             if hadInsertion:
 *                 alignmentChars.append("!")             # <<<<<<<<<<<<<<
 *             else:
 *                 alignmentChars.append(".")
 */
        __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_alignmentChars, __pyx_kp_s__7); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 714, __pyx_L1_error)

        /* "chaplotype.pyx":713
 *         elif theChar2 == hapSeq[hapIndex]:
 * 
 *             if hadInsertion:             # <<<<<<<<<<<<<<
 *                 alignmentChars.append("!")
 *             else:
 */
        goto __pyx_L9;
      }

      /* "chaplotype.pyx":716
 *                 alignmentChars.append("!")
 *             else:
 *                 alignmentChars.append(".")             # <<<<<<<<<<<<<<
 * 
 *             hadInsertion = False
 */
      /*else*/ {
        __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_alignmentChars, __pyx_kp_s__8); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 716, __pyx_L1_error)
      }
      __pyx_L9:;

      /* "chaplotype.pyx":718
 *                 alignmentChars.append(".")
 * 
 *             hadInsertion = False             # <<<<<<<<<<<<<<
 * 
 *             qualIndex += 1
 */
      __pyx_v_hadInsertion = 0;

      /* "chaplotype.pyx":720
 *             hadInsertion = False
 * 
 *             qualIndex += 1             # <<<<<<<<<<<<<<
 *             hapIndex += 1
 * 
 */
      __pyx_v_qualIndex = (__pyx_v_qualIndex + 1);

      /* "chaplotype.pyx":721
 * 
 *             qualIndex += 1
 *             hapIndex += 1             # <<<<<<<<<<<<<<
 * 
 *         else:
 */
      __pyx_v_hapIndex = (__pyx_v_hapIndex + 1);

      /* "chaplotype.pyx":711
 *             hadInsertion = True
 * 
 *         elif theChar2 == hapSeq[hapIndex]:             # <<<<<<<<<<<<<<
 * 
 *             if hadInsertion:
 */
      goto __pyx_L8;
    }

    /* "chaplotype.pyx":724
 * 
 *         else:
 *             newChar = None             # <<<<<<<<<<<<<<
 * 
 *             if readQuals[qualIndex] > minQual:
 */
    /*else*/ {
      __Pyx_INCREF(Py_None);
      __Pyx_XDECREF_SET(__pyx_v_newChar, Py_None);

      /* "chaplotype.pyx":726
 *             newChar = None
 * 
 *             if readQuals[qualIndex] > minQual:             # <<<<<<<<<<<<<<
 *                 newChar = theChar2.lower()
 *             else:
 */
      __pyx_t_11 = (((__pyx_v_readQuals[__pyx_v_qualIndex]) > __pyx_v_minQual) != 0);
      if (__pyx_t_11) {

        /* "chaplotype.pyx":727
 * 
 *             if readQuals[qualIndex] > minQual:
 *                 newChar = theChar2.lower()             # <<<<<<<<<<<<<<
 *             else:
 *                 newChar = "n"
 */
        __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_theChar2, __pyx_n_s_lower); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 727, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __pyx_t_6 = NULL;
        if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
          __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_2);
          if (likely(__pyx_t_6)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
            __Pyx_INCREF(__pyx_t_6);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_2, function);
          }
        }
        __pyx_t_7 = (__pyx_t_6) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
        __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
        if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 727, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __Pyx_DECREF_SET(__pyx_v_newChar, __pyx_t_7);
        __pyx_t_7 = 0;

        /* "chaplotype.pyx":726
 *             newChar = None
 * 
 *             if readQuals[qualIndex] > minQual:             # <<<<<<<<<<<<<<
 *                 newChar = theChar2.lower()
 *             else:
 */
        goto __pyx_L10;
      }

      /* "chaplotype.pyx":729
 *                 newChar = theChar2.lower()
 *             else:
 *                 newChar = "n"             # <<<<<<<<<<<<<<
 * 
 *             if hadInsertion:
 */
      /*else*/ {
        __Pyx_INCREF(__pyx_n_s_n);
        __Pyx_DECREF_SET(__pyx_v_newChar, __pyx_n_s_n);
      }
      __pyx_L10:;

      /* "chaplotype.pyx":731
 *                 newChar = "n"
 * 
 *             if hadInsertion:             # <<<<<<<<<<<<<<
 *                 newChar = newChar.upper()
 * 
 */
      __pyx_t_11 = (__pyx_v_hadInsertion != 0);
      if (__pyx_t_11) {

        /* "chaplotype.pyx":732
 * 
 *             if hadInsertion:
 *                 newChar = newChar.upper()             # <<<<<<<<<<<<<<
 * 
 *             alignmentChars.append( newChar )
 */
        __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_newChar, __pyx_n_s_upper); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 732, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __pyx_t_6 = NULL;
        if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
          __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_2);
          if (likely(__pyx_t_6)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
            __Pyx_INCREF(__pyx_t_6);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_2, function);
          }
        }
        __pyx_t_7 = (__pyx_t_6) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6) : __Pyx_PyObject_CallNoArg(__pyx_t_2);
        __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
        if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 732, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __Pyx_DECREF_SET(__pyx_v_newChar, __pyx_t_7);
        __pyx_t_7 = 0;

        /* "chaplotype.pyx":731
 *                 newChar = "n"
 * 
 *             if hadInsertion:             # <<<<<<<<<<<<<<
 *                 newChar = newChar.upper()
 * 
 */
      }

      /* "chaplotype.pyx":734
 *                 newChar = newChar.upper()
 * 
 *             alignmentChars.append( newChar )             # <<<<<<<<<<<<<<
 *             hadInsertion = False
 * 
 */
      __pyx_t_12 = __Pyx_PyList_Append(__pyx_v_alignmentChars, __pyx_v_newChar); if (unlikely(__pyx_t_12 == ((int)-1))) __PYX_ERR(0, 734, __pyx_L1_error)

      /* "chaplotype.pyx":735
 * 
 *             alignmentChars.append( newChar )
 *             hadInsertion = False             # <<<<<<<<<<<<<<
 * 
 *             qualIndex += 1
 */
      __pyx_v_hadInsertion = 0;

      /* "chaplotype.pyx":737
 *             hadInsertion = False
 * 
 *             qualIndex += 1             # <<<<<<<<<<<<<<
 *             hapIndex += 1
 * 
 */
      __pyx_v_qualIndex = (__pyx_v_qualIndex + 1);

      /* "chaplotype.pyx":738
 * 
 *             qualIndex += 1
 *             hapIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     logger.debug("".join(alignmentChars) + " Score = %s" %(alignScore))
 */
      __pyx_v_hapIndex = (__pyx_v_hapIndex + 1);
    }
    __pyx_L8:;

    /* "chaplotype.pyx":694
 *     cdef int hadInsertion = False
 * 
 *     for theChar1,theChar2 in zip(aln1Str,aln2Str):             # <<<<<<<<<<<<<<
 * 
 *         if hapIndex >= len(hapSeq):
 */
  }
  __pyx_L4_break:;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":740
 *             hapIndex += 1
 * 
 *     logger.debug("".join(alignmentChars) + " Score = %s" %(alignScore))             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_logger); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  __pyx_t_7 = __Pyx_PyString_Join(__pyx_kp_s_, __pyx_v_alignmentChars); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_7);
  __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_alignScore); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __pyx_t_8 = __Pyx_PyString_Format(__pyx_kp_s_Score_s, __pyx_t_6); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_8);
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_6 = PyNumber_Add(__pyx_t_7, __pyx_t_8); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
  __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
  __pyx_t_8 = NULL;
  if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_8)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_8);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_1 = (__pyx_t_8) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_8, __pyx_t_6) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6);
  __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 740, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":680
 * ###################################################################################################
 * 
 * cdef void logAlignmentOfReadToHaplotype(Haplotype hap, char* readSeq, char* readQuals, char* aln1, char* aln2, int mapPos, int alignScore, options):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin: uses the logger to output a string representation of
 */

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_WriteUnraisable("chaplotype.logAlignmentOfReadToHaplotype", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_alignmentChars);
  __Pyx_XDECREF(__pyx_v_hapSeq);
  __Pyx_XDECREF(__pyx_v_aln1Str);
  __Pyx_XDECREF(__pyx_v_aln2Str);
  __Pyx_XDECREF(__pyx_v_theChar1);
  __Pyx_XDECREF(__pyx_v_theChar2);
  __Pyx_XDECREF(__pyx_v_newChar);
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pxd":250
 * 
 * # And here are accessor functions for the bit-fields
 * cdef inline int Read_IsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FREVERSE) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":251
 * # And here are accessor functions for the bit-fields
 * cdef inline int Read_IsReverse(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FREVERSE) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 16) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":250
 * 
 * # And here are accessor functions for the bit-fields
 * cdef inline int Read_IsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FREVERSE) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":253
 *     return ( (theRead.bitFlag & BAM_FREVERSE) != 0)
 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsPaired(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":254
 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 1) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":253
 *     return ( (theRead.bitFlag & BAM_FREVERSE) != 0)
 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":256
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)
 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsProperPair(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":257
 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 2) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":256
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)
 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":259
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsDuplicate(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":260
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 0x400) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":259
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":262
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":263
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 4) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":262
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":265
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":266
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 8) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":265
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":268
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":269
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 32) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":268
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":271
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":272
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 0x200) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":271
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":274
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReadOne(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":275
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 64) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":274
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":277
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsSecondaryAlignment(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":278
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 0x100) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":277
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":280
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":281
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 0x800) != 0);
  goto __pyx_L0;

  /* "htslibWrapper.pxd":280
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 */

  /* function exit code */
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pxd":283
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FREVERSE)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_SetIsNotReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":284
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag &= (~BAM_FREVERSE)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag & (~16));

  /* "htslibWrapper.pxd":283
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FREVERSE)
 * 
 */

  /* function exit code */
  __pyx_r = 0;
  return __pyx_r;
}

/* "htslibWrapper.pxd":286
 *     theRead.bitFlag &= (~BAM_FREVERSE)
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FREVERSE
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_SetIsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  int __pyx_r;

  /* "htslibWrapper.pxd":287
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FREVERSE             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 16);

  /* "htslibWrapper.pxd":286
 *     theRead.bitFlag &= (~BAM_FREVERSE)
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FREVERSE
 * 
 */

  /* function exit code */
  __pyx_r = 0;
  return __pyx_r;
}

/* "htslibWrapper.pxd":289
 *     theRead.bitFlag |= BAM_FREVERSE
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FQCFAIL
 * 
 */

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":290
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FQCFAIL             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 0x200);

  /* "htslibWrapper.pxd":289
 *     theRead.bitFlag |= BAM_FREVERSE
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FQCFAIL
 * 
 */

  /* function exit code */
}

/* "htslibWrapper.pxd":292
 *     theRead.bitFlag |= BAM_FQCFAIL
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 */

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":293
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FCOMPRESSED             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 0x800);

  /* "htslibWrapper.pxd":292
 *     theRead.bitFlag |= BAM_FQCFAIL
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 */

  /* function exit code */
}

/* "htslibWrapper.pxd":295
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)
 * 
 */

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":296
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag & (~0x800));

  /* "htslibWrapper.pxd":295
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)
 * 
 */

  /* function exit code */
}
static struct __pyx_vtabstruct_10chaplotype_Haplotype __pyx_vtable_10chaplotype_Haplotype;

static PyObject *__pyx_tp_new_10chaplotype_Haplotype(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
  struct __pyx_obj_10chaplotype_Haplotype *p;
  PyObject *o;
  o = (*t->tp_alloc)(t, 0);
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_10chaplotype_Haplotype *)o);
  p->__pyx_vtab = __pyx_vtabptr_10chaplotype_Haplotype;
  p->refName = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->variants = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->haplotypeSequence = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->shortHaplotypeSequence = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->refFile = ((struct __pyx_obj_9fastafile_FastaFile *)Py_None); Py_INCREF(Py_None);
  p->options = Py_None; Py_INCREF(Py_None);
  p->referenceSequence = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->shortReferenceSequence = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->longVar = ((struct __pyx_obj_7variant_Variant *)Py_None); Py_INCREF(Py_None);
  return o;
}

static void __pyx_tp_dealloc_10chaplotype_Haplotype(PyObject *o) {
  struct __pyx_obj_10chaplotype_Haplotype *p = (struct __pyx_obj_10chaplotype_Haplotype *)o;
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_10chaplotype_9Haplotype_3__dealloc__(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  Py_CLEAR(p->refName);
  Py_CLEAR(p->variants);
  Py_CLEAR(p->haplotypeSequence);
  Py_CLEAR(p->shortHaplotypeSequence);
  Py_CLEAR(p->refFile);
  Py_CLEAR(p->options);
  Py_CLEAR(p->referenceSequence);
  Py_CLEAR(p->shortReferenceSequence);
  Py_CLEAR(p->longVar);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_10chaplotype_Haplotype(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_10chaplotype_Haplotype *p = (struct __pyx_obj_10chaplotype_Haplotype *)o;
  if (p->variants) {
    e = (*v)(p->variants, a); if (e) return e;
  }
  if (p->refFile) {
    e = (*v)(((PyObject *)p->refFile), a); if (e) return e;
  }
  if (p->options) {
    e = (*v)(p->options, a); if (e) return e;
  }
  if (p->longVar) {
    e = (*v)(((PyObject *)p->longVar), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_10chaplotype_Haplotype(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_10chaplotype_Haplotype *p = (struct __pyx_obj_10chaplotype_Haplotype *)o;
  tmp = ((PyObject*)p->variants);
  p->variants = ((PyObject*)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->refFile);
  p->refFile = ((struct __pyx_obj_9fastafile_FastaFile *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->options);
  p->options = Py_None; Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->longVar);
  p->longVar = ((struct __pyx_obj_7variant_Variant *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyMethodDef __pyx_methods_10chaplotype_Haplotype[] = {
  {"__copy__", (PyCFunction)__pyx_pw_10chaplotype_9Haplotype_5__copy__, METH_NOARGS, __pyx_doc_10chaplotype_9Haplotype_4__copy__},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_10chaplotype_9Haplotype_15__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_10chaplotype_9Haplotype_17__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_10chaplotype_Haplotype = {
  PyVarObject_HEAD_INIT(0, 0)
  "chaplotype.Haplotype", /*tp_name*/
  sizeof(struct __pyx_obj_10chaplotype_Haplotype), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_10chaplotype_Haplotype, /*tp_dealloc*/
  0, /*tp_print*/
  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_10chaplotype_9Haplotype_13__repr__, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  __pyx_pw_10chaplotype_9Haplotype_9__hash__, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pw_10chaplotype_9Haplotype_11__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_HAVE_GC, /*tp_flags*/
  "\n    Class to encapsulate a single haplotype. This will store all the\n    variants pertaining to this haplotype, as well as the reference\n    sequence, all supporting reads, and the start and end positions of\n    this haplotype in the reference.\n    ", /*tp_doc*/
  __pyx_tp_traverse_10chaplotype_Haplotype, /*tp_traverse*/
  __pyx_tp_clear_10chaplotype_Haplotype, /*tp_clear*/
  __pyx_pw_10chaplotype_9Haplotype_7__richcmp__, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_10chaplotype_Haplotype, /*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*/
  __pyx_pw_10chaplotype_9Haplotype_1__init__, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_10chaplotype_Haplotype, /*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
};

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_chaplotype(PyObject* module); /*proto*/
static PyModuleDef_Slot __pyx_moduledef_slots[] = {
  {Py_mod_create, (void*)__pyx_pymod_create},
  {Py_mod_exec, (void*)__pyx_pymod_exec_chaplotype},
  {0, NULL}
};
#endif

static struct PyModuleDef __pyx_moduledef = {
    PyModuleDef_HEAD_INIT,
    "chaplotype",
    __pyx_k_module_containing_various_class, /* 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_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0},
  {&__pyx_kp_s_Could_not_allocate_haplotype_cac, __pyx_k_Could_not_allocate_haplotype_cac, sizeof(__pyx_k_Could_not_allocate_haplotype_cac), 0, 0, 1, 0},
  {&__pyx_kp_s_Could_not_reallocate_haplotype_c, __pyx_k_Could_not_reallocate_haplotype_c, sizeof(__pyx_k_Could_not_reallocate_haplotype_c), 0, 0, 1, 0},
  {&__pyx_n_s_HP, __pyx_k_HP, sizeof(__pyx_k_HP), 0, 0, 1, 1},
  {&__pyx_kp_s_Haplotype, __pyx_k_Haplotype, sizeof(__pyx_k_Haplotype), 0, 0, 1, 0},
  {&__pyx_n_s_Haplotype_2, __pyx_k_Haplotype_2, sizeof(__pyx_k_Haplotype_2), 0, 0, 1, 1},
  {&__pyx_kp_s_Haplotype_Reference_s_s_s, __pyx_k_Haplotype_Reference_s_s_s, sizeof(__pyx_k_Haplotype_Reference_s_s_s), 0, 0, 1, 0},
  {&__pyx_kp_s_Haplotype_is_too_long_Max_allowe, __pyx_k_Haplotype_is_too_long_Max_allowe, sizeof(__pyx_k_Haplotype_is_too_long_Max_allowe), 0, 0, 1, 0},
  {&__pyx_kp_s_Haplotype_with_vars_s_has_len_s, __pyx_k_Haplotype_with_vars_s_has_len_s, sizeof(__pyx_k_Haplotype_with_vars_s_has_len_s), 0, 0, 1, 0},
  {&__pyx_kp_s_Internal_error_encountered_negat, __pyx_k_Internal_error_encountered_negat, sizeof(__pyx_k_Internal_error_encountered_negat), 0, 0, 1, 0},
  {&__pyx_n_s_Log, __pyx_k_Log, sizeof(__pyx_k_Log), 0, 0, 1, 1},
  {&__pyx_kp_s_Oh_no_The_bridge_is_gone, __pyx_k_Oh_no_The_bridge_is_gone, sizeof(__pyx_k_Oh_no_The_bridge_is_gone), 0, 0, 1, 0},
  {&__pyx_kp_s_Op_code_s_not_implemented_in_hap, __pyx_k_Op_code_s_not_implemented_in_hap, sizeof(__pyx_k_Op_code_s_not_implemented_in_hap), 0, 0, 1, 0},
  {&__pyx_kp_s_Out_of_memory_in_cHaplotype_alig, __pyx_k_Out_of_memory_in_cHaplotype_alig, sizeof(__pyx_k_Out_of_memory_in_cHaplotype_alig), 0, 0, 1, 0},
  {&__pyx_n_s_SC, __pyx_k_SC, sizeof(__pyx_k_SC), 0, 0, 1, 1},
  {&__pyx_kp_s_Score_s, __pyx_k_Score_s, sizeof(__pyx_k_Score_s), 0, 0, 1, 0},
  {&__pyx_n_s_SeqLength, __pyx_k_SeqLength, sizeof(__pyx_k_SeqLength), 0, 0, 1, 1},
  {&__pyx_n_s_StandardError, __pyx_k_StandardError, sizeof(__pyx_k_StandardError), 0, 0, 1, 1},
  {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
  {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
  {&__pyx_kp_s__2, __pyx_k__2, sizeof(__pyx_k__2), 0, 0, 1, 0},
  {&__pyx_kp_s__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 0, 1, 0},
  {&__pyx_kp_s__6, __pyx_k__6, sizeof(__pyx_k__6), 0, 0, 1, 0},
  {&__pyx_kp_s__7, __pyx_k__7, sizeof(__pyx_k__7), 0, 0, 1, 0},
  {&__pyx_kp_s__8, __pyx_k__8, sizeof(__pyx_k__8), 0, 0, 1, 0},
  {&__pyx_n_s_calculateFlankScore, __pyx_k_calculateFlankScore, sizeof(__pyx_k_calculateFlankScore), 0, 0, 1, 1},
  {&__pyx_n_s_chr, __pyx_k_chr, sizeof(__pyx_k_chr), 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_kp_s_cpos_s_end_pos_s_Variants_are_s, __pyx_k_cpos_s_end_pos_s_Variants_are_s, sizeof(__pyx_k_cpos_s_end_pos_s_Variants_are_s), 0, 0, 1, 0},
  {&__pyx_n_s_debug, __pyx_k_debug, sizeof(__pyx_k_debug), 0, 0, 1, 1},
  {&__pyx_n_s_endPos, __pyx_k_endPos, sizeof(__pyx_k_endPos), 0, 0, 1, 1},
  {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1},
  {&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1},
  {&__pyx_n_s_getLogger, __pyx_k_getLogger, sizeof(__pyx_k_getLogger), 0, 0, 1, 1},
  {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1},
  {&__pyx_n_s_idx, __pyx_k_idx, sizeof(__pyx_k_idx), 0, 0, 1, 1},
  {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
  {&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1},
  {&__pyx_n_s_logger, __pyx_k_logger, sizeof(__pyx_k_logger), 0, 0, 1, 1},
  {&__pyx_n_s_logging, __pyx_k_logging, sizeof(__pyx_k_logging), 0, 0, 1, 1},
  {&__pyx_n_s_lower, __pyx_k_lower, sizeof(__pyx_k_lower), 0, 0, 1, 1},
  {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_math, __pyx_k_math, sizeof(__pyx_k_math), 0, 0, 1, 1},
  {&__pyx_n_s_max, __pyx_k_max, sizeof(__pyx_k_max), 0, 0, 1, 1},
  {&__pyx_n_s_maxReadLength, __pyx_k_maxReadLength, sizeof(__pyx_k_maxReadLength), 0, 0, 1, 1},
  {&__pyx_n_s_min, __pyx_k_min, sizeof(__pyx_k_min), 0, 0, 1, 1},
  {&__pyx_n_s_minBaseQual, __pyx_k_minBaseQual, sizeof(__pyx_k_minBaseQual), 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_options, __pyx_k_options, sizeof(__pyx_k_options), 0, 0, 1, 1},
  {&__pyx_n_s_pi, __pyx_k_pi, sizeof(__pyx_k_pi), 0, 0, 1, 1},
  {&__pyx_n_s_pow, __pyx_k_pow, sizeof(__pyx_k_pow), 0, 0, 1, 1},
  {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1},
  {&__pyx_n_s_q, __pyx_k_q, sizeof(__pyx_k_q), 0, 0, 1, 1},
  {&__pyx_n_s_random, __pyx_k_random, sizeof(__pyx_k_random), 0, 0, 1, 1},
  {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 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_refFile, __pyx_k_refFile, sizeof(__pyx_k_refFile), 0, 0, 1, 1},
  {&__pyx_n_s_refName, __pyx_k_refName, sizeof(__pyx_k_refName), 0, 0, 1, 1},
  {&__pyx_n_s_reversed, __pyx_k_reversed, sizeof(__pyx_k_reversed), 0, 0, 1, 1},
  {&__pyx_kp_s_s_s_s, __pyx_k_s_s_s, sizeof(__pyx_k_s_s_s), 0, 0, 1, 0},
  {&__pyx_kp_s_self_hapSequenceHash_self_hapSeq, __pyx_k_self_hapSequenceHash_self_hapSeq, sizeof(__pyx_k_self_hapSequenceHash_self_hapSeq), 0, 0, 1, 0},
  {&__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_startPos, __pyx_k_startPos, sizeof(__pyx_k_startPos), 0, 0, 1, 1},
  {&__pyx_n_s_str, __pyx_k_str, sizeof(__pyx_k_str), 0, 0, 1, 1},
  {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_upper, __pyx_k_upper, sizeof(__pyx_k_upper), 0, 0, 1, 1},
  {&__pyx_n_s_varSource, __pyx_k_varSource, sizeof(__pyx_k_varSource), 0, 0, 1, 1},
  {&__pyx_n_s_variants, __pyx_k_variants, sizeof(__pyx_k_variants), 0, 0, 1, 1},
  {&__pyx_n_s_verbosity, __pyx_k_verbosity, sizeof(__pyx_k_verbosity), 0, 0, 1, 1},
  {&__pyx_n_s_zip, __pyx_k_zip, sizeof(__pyx_k_zip), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 64, __pyx_L1_error)
  __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 67, __pyx_L1_error)
  __pyx_builtin_chr = __Pyx_GetBuiltinName(__pyx_n_s_chr); if (!__pyx_builtin_chr) __PYX_ERR(0, 67, __pyx_L1_error)
  __pyx_builtin_min = __Pyx_GetBuiltinName(__pyx_n_s_min); if (!__pyx_builtin_min) __PYX_ERR(0, 153, __pyx_L1_error)
  __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) __PYX_ERR(0, 154, __pyx_L1_error)
  __pyx_builtin_StandardError = __Pyx_GetBuiltinName(__pyx_n_s_StandardError); if (!__pyx_builtin_StandardError) __PYX_ERR(0, 183, __pyx_L1_error)
  __pyx_builtin_reversed = __Pyx_GetBuiltinName(__pyx_n_s_reversed); if (!__pyx_builtin_reversed) __PYX_ERR(0, 483, __pyx_L1_error)
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 586, __pyx_L1_error)
  __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
  __pyx_builtin_zip = __Pyx_GetBuiltinName(__pyx_n_s_zip); if (!__pyx_builtin_zip) __PYX_ERR(0, 694, __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("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 */
  __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_self_hapSequenceHash_self_hapSeq); if (unlikely(!__pyx_tuple__3)) __PYX_ERR(1, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__3);
  __Pyx_GIVEREF(__pyx_tuple__3);

  /* "(tree fragment)":4
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("self.hapSequenceHash,self.hapSequenceNextArray,self.likelihoodCache,self.mapCounts cannot be converted to a Python object for pickling")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_self_hapSequenceHash_self_hapSeq); if (unlikely(!__pyx_tuple__4)) __PYX_ERR(1, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__4);
  __Pyx_GIVEREF(__pyx_tuple__4);

  /* "chaplotype.pyx":39
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_tuple__9 = PyTuple_Pack(1, __pyx_n_s_Log); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(0, 39, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__9);
  __Pyx_GIVEREF(__pyx_tuple__9);
  __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(0, 1, __pyx_L1_error);
  __pyx_float_1_0eneg_3 = PyFloat_FromDouble(1.0e-3); if (unlikely(!__pyx_float_1_0eneg_3)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_1_1eneg_4 = PyFloat_FromDouble(1.1e-4); if (unlikely(!__pyx_float_1_1eneg_4)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_1_4eneg_3 = PyFloat_FromDouble(1.4e-3); if (unlikely(!__pyx_float_1_4eneg_3)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_2_4eneg_4 = PyFloat_FromDouble(2.4e-4); if (unlikely(!__pyx_float_2_4eneg_4)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_2_9eneg_5 = PyFloat_FromDouble(2.9e-5); if (unlikely(!__pyx_float_2_9eneg_5)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_4_3eneg_4 = PyFloat_FromDouble(4.3e-4); if (unlikely(!__pyx_float_4_3eneg_4)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_4_3eneg_5 = PyFloat_FromDouble(4.3e-5); if (unlikely(!__pyx_float_4_3eneg_5)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_float_5_7eneg_4 = PyFloat_FromDouble(5.7e-4); if (unlikely(!__pyx_float_5_7eneg_4)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_11 = PyInt_FromLong(11); if (unlikely(!__pyx_int_11)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_20 = PyInt_FromLong(20); if (unlikely(!__pyx_int_20)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_21 = PyInt_FromLong(21); if (unlikely(!__pyx_int_21)) __PYX_ERR(0, 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_v_10chaplotype_per_base_indel_errors = ((PyObject*)Py_None); Py_INCREF(Py_None);
  __pyx_v_10chaplotype_homopolq = ((PyObject*)Py_None); Py_INCREF(Py_None);
  __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 ---*/
  if (__Pyx_ExportFunction("computeOverlapOfReadAndHaplotype", (void (*)(void))__pyx_f_10chaplotype_computeOverlapOfReadAndHaplotype, "int (int, int, __pyx_t_13htslibWrapper_cAlignedRead *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_type_init_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
  /*--- Type init code ---*/
  __pyx_vtabptr_10chaplotype_Haplotype = &__pyx_vtable_10chaplotype_Haplotype;
  __pyx_vtable_10chaplotype_Haplotype.alignReads = (double *(*)(struct __pyx_obj_10chaplotype_Haplotype *, int, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, int))__pyx_f_10chaplotype_9Haplotype_alignReads;
  __pyx_vtable_10chaplotype_Haplotype.alignSingleRead = (double (*)(struct __pyx_obj_10chaplotype_Haplotype *, __pyx_t_13htslibWrapper_cAlignedRead *, int))__pyx_f_10chaplotype_9Haplotype_alignSingleRead;
  __pyx_vtable_10chaplotype_Haplotype.getReferenceSequence = (char *(*)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args))__pyx_f_10chaplotype_9Haplotype_getReferenceSequence;
  __pyx_vtable_10chaplotype_Haplotype.getMutatedSequence = (char *(*)(struct __pyx_obj_10chaplotype_Haplotype *))__pyx_f_10chaplotype_9Haplotype_getMutatedSequence;
  __pyx_vtable_10chaplotype_Haplotype.getShortHaplotypeSequence = (char *(*)(struct __pyx_obj_10chaplotype_Haplotype *))__pyx_f_10chaplotype_9Haplotype_getShortHaplotypeSequence;
  __pyx_vtable_10chaplotype_Haplotype.vcfINFO = (PyObject *(*)(struct __pyx_obj_10chaplotype_Haplotype *))__pyx_f_10chaplotype_9Haplotype_vcfINFO;
  __pyx_vtable_10chaplotype_Haplotype.getSequenceContext = (PyObject *(*)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *))__pyx_f_10chaplotype_9Haplotype_getSequenceContext;
  __pyx_vtable_10chaplotype_Haplotype.homopolymerLengthForOneVariant = (int (*)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *))__pyx_f_10chaplotype_9Haplotype_homopolymerLengthForOneVariant;
  __pyx_vtable_10chaplotype_Haplotype.homopolymerLengths = (PyObject *(*)(struct __pyx_obj_10chaplotype_Haplotype *))__pyx_f_10chaplotype_9Haplotype_homopolymerLengths;
  __pyx_vtable_10chaplotype_Haplotype.annotateWithGapOpen = (void (*)(struct __pyx_obj_10chaplotype_Haplotype *))__pyx_f_10chaplotype_9Haplotype_annotateWithGapOpen;
  if (PyType_Ready(&__pyx_type_10chaplotype_Haplotype) < 0) __PYX_ERR(0, 120, __pyx_L1_error)
  __pyx_type_10chaplotype_Haplotype.tp_print = 0;
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_10chaplotype_Haplotype.tp_dictoffset && __pyx_type_10chaplotype_Haplotype.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_10chaplotype_Haplotype.tp_getattro = __Pyx_PyObject_GenericGetAttrNoDict;
  }
  #if CYTHON_COMPILING_IN_CPYTHON
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_10chaplotype_Haplotype, "__init__"); if (unlikely(!wrapper)) __PYX_ERR(0, 120, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_10chaplotype_9Haplotype___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_10chaplotype_9Haplotype___init__.doc = __pyx_doc_10chaplotype_9Haplotype___init__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10chaplotype_9Haplotype___init__;
    }
  }
  #endif
  #if CYTHON_COMPILING_IN_CPYTHON
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_10chaplotype_Haplotype, "__hash__"); if (unlikely(!wrapper)) __PYX_ERR(0, 120, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_10chaplotype_9Haplotype_8__hash__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_10chaplotype_9Haplotype_8__hash__.doc = __pyx_doc_10chaplotype_9Haplotype_8__hash__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10chaplotype_9Haplotype_8__hash__;
    }
  }
  #endif
  #if CYTHON_COMPILING_IN_CPYTHON
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_10chaplotype_Haplotype, "__str__"); if (unlikely(!wrapper)) __PYX_ERR(0, 120, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_10chaplotype_9Haplotype_10__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_10chaplotype_9Haplotype_10__str__.doc = __pyx_doc_10chaplotype_9Haplotype_10__str__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10chaplotype_9Haplotype_10__str__;
    }
  }
  #endif
  #if CYTHON_COMPILING_IN_CPYTHON
  {
    PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_10chaplotype_Haplotype, "__repr__"); if (unlikely(!wrapper)) __PYX_ERR(0, 120, __pyx_L1_error)
    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
      __pyx_wrapperbase_10chaplotype_9Haplotype_12__repr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
      __pyx_wrapperbase_10chaplotype_9Haplotype_12__repr__.doc = __pyx_doc_10chaplotype_9Haplotype_12__repr__;
      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10chaplotype_9Haplotype_12__repr__;
    }
  }
  #endif
  if (__Pyx_SetVtable(__pyx_type_10chaplotype_Haplotype.tp_dict, __pyx_vtabptr_10chaplotype_Haplotype) < 0) __PYX_ERR(0, 120, __pyx_L1_error)
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Haplotype_2, (PyObject *)&__pyx_type_10chaplotype_Haplotype) < 0) __PYX_ERR(0, 120, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_10chaplotype_Haplotype) < 0) __PYX_ERR(0, 120, __pyx_L1_error)
  __pyx_ptype_10chaplotype_Haplotype = &__pyx_type_10chaplotype_Haplotype;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_type_import_code(void) {
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
  /*--- Type import code ---*/
  __pyx_t_1 = PyImport_ImportModule("fastafile"); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_9fastafile_FastaIndex = __Pyx_ImportType(__pyx_t_1, "fastafile", "FastaIndex", sizeof(struct __pyx_obj_9fastafile_FastaIndex), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_9fastafile_FastaIndex) __PYX_ERR(2, 1, __pyx_L1_error)
  __pyx_vtabptr_9fastafile_FastaIndex = (struct __pyx_vtabstruct_9fastafile_FastaIndex*)__Pyx_GetVtable(__pyx_ptype_9fastafile_FastaIndex->tp_dict); if (unlikely(!__pyx_vtabptr_9fastafile_FastaIndex)) __PYX_ERR(2, 1, __pyx_L1_error)
  __pyx_ptype_9fastafile_FastaFile = __Pyx_ImportType(__pyx_t_1, "fastafile", "FastaFile", sizeof(struct __pyx_obj_9fastafile_FastaFile), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_9fastafile_FastaFile) __PYX_ERR(2, 5, __pyx_L1_error)
  __pyx_vtabptr_9fastafile_FastaFile = (struct __pyx_vtabstruct_9fastafile_FastaFile*)__Pyx_GetVtable(__pyx_ptype_9fastafile_FastaFile->tp_dict); if (unlikely(!__pyx_vtabptr_9fastafile_FastaFile)) __PYX_ERR(2, 5, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 9, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", 
  #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000
  sizeof(PyTypeObject),
  #else
  sizeof(PyHeapTypeObject),
  #endif
  __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(3, 9, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 8, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(4, 8, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(5, 15, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(5, 15, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule("htslibWrapper"); if (unlikely(!__pyx_t_1)) __PYX_ERR(6, 203, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_13htslibWrapper_Samfile = __Pyx_ImportType(__pyx_t_1, "htslibWrapper", "Samfile", sizeof(struct __pyx_obj_13htslibWrapper_Samfile), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_13htslibWrapper_Samfile) __PYX_ERR(6, 203, __pyx_L1_error)
  __pyx_vtabptr_13htslibWrapper_Samfile = (struct __pyx_vtabstruct_13htslibWrapper_Samfile*)__Pyx_GetVtable(__pyx_ptype_13htslibWrapper_Samfile->tp_dict); if (unlikely(!__pyx_vtabptr_13htslibWrapper_Samfile)) __PYX_ERR(6, 203, __pyx_L1_error)
  __pyx_ptype_13htslibWrapper_ReadIterator = __Pyx_ImportType(__pyx_t_1, "htslibWrapper", "ReadIterator", sizeof(struct __pyx_obj_13htslibWrapper_ReadIterator), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_13htslibWrapper_ReadIterator) __PYX_ERR(6, 222, __pyx_L1_error)
  __pyx_vtabptr_13htslibWrapper_ReadIterator = (struct __pyx_vtabstruct_13htslibWrapper_ReadIterator*)__Pyx_GetVtable(__pyx_ptype_13htslibWrapper_ReadIterator->tp_dict); if (unlikely(!__pyx_vtabptr_13htslibWrapper_ReadIterator)) __PYX_ERR(6, 222, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule("variant"); if (unlikely(!__pyx_t_1)) __PYX_ERR(7, 17, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7variant_Variant = __Pyx_ImportType(__pyx_t_1, "variant", "Variant", sizeof(struct __pyx_obj_7variant_Variant), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7variant_Variant) __PYX_ERR(7, 17, __pyx_L1_error)
  __pyx_vtabptr_7variant_Variant = (struct __pyx_vtabstruct_7variant_Variant*)__Pyx_GetVtable(__pyx_ptype_7variant_Variant->tp_dict); if (unlikely(!__pyx_vtabptr_7variant_Variant)) __PYX_ERR(7, 17, __pyx_L1_error)
  __pyx_ptype_7variant_VariantCandidateGenerator = __Pyx_ImportType(__pyx_t_1, "variant", "VariantCandidateGenerator", sizeof(struct __pyx_obj_7variant_VariantCandidateGenerator), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7variant_VariantCandidateGenerator) __PYX_ERR(7, 44, __pyx_L1_error)
  __pyx_vtabptr_7variant_VariantCandidateGenerator = (struct __pyx_vtabstruct_7variant_VariantCandidateGenerator*)__Pyx_GetVtable(__pyx_ptype_7variant_VariantCandidateGenerator->tp_dict); if (unlikely(!__pyx_vtabptr_7variant_VariantCandidateGenerator)) __PYX_ERR(7, 44, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_variable_import_code(void) {
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0);
  /*--- Variable import code ---*/
  __pyx_t_1 = PyImport_ImportModule("variant"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_1, "PLATYPUS_VAR", (void **)&__pyx_vp_7variant_PLATYPUS_VAR, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_1, "FILE_VAR", (void **)&__pyx_vp_7variant_FILE_VAR, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_1, "ASSEMBLER_VAR", (void **)&__pyx_vp_7variant_ASSEMBLER_VAR, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_2 = PyImport_ImportModule("calign"); if (!__pyx_t_2) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_2, "hash_nucs", (void **)&__pyx_vp_6calign_hash_nucs, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_2, "hash_size", (void **)&__pyx_vp_6calign_hash_size, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportVoidPtr(__pyx_t_2, "max_sequence_length", (void **)&__pyx_vp_6calign_max_sequence_length, "int") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_function_import_code(void) {
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0);
  /*--- Function import code ---*/
  __pyx_t_1 = PyImport_ImportModule("calign"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_1, "hash_sequence", (void (**)(void))&__pyx_f_6calign_hash_sequence, "short *(char *, int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_1, "hash_sequence_multihit", (void (**)(void))&__pyx_f_6calign_hash_sequence_multihit, "void (char *, int, short **, short **)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_1, "mapAndAlignReadToHaplotype", (void (**)(void))&__pyx_f_6calign_mapAndAlignReadToHaplotype, "int (char *, char *, int, int, int, int, short *, short *, short *, char *, int, int, char *, int *, int, int, int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_1, "hashReadForMapping", (void (**)(void))&__pyx_f_6calign_hashReadForMapping, "void (__pyx_t_13htslibWrapper_cAlignedRead *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_RefNannyFinishContext();
  return -1;
}


#if PY_MAJOR_VERSION < 3
#ifdef CYTHON_NO_PYINIT_EXPORT
#define __Pyx_PyMODINIT_FUNC void
#else
#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
#endif
#else
#ifdef CYTHON_NO_PYINIT_EXPORT
#define __Pyx_PyMODINIT_FUNC PyObject *
#else
#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
#endif
#endif


#if PY_MAJOR_VERSION < 3
__Pyx_PyMODINIT_FUNC initchaplotype(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC initchaplotype(void)
#else
__Pyx_PyMODINIT_FUNC PyInit_chaplotype(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC PyInit_chaplotype(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_chaplotype(PyObject *__pyx_pyinit_module)
#endif
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  double __pyx_t_3;
  long __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  Py_ssize_t __pyx_t_7;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  __Pyx_RefNannyDeclarations
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  if (__pyx_m) {
    if (__pyx_m == __pyx_pyinit_module) return 0;
    PyErr_SetString(PyExc_RuntimeError, "Module 'chaplotype' 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_chaplotype(void)", 0);
  if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 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(0, 1, __pyx_L1_error)
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
  #ifdef __Pyx_CyFunction_USED
  if (__pyx_CyFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Coroutine_USED
  if (__pyx_Coroutine_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_AsyncGen_USED
  if (__pyx_AsyncGen_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_StopAsyncIteration_USED
  if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  #ifdef WITH_THREAD /* Python build with threading support? */
  PyEval_InitThreads();
  #endif
  #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("chaplotype", __pyx_methods, __pyx_k_module_containing_various_class, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_cython_runtime = PyImport_AddModule((char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error)
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  /*--- Initialize various global constants etc. ---*/
  if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 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(0, 1, __pyx_L1_error)
  #endif
  if (__pyx_module_is_main_chaplotype) {
    if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
    if (!PyDict_GetItemString(modules, "chaplotype")) {
      if (unlikely(PyDict_SetItemString(modules, "chaplotype", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Constants init code ---*/
  if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Global type/function init code ---*/
  (void)__Pyx_modinit_global_init_code();
  (void)__Pyx_modinit_variable_export_code();
  if (unlikely(__Pyx_modinit_function_export_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_type_init_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_type_import_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_variable_import_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_function_import_code() != 0)) goto __pyx_L1_error;
  /*--- Execution code ---*/
  #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
  if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif

  /* "chaplotype.pyx":9
 * 
 * import cython
 * import logging             # <<<<<<<<<<<<<<
 * import math
 * import random
 */
  __pyx_t_1 = __Pyx_Import(__pyx_n_s_logging, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 9, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_logging, __pyx_t_1) < 0) __PYX_ERR(0, 9, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":10
 * import cython
 * import logging
 * import math             # <<<<<<<<<<<<<<
 * import random
 * 
 */
  __pyx_t_1 = __Pyx_Import(__pyx_n_s_math, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 10, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_math, __pyx_t_1) < 0) __PYX_ERR(0, 10, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":11
 * import logging
 * import math
 * import random             # <<<<<<<<<<<<<<
 * 
 * cimport cython
 */
  __pyx_t_1 = __Pyx_Import(__pyx_n_s_random, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 11, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_random, __pyx_t_1) < 0) __PYX_ERR(0, 11, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":39
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_logging); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 39, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_getLogger); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 39, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 39, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_logger, __pyx_t_1) < 0) __PYX_ERR(0, 39, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "chaplotype.pyx":43
 * ###################################################################################################
 * 
 * cdef double PI = math.pi             # <<<<<<<<<<<<<<
 * cdef double mLTOT = -0.23025850929940459    # Minus log ten over ten
 * 
 */
  __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_math); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 43, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_pi); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 43, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_3 = __pyx_PyFloat_AsDouble(__pyx_t_2); if (unlikely((__pyx_t_3 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 43, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_v_10chaplotype_PI = __pyx_t_3;

  /* "chaplotype.pyx":44
 * 
 * cdef double PI = math.pi
 * cdef double mLTOT = -0.23025850929940459    # Minus log ten over ten             # <<<<<<<<<<<<<<
 * 
 * cdef extern from "math.h":
 */
  __pyx_v_10chaplotype_mLTOT = -0.23025850929940459;

  /* "chaplotype.pyx":64
 * 
 * # Some nasty global variables
 * cdef list per_base_indel_errors = [2.9e-5, 2.9e-5, 2.9e-5, 2.9e-5, 4.3e-5, 1.1e-4, 2.4e-4, 5.7e-4, 1.0e-3, 1.4e-3] + [ 1.4e-3 + 4.3e-4*(n-10) for n in range(11,50) ]             # <<<<<<<<<<<<<<
 * 
 * # homopolymer indel error model
 */
  __pyx_t_2 = PyList_New(10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 64, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_INCREF(__pyx_float_2_9eneg_5);
  __Pyx_GIVEREF(__pyx_float_2_9eneg_5);
  PyList_SET_ITEM(__pyx_t_2, 0, __pyx_float_2_9eneg_5);
  __Pyx_INCREF(__pyx_float_2_9eneg_5);
  __Pyx_GIVEREF(__pyx_float_2_9eneg_5);
  PyList_SET_ITEM(__pyx_t_2, 1, __pyx_float_2_9eneg_5);
  __Pyx_INCREF(__pyx_float_2_9eneg_5);
  __Pyx_GIVEREF(__pyx_float_2_9eneg_5);
  PyList_SET_ITEM(__pyx_t_2, 2, __pyx_float_2_9eneg_5);
  __Pyx_INCREF(__pyx_float_2_9eneg_5);
  __Pyx_GIVEREF(__pyx_float_2_9eneg_5);
  PyList_SET_ITEM(__pyx_t_2, 3, __pyx_float_2_9eneg_5);
  __Pyx_INCREF(__pyx_float_4_3eneg_5);
  __Pyx_GIVEREF(__pyx_float_4_3eneg_5);
  PyList_SET_ITEM(__pyx_t_2, 4, __pyx_float_4_3eneg_5);
  __Pyx_INCREF(__pyx_float_1_1eneg_4);
  __Pyx_GIVEREF(__pyx_float_1_1eneg_4);
  PyList_SET_ITEM(__pyx_t_2, 5, __pyx_float_1_1eneg_4);
  __Pyx_INCREF(__pyx_float_2_4eneg_4);
  __Pyx_GIVEREF(__pyx_float_2_4eneg_4);
  PyList_SET_ITEM(__pyx_t_2, 6, __pyx_float_2_4eneg_4);
  __Pyx_INCREF(__pyx_float_5_7eneg_4);
  __Pyx_GIVEREF(__pyx_float_5_7eneg_4);
  PyList_SET_ITEM(__pyx_t_2, 7, __pyx_float_5_7eneg_4);
  __Pyx_INCREF(__pyx_float_1_0eneg_3);
  __Pyx_GIVEREF(__pyx_float_1_0eneg_3);
  PyList_SET_ITEM(__pyx_t_2, 8, __pyx_float_1_0eneg_3);
  __Pyx_INCREF(__pyx_float_1_4eneg_3);
  __Pyx_GIVEREF(__pyx_float_1_4eneg_3);
  PyList_SET_ITEM(__pyx_t_2, 9, __pyx_float_1_4eneg_3);
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 64, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  for (__pyx_t_4 = 11; __pyx_t_4 < 50; __pyx_t_4+=1) {
    __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    if (PyDict_SetItem(__pyx_d, __pyx_n_s_n, __pyx_t_5) < 0) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_n); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_6 = __Pyx_PyInt_SubtractObjC(__pyx_t_5, __pyx_int_10, 10, 0, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = PyNumber_Multiply(__pyx_float_4_3eneg_4, __pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
    __pyx_t_6 = __Pyx_PyFloat_AddCObj(__pyx_float_1_4eneg_3, __pyx_t_5, 1.4e-3, 0, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_6);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_6))) __PYX_ERR(0, 64, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  }
  __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_XGOTREF(__pyx_v_10chaplotype_per_base_indel_errors);
  __Pyx_DECREF_SET(__pyx_v_10chaplotype_per_base_indel_errors, ((PyObject*)__pyx_t_6));
  __Pyx_GIVEREF(__pyx_t_6);
  __pyx_t_6 = 0;

  /* "chaplotype.pyx":67
 * 
 * # homopolymer indel error model
 * cdef bytes homopolq = bytes(''.join([chr(int(33.5 + 10*log( (idx+1)*q )/log(0.1) )) for idx,q in enumerate(per_base_indel_errors)]))             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 67, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_INCREF(__pyx_int_0);
  __pyx_t_1 = __pyx_int_0;
  __pyx_t_2 = __pyx_v_10chaplotype_per_base_indel_errors; __Pyx_INCREF(__pyx_t_2); __pyx_t_7 = 0;
  for (;;) {
    if (__pyx_t_7 >= 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_7); __Pyx_INCREF(__pyx_t_5); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(0, 67, __pyx_L1_error)
    #else
    __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    #endif
    if (PyDict_SetItem(__pyx_d, __pyx_n_s_q, __pyx_t_5) < 0) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    if (PyDict_SetItem(__pyx_d, __pyx_n_s_idx, __pyx_t_1) < 0) __PYX_ERR(0, 67, __pyx_L1_error)
    __pyx_t_5 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_1);
    __pyx_t_1 = __pyx_t_5;
    __pyx_t_5 = 0;
    __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_8 = __Pyx_PyInt_AddObjC(__pyx_t_5, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_8);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_q); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __pyx_t_9 = PyNumber_Multiply(__pyx_t_8, __pyx_t_5); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_9);
    __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_3 = __pyx_PyFloat_AsDouble(__pyx_t_9); if (unlikely((__pyx_t_3 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    __pyx_t_9 = __Pyx_PyInt_FromDouble((33.5 + ((10.0 * log(__pyx_t_3)) / log(0.1)))); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_9);
    __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_chr, __pyx_t_9); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
    if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_5))) __PYX_ERR(0, 67, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyString_Join(__pyx_kp_s_, __pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 67, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
  __pyx_t_6 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyBytes_Type)), __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 67, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_XGOTREF(__pyx_v_10chaplotype_homopolq);
  __Pyx_DECREF_SET(__pyx_v_10chaplotype_homopolq, ((PyObject*)__pyx_t_6));
  __Pyx_GIVEREF(__pyx_t_6);
  __pyx_t_6 = 0;

  /* "chaplotype.pyx":1
 * """             # <<<<<<<<<<<<<<
 * module containing various classes and functions for use in generating
 * and processing haplotypes.
 */
  __pyx_t_6 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_6);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_6) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;

  /* "htslibWrapper.pxd":295
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)
 * 
 */

  /*--- Wrapped vars code ---*/

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init chaplotype", __pyx_clineno, __pyx_lineno, __pyx_filename);
    }
    Py_CLEAR(__pyx_m);
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init chaplotype");
  }
  __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);
}

/* 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_CheckExact(key)) || 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
                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(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
                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(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;
}

/* PyIntBinop */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) {
    (void)inplace;
    (void)zerodivision_check;
    #if PY_MAJOR_VERSION < 3
    if (likely(PyInt_CheckExact(op1))) {
        const long b = intval;
        long x;
        long a = PyInt_AS_LONG(op1);
            x = (long)((unsigned long)a - b);
            if (likely((x^a) >= 0 || (x^~b) >= 0))
                return PyInt_FromLong(x);
            return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
    }
    #endif
    #if CYTHON_USE_PYLONG_INTERNALS
    if (likely(PyLong_CheckExact(op1))) {
        const long b = intval;
        long a, x;
#ifdef HAVE_LONG_LONG
        const PY_LONG_LONG llb = intval;
        PY_LONG_LONG lla, llx;
#endif
        const digit* digits = ((PyLongObject*)op1)->ob_digit;
        const Py_ssize_t size = Py_SIZE(op1);
        if (likely(__Pyx_sst_abs(size) <= 1)) {
            a = likely(size) ? digits[0] : 0;
            if (size == -1) a = -a;
        } else {
            switch (size) {
                case -2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case -3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case -4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
            }
        }
                x = a - b;
            return PyLong_FromLong(x);
#ifdef HAVE_LONG_LONG
        long_long:
                llx = lla - llb;
            return PyLong_FromLongLong(llx);
#endif
        
        
    }
    #endif
    if (PyFloat_CheckExact(op1)) {
        const long b = intval;
        double a = PyFloat_AS_DOUBLE(op1);
            double result;
            PyFPE_START_PROTECT("subtract", return NULL)
            result = ((double)a) - (double)b;
            PyFPE_END_PROTECT(result)
            return PyFloat_FromDouble(result);
    }
    return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2);
}
#endif

/* 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

/* 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;
}

/* 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, int 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, nargs,
                               k, (int)nk,
                               d, (int)nd, kwdefs, closure);
#else
    result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
                               args, 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 = func->ob_type->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 (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) {
            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

/* 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);
}

/* 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;
}

/* 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_COMPILING_IN_PYPY
        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);
#else
        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);
        }
#endif
    }
bad:
    Py_XDECREF(owned_instance);
    return;
}
#endif

/* BytesEquals */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
#if CYTHON_COMPILING_IN_PYPY
    return PyObject_RichCompareBool(s1, s2, equals);
#else
    if (s1 == s2) {
        return (equals == Py_EQ);
    } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
        const char *ps1, *ps2;
        Py_ssize_t length = PyBytes_GET_SIZE(s1);
        if (length != PyBytes_GET_SIZE(s2))
            return (equals == Py_NE);
        ps1 = PyBytes_AS_STRING(s1);
        ps2 = PyBytes_AS_STRING(s2);
        if (ps1[0] != ps2[0]) {
            return (equals == Py_NE);
        } else if (length == 1) {
            return (equals == Py_EQ);
        } else {
            int result;
#if CYTHON_USE_UNICODE_INTERNALS
            Py_hash_t hash1, hash2;
            hash1 = ((PyBytesObject*)s1)->ob_shash;
            hash2 = ((PyBytesObject*)s2)->ob_shash;
            if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
                return (equals == Py_NE);
            }
#endif
            result = memcmp(ps1, ps2, (size_t)length);
            return (equals == Py_EQ) ? (result == 0) : (result != 0);
        }
    } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
        return (equals == Py_NE);
    } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
        return (equals == Py_NE);
    } else {
        int result;
        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
        if (!py_result)
            return -1;
        result = __Pyx_PyObject_IsTrue(py_result);
        Py_DECREF(py_result);
        return result;
    }
#endif
}

/* 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();
#ifdef _MSC_VER
    else state = (PyGILState_STATE)-1;
#endif
#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
}

/* PyIntCompare */
static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED long inplace) {
    if (op1 == op2) {
        Py_RETURN_TRUE;
    }
    #if PY_MAJOR_VERSION < 3
    if (likely(PyInt_CheckExact(op1))) {
        const long b = intval;
        long a = PyInt_AS_LONG(op1);
        if (a == b) Py_RETURN_TRUE; else Py_RETURN_FALSE;
    }
    #endif
    #if CYTHON_USE_PYLONG_INTERNALS
    if (likely(PyLong_CheckExact(op1))) {
        int unequal;
        unsigned long uintval;
        Py_ssize_t size = Py_SIZE(op1);
        const digit* digits = ((PyLongObject*)op1)->ob_digit;
        if (intval == 0) {
            if (size == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE;
        } else if (intval < 0) {
            if (size >= 0)
                Py_RETURN_FALSE;
            intval = -intval;
            size = -size;
        } else {
            if (size <= 0)
                Py_RETURN_FALSE;
        }
        uintval = (unsigned long) intval;
#if PyLong_SHIFT * 4 < SIZEOF_LONG*8
        if (uintval >> (PyLong_SHIFT * 4)) {
            unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
                 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
        } else
#endif
#if PyLong_SHIFT * 3 < SIZEOF_LONG*8
        if (uintval >> (PyLong_SHIFT * 3)) {
            unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
                 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
        } else
#endif
#if PyLong_SHIFT * 2 < SIZEOF_LONG*8
        if (uintval >> (PyLong_SHIFT * 2)) {
            unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
                 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
        } else
#endif
#if PyLong_SHIFT * 1 < SIZEOF_LONG*8
        if (uintval >> (PyLong_SHIFT * 1)) {
            unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
                 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
        } else
#endif
            unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK));
        if (unequal == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE;
    }
    #endif
    if (PyFloat_CheckExact(op1)) {
        const long b = intval;
        double a = PyFloat_AS_DOUBLE(op1);
        if ((double)a == (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE;
    }
    return (
        PyObject_RichCompare(op1, op2, Py_EQ));
}

/* PyIntBinop */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) {
    (void)inplace;
    (void)zerodivision_check;
    #if PY_MAJOR_VERSION < 3
    if (likely(PyInt_CheckExact(op1))) {
        const long b = intval;
        long x;
        long a = PyInt_AS_LONG(op1);
            x = (long)((unsigned long)a + b);
            if (likely((x^a) >= 0 || (x^b) >= 0))
                return PyInt_FromLong(x);
            return PyLong_Type.tp_as_number->nb_add(op1, op2);
    }
    #endif
    #if CYTHON_USE_PYLONG_INTERNALS
    if (likely(PyLong_CheckExact(op1))) {
        const long b = intval;
        long a, x;
#ifdef HAVE_LONG_LONG
        const PY_LONG_LONG llb = intval;
        PY_LONG_LONG lla, llx;
#endif
        const digit* digits = ((PyLongObject*)op1)->ob_digit;
        const Py_ssize_t size = Py_SIZE(op1);
        if (likely(__Pyx_sst_abs(size) <= 1)) {
            a = likely(size) ? digits[0] : 0;
            if (size == -1) a = -a;
        } else {
            switch (size) {
                case -2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case -3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case -4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                case 4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
#ifdef HAVE_LONG_LONG
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
#endif
                    }
                    CYTHON_FALLTHROUGH;
                default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
            }
        }
                x = a + b;
            return PyLong_FromLong(x);
#ifdef HAVE_LONG_LONG
        long_long:
                llx = lla + llb;
            return PyLong_FromLongLong(llx);
#endif
        
        
    }
    #endif
    if (PyFloat_CheckExact(op1)) {
        const long b = intval;
        double a = PyFloat_AS_DOUBLE(op1);
            double result;
            PyFPE_START_PROTECT("add", return NULL)
            result = ((double)a) + (double)b;
            PyFPE_END_PROTECT(result)
            return PyFloat_FromDouble(result);
    }
    return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2);
}
#endif

/* StringJoin */
#if !CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
    return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL);
}
#endif

/* 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));
}

/* ObjectGetItem */
#if CYTHON_USE_TYPE_SLOTS
static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) {
    PyObject *runerr;
    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

/* 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
#ifdef __Pyx_CyFunction_USED
    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

/* 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);
}

/* 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");
}

/* 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
}

/* UnpackItemEndCheck */
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
    if (unlikely(retval)) {
        Py_DECREF(retval);
        __Pyx_RaiseTooManyValuesError(expected);
        return -1;
    } else {
        return __Pyx_IterFinish();
    }
    return 0;
}

/* UnicodeEquals */
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
#if CYTHON_COMPILING_IN_PYPY
    return PyObject_RichCompareBool(s1, s2, equals);
#else
#if PY_MAJOR_VERSION < 3
    PyObject* owned_ref = NULL;
#endif
    int s1_is_unicode, s2_is_unicode;
    if (s1 == s2) {
        goto return_eq;
    }
    s1_is_unicode = PyUnicode_CheckExact(s1);
    s2_is_unicode = PyUnicode_CheckExact(s2);
#if PY_MAJOR_VERSION < 3
    if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
        owned_ref = PyUnicode_FromObject(s2);
        if (unlikely(!owned_ref))
            return -1;
        s2 = owned_ref;
        s2_is_unicode = 1;
    } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
        owned_ref = PyUnicode_FromObject(s1);
        if (unlikely(!owned_ref))
            return -1;
        s1 = owned_ref;
        s1_is_unicode = 1;
    } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
        return __Pyx_PyBytes_Equals(s1, s2, equals);
    }
#endif
    if (s1_is_unicode & s2_is_unicode) {
        Py_ssize_t length;
        int kind;
        void *data1, *data2;
        if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
            return -1;
        length = __Pyx_PyUnicode_GET_LENGTH(s1);
        if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
            goto return_ne;
        }
#if CYTHON_USE_UNICODE_INTERNALS
        {
            Py_hash_t hash1, hash2;
        #if CYTHON_PEP393_ENABLED
            hash1 = ((PyASCIIObject*)s1)->hash;
            hash2 = ((PyASCIIObject*)s2)->hash;
        #else
            hash1 = ((PyUnicodeObject*)s1)->hash;
            hash2 = ((PyUnicodeObject*)s2)->hash;
        #endif
            if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
                goto return_ne;
            }
        }
#endif
        kind = __Pyx_PyUnicode_KIND(s1);
        if (kind != __Pyx_PyUnicode_KIND(s2)) {
            goto return_ne;
        }
        data1 = __Pyx_PyUnicode_DATA(s1);
        data2 = __Pyx_PyUnicode_DATA(s2);
        if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
            goto return_ne;
        } else if (length == 1) {
            goto return_eq;
        } else {
            int result = memcmp(data1, data2, (size_t)(length * kind));
            #if PY_MAJOR_VERSION < 3
            Py_XDECREF(owned_ref);
            #endif
            return (equals == Py_EQ) ? (result == 0) : (result != 0);
        }
    } else if ((s1 == Py_None) & s2_is_unicode) {
        goto return_ne;
    } else if ((s2 == Py_None) & s1_is_unicode) {
        goto return_ne;
    } else {
        int result;
        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
        #if PY_MAJOR_VERSION < 3
        Py_XDECREF(owned_ref);
        #endif
        if (!py_result)
            return -1;
        result = __Pyx_PyObject_IsTrue(py_result);
        Py_DECREF(py_result);
        return result;
    }
return_eq:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(owned_ref);
    #endif
    return (equals == Py_EQ);
return_ne:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(owned_ref);
    #endif
    return (equals == Py_NE);
#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

/* SetVTable */
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000
    PyObject *ob = PyCapsule_New(vtable, 0, 0);
#else
    PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
#endif
    if (!ob)
        goto bad;
    if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
        goto bad;
    Py_DECREF(ob);
    return 0;
bad:
    Py_XDECREF(ob);
    return -1;
}

/* 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);
  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_reduce_ex = NULL;
    PyObject *reduce = NULL;
    PyObject *reduce_ex = NULL;
    PyObject *reduce_cython = NULL;
    PyObject *setstate = NULL;
    PyObject *setstate_cython = NULL;
#if CYTHON_USE_PYTYPE_LOOKUP
    if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD;
#else
    if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD;
#endif
#if CYTHON_USE_PYTYPE_LOOKUP
    object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
#else
    object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
#endif
    reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto 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 BAD;
#else
        object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD;
#endif
        reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD;
        if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
            reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD;
            ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD;
            ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto 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_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD;
                ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD;
                ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD;
            }
            PyType_Modified((PyTypeObject*)type_obj);
        }
    }
    goto GOOD;
BAD:
    if (!PyErr_Occurred())
        PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name);
    ret = -1;
GOOD:
#if !CYTHON_USE_PYTYPE_LOOKUP
    Py_XDECREF(object_reduce);
    Py_XDECREF(object_reduce_ex);
#endif
    Py_XDECREF(reduce);
    Py_XDECREF(reduce_ex);
    Py_XDECREF(reduce_cython);
    Py_XDECREF(setstate);
    Py_XDECREF(setstate_cython);
    return ret;
}

/* TypeImport */
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name,
    size_t size, enum __Pyx_ImportType_CheckSize check_size)
{
    PyObject *result = 0;
    char warning[200];
    Py_ssize_t basicsize;
#ifdef Py_LIMITED_API
    PyObject *py_basicsize;
#endif
    result = PyObject_GetAttrString(module, class_name);
    if (!result)
        goto bad;
    if (!PyType_Check(result)) {
        PyErr_Format(PyExc_TypeError,
            "%.200s.%.200s is not a type object",
            module_name, class_name);
        goto bad;
    }
#ifndef Py_LIMITED_API
    basicsize = ((PyTypeObject *)result)->tp_basicsize;
#else
    py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
    if (!py_basicsize)
        goto bad;
    basicsize = PyLong_AsSsize_t(py_basicsize);
    Py_DECREF(py_basicsize);
    py_basicsize = 0;
    if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
        goto bad;
#endif
    if ((size_t)basicsize < size) {
        PyErr_Format(PyExc_ValueError,
            "%.200s.%.200s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        goto bad;
    }
    if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) {
        PyErr_Format(PyExc_ValueError,
            "%.200s.%.200s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        goto bad;
    }
    else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) {
        PyOS_snprintf(warning, sizeof(warning),
            "%s.%s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
    }
    return (PyTypeObject *)result;
bad:
    Py_XDECREF(result);
    return NULL;
}
#endif

/* GetVTable */
static void* __Pyx_GetVtable(PyObject *dict) {
    void* ptr;
    PyObject *ob = PyObject_GetItem(dict, __pyx_n_s_pyx_vtable);
    if (!ob)
        goto bad;
#if PY_VERSION_HEX >= 0x02070000
    ptr = PyCapsule_GetPointer(ob, 0);
#else
    ptr = PyCObject_AsVoidPtr(ob);
#endif
    if (!ptr && !PyErr_Occurred())
        PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
    Py_DECREF(ob);
    return ptr;
bad:
    Py_XDECREF(ob);
    return NULL;
}

/* 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 (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;
}

/* PyFloatBinop */
#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyFloat_AddCObj(PyObject *op1, PyObject *op2, double floatval, int inplace, int zerodivision_check) {
    const double a = floatval;
    double b, result;
    (void)inplace;
    (void)zerodivision_check;
    if (likely(PyFloat_CheckExact(op2))) {
        b = PyFloat_AS_DOUBLE(op2);
        
    } else
    #if PY_MAJOR_VERSION < 3
    if (likely(PyInt_CheckExact(op2))) {
        b = (double) PyInt_AS_LONG(op2);
        
    } else
    #endif
    if (likely(PyLong_CheckExact(op2))) {
        #if CYTHON_USE_PYLONG_INTERNALS
        const digit* digits = ((PyLongObject*)op2)->ob_digit;
        const Py_ssize_t size = Py_SIZE(op2);
        switch (size) {
            case  0: b = 0.0; break;
            case -1: b = -(double) digits[0]; break;
            case  1: b = (double) digits[0]; break;
            case -2:
            case 2:
                if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (1 * PyLong_SHIFT < 53))) {
                    b = (double) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                    if ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) {
                        if (size == -2)
                            b = -b;
                        break;
                    }
                }
                CYTHON_FALLTHROUGH;
            case -3:
            case 3:
                if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (2 * PyLong_SHIFT < 53))) {
                    b = (double) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                    if ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) {
                        if (size == -3)
                            b = -b;
                        break;
                    }
                }
                CYTHON_FALLTHROUGH;
            case -4:
            case 4:
                if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT && ((8 * sizeof(unsigned long) < 53) || (3 * PyLong_SHIFT < 53))) {
                    b = (double) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                    if ((8 * sizeof(unsigned long) < 53) || (4 * PyLong_SHIFT < 53) || (b < (double) ((PY_LONG_LONG)1 << 53))) {
                        if (size == -4)
                            b = -b;
                        break;
                    }
                }
                CYTHON_FALLTHROUGH;
            default:
        #else
        {
        #endif
            b = PyLong_AsDouble(op2);
            if (unlikely(b == -1.0 && PyErr_Occurred())) return NULL;
            
        }
    } else {
        return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2);
    }
        
        PyFPE_START_PROTECT("add", return NULL)
        result = a + b;
        PyFPE_END_PROTECT(result)
        return PyFloat_FromDouble(result);
}
#endif

/* PyIntFromDouble */
  #if PY_MAJOR_VERSION < 3
static CYTHON_INLINE PyObject* __Pyx_PyInt_FromDouble(double value) {
    if (value >= (double)LONG_MIN && value <= (double)LONG_MAX) {
        return PyInt_FromLong((long)value);
    }
    return PyLong_FromDouble(value);
}
#endif

/* CLineInTraceback */
  #ifndef CYTHON_CLINE_IN_TRACEBACK
static int __Pyx_CLineForTraceback(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;
        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"
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
            const char *funcname, int c_line,
            int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyObject *py_srcfile = 0;
    PyObject *py_funcname = 0;
    #if PY_MAJOR_VERSION < 3
    py_srcfile = PyString_FromString(filename);
    #else
    py_srcfile = PyUnicode_FromString(filename);
    #endif
    if (!py_srcfile) goto bad;
    if (c_line) {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #else
        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #endif
    }
    else {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromString(funcname);
        #else
        py_funcname = PyUnicode_FromString(funcname);
        #endif
    }
    if (!py_funcname) goto bad;
    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);
    Py_DECREF(py_funcname);
    return py_code;
bad:
    Py_XDECREF(py_srcfile);
    Py_XDECREF(py_funcname);
    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;
    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) {
        py_code = __Pyx_CreateCodeObjectForTraceback(
            funcname, c_line, py_line, filename);
        if (!py_code) goto bad;
        __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;\
    }

/* CIntToPy */
  static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
    const int neg_one = (int) ((int) 0 - (int) 1), const_zero = (int) 0;
    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) {
    const long neg_one = (long) ((long) 0 - (long) 1), const_zero = (long) 0;
    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_char(char value) {
    const char neg_one = (char) ((char) 0 - (char) 1), const_zero = (char) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(char) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(char) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(char) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(char) <= 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(char),
                                     little, !is_unsigned);
    }
}

/* CIntFromPy */
  static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
    const int neg_one = (int) ((int) 0 - (int) 1), const_zero = (int) 0;
    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
            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 PY_LONG_LONG __Pyx_PyInt_As_PY_LONG_LONG(PyObject *x) {
    const PY_LONG_LONG neg_one = (PY_LONG_LONG) ((PY_LONG_LONG) 0 - (PY_LONG_LONG) 1), const_zero = (PY_LONG_LONG) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(PY_LONG_LONG) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (PY_LONG_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 (PY_LONG_LONG) 0;
                case  1: __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, digit, digits[0])
                case 2:
                    if (8 * sizeof(PY_LONG_LONG) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) >= 2 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((((PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(PY_LONG_LONG) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) >= 3 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((((((PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(PY_LONG_LONG) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_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(PY_LONG_LONG) >= 4 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((((((((PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            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 (PY_LONG_LONG) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(PY_LONG_LONG) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(PY_LONG_LONG, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(PY_LONG_LONG) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(PY_LONG_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 (PY_LONG_LONG) 0;
                case -1: __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(PY_LONG_LONG,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(PY_LONG_LONG) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((PY_LONG_LONG)-1)*(((((PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(PY_LONG_LONG) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) ((((((PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((PY_LONG_LONG)-1)*(((((((PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(PY_LONG_LONG) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_LONG, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) ((((((((PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_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(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) (((PY_LONG_LONG)-1)*(((((((((PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(PY_LONG_LONG) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(PY_LONG_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(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                            return (PY_LONG_LONG) ((((((((((PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (PY_LONG_LONG)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(PY_LONG_LONG) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(PY_LONG_LONG, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(PY_LONG_LONG) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(PY_LONG_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
            PY_LONG_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 (PY_LONG_LONG) -1;
        }
    } else {
        PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (PY_LONG_LONG) -1;
        val = __Pyx_PyInt_As_PY_LONG_LONG(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to PY_LONG_LONG");
    return (PY_LONG_LONG) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to PY_LONG_LONG");
    return (PY_LONG_LONG) -1;
}

/* CIntFromPy */
  static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
    const long neg_one = (long) ((long) 0 - (long) 1), const_zero = (long) 0;
    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
            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

/* CheckBinaryVersion */
  static int __Pyx_check_binary_version(void) {
    char ctversion[4], rtversion[4];
    PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
    PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
    if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
        char message[200];
        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;
}

/* FunctionExport */
  static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    union {
        void (*fp)(void);
        void *p;
    } tmp;
    d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__");
    if (!d) {
        PyErr_Clear();
        d = PyDict_New();
        if (!d)
            goto bad;
        Py_INCREF(d);
        if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0)
            goto bad;
    }
    tmp.fp = f;
#if PY_VERSION_HEX >= 0x02070000
    cobj = PyCapsule_New(tmp.p, sig, 0);
#else
    cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0);
#endif
    if (!cobj)
        goto bad;
    if (PyDict_SetItemString(d, name, cobj) < 0)
        goto bad;
    Py_DECREF(cobj);
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(cobj);
    Py_XDECREF(d);
    return -1;
}

/* VoidPtrImport */
  #ifndef __PYX_HAVE_RT_ImportVoidPtr
#define __PYX_HAVE_RT_ImportVoidPtr
static int __Pyx_ImportVoidPtr(PyObject *module, const char *name, void **p, const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
    if (!d)
        goto bad;
    cobj = PyDict_GetItemString(d, name);
    if (!cobj) {
        PyErr_Format(PyExc_ImportError,
            "%.200s does not export expected C variable %.200s",
                PyModule_GetName(module), name);
        goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000
    if (!PyCapsule_IsValid(cobj, sig)) {
        PyErr_Format(PyExc_TypeError,
            "C variable %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), name, sig, PyCapsule_GetName(cobj));
        goto bad;
    }
    *p = PyCapsule_GetPointer(cobj, sig);
#else
    {const char *desc, *s1, *s2;
    desc = (const char *)PyCObject_GetDesc(cobj);
    if (!desc)
        goto bad;
    s1 = desc; s2 = sig;
    while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
    if (*s1 != *s2) {
        PyErr_Format(PyExc_TypeError,
            "C variable %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), name, sig, desc);
        goto bad;
    }
    *p = PyCObject_AsVoidPtr(cobj);}
#endif
    if (!(*p))
        goto bad;
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(d);
    return -1;
}
#endif

/* FunctionImport */
  #ifndef __PYX_HAVE_RT_ImportFunction
#define __PYX_HAVE_RT_ImportFunction
static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    union {
        void (*fp)(void);
        void *p;
    } tmp;
    d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
    if (!d)
        goto bad;
    cobj = PyDict_GetItemString(d, funcname);
    if (!cobj) {
        PyErr_Format(PyExc_ImportError,
            "%.200s does not export expected C function %.200s",
                PyModule_GetName(module), funcname);
        goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000
    if (!PyCapsule_IsValid(cobj, sig)) {
        PyErr_Format(PyExc_TypeError,
            "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
        goto bad;
    }
    tmp.p = PyCapsule_GetPointer(cobj, sig);
#else
    {const char *desc, *s1, *s2;
    desc = (const char *)PyCObject_GetDesc(cobj);
    if (!desc)
        goto bad;
    s1 = desc; s2 = sig;
    while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
    if (*s1 != *s2) {
        PyErr_Format(PyExc_TypeError,
            "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), funcname, sig, desc);
        goto bad;
    }
    tmp.p = PyCObject_AsVoidPtr(cobj);}
#endif
    *f = tmp.fp;
    if (!(*f))
        goto bad;
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(d);
    return -1;
}
#endif

/* 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 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 */
