/* 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__assembler
#define __PYX_HAVE_API__assembler
/* 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/assembler.pyx",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "cython/htslibWrapper.pxd",
  "cython/fastafile.pxd",
  "cython/cwindow.pxd",
  "cython/variant.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_13htslibWrapper_ReadIterator;
struct __pyx_obj_9fastafile_FastaIndex;
struct __pyx_obj_9fastafile_FastaFile;
struct __pyx_obj_7cwindow_ReadArray;
struct __pyx_obj_7cwindow_bamReadBuffer;
struct __pyx_obj_7variant_Variant;
struct __pyx_obj_7variant_VariantCandidateGenerator;
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_t_9assembler_Node;
typedef struct __pyx_t_9assembler_Node __pyx_t_9assembler_Node;
struct __pyx_t_9assembler_NodeStack;
typedef struct __pyx_t_9assembler_NodeStack __pyx_t_9assembler_NodeStack;
struct __pyx_t_9assembler_Edge;
typedef struct __pyx_t_9assembler_Edge __pyx_t_9assembler_Edge;
struct __pyx_t_9assembler_EdgeStack;
typedef struct __pyx_t_9assembler_EdgeStack __pyx_t_9assembler_EdgeStack;
struct __pyx_t_9assembler_NodeDict;
typedef struct __pyx_t_9assembler_NodeDict __pyx_t_9assembler_NodeDict;
struct __pyx_t_9assembler_Path;
typedef struct __pyx_t_9assembler_Path __pyx_t_9assembler_Path;
struct __pyx_t_9assembler_PathStack;
typedef struct __pyx_t_9assembler_PathStack __pyx_t_9assembler_PathStack;
struct __pyx_t_9assembler_DeBruijnGraph;
typedef struct __pyx_t_9assembler_DeBruijnGraph __pyx_t_9assembler_DeBruijnGraph;

/* "assembler.pyx":73
 * 
 * # Represents a node in the graph
 * ctypedef struct Node:             # <<<<<<<<<<<<<<
 *     Edge* edges[4]
 *     char* sequence
 */
struct __pyx_t_9assembler_Node {
  __pyx_t_9assembler_Edge *edges[4];
  char *sequence;
  int colours;
  int position;
  int kmerSize;
  int nEdges;
  double weight;
  char dfsColour;
};

/* "assembler.pyx":84
 * 
 * # Simple implementation of a stack, for storing nodes.
 * ctypedef struct NodeStack:             # <<<<<<<<<<<<<<
 *     Node** elements
 *     int capacity
 */
struct __pyx_t_9assembler_NodeStack {
  __pyx_t_9assembler_Node **elements;
  int capacity;
  int top;
};

/* "assembler.pyx":69
 * 
 * # Forward declaration of Edge struct, so it can be referred to in Node.
 * ctypedef struct Edge             # <<<<<<<<<<<<<<
 * ctypedef struct EdgeStack
 * 
 */
struct __pyx_t_9assembler_Edge {
  __pyx_t_9assembler_Node *startNode;
  __pyx_t_9assembler_Node *endNode;
  double weight;
};

/* "assembler.pyx":70
 * # Forward declaration of Edge struct, so it can be referred to in Node.
 * ctypedef struct Edge
 * ctypedef struct EdgeStack             # <<<<<<<<<<<<<<
 * 
 * # Represents a node in the graph
 */
struct __pyx_t_9assembler_EdgeStack {
  __pyx_t_9assembler_Edge **elements;
  int capacity;
  int top;
};

/* "assembler.pyx":102
 * 
 * # A dictionary of Nodes
 * ctypedef struct NodeDict:             # <<<<<<<<<<<<<<
 *     Node*** buckets
 *     int* bucketSize
 */
struct __pyx_t_9assembler_NodeDict {
  __pyx_t_9assembler_Node ***buckets;
  int *bucketSize;
  int nBuckets;
};

/* "assembler.pyx":108
 * 
 * # Hold a path through the graph
 * ctypedef struct Path:             # <<<<<<<<<<<<<<
 *     NodeStack* nodes
 *     int nNodes
 */
struct __pyx_t_9assembler_Path {
  __pyx_t_9assembler_NodeStack *nodes;
  int nNodes;
  int isBubble;
  double weight;
};

/* "assembler.pyx":115
 * 
 * # A stack of paths
 * ctypedef struct PathStack:             # <<<<<<<<<<<<<<
 *     Path** elements
 *     int capacity
 */
struct __pyx_t_9assembler_PathStack {
  __pyx_t_9assembler_Path **elements;
  int capacity;
  int top;
};

/* "assembler.pyx":121
 * 
 * # A graph
 * ctypedef struct DeBruijnGraph:             # <<<<<<<<<<<<<<
 *     int kmerSize
 *     NodeStack* allNodes
 */
struct __pyx_t_9assembler_DeBruijnGraph {
  int kmerSize;
  __pyx_t_9assembler_NodeStack *allNodes;
  __pyx_t_9assembler_NodeDict *nodes;
};

/* "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;
};


/* "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;
};


/* "cwindow.pxd":13
 * ###################################################################################################
 * 
 * cdef class ReadArray:             # <<<<<<<<<<<<<<
 *     cdef cAlignedRead** array
 *     cdef cAlignedRead** windowStart
 */
struct __pyx_obj_7cwindow_ReadArray {
  PyObject_HEAD
  struct __pyx_vtabstruct_7cwindow_ReadArray *__pyx_vtab;
  __pyx_t_13htslibWrapper_cAlignedRead **array;
  __pyx_t_13htslibWrapper_cAlignedRead **windowStart;
  __pyx_t_13htslibWrapper_cAlignedRead **windowEnd;
  int __pyx___size;
  int __pyx___capacity;
  int __pyx___longestRead;
};


/* "cwindow.pxd":29
 * ###################################################################################################
 * 
 * cdef class bamReadBuffer:             # <<<<<<<<<<<<<<
 *     cdef char* chrom
 *     cdef int chromID
 */
struct __pyx_obj_7cwindow_bamReadBuffer {
  PyObject_HEAD
  struct __pyx_vtabstruct_7cwindow_bamReadBuffer *__pyx_vtab;
  char *chrom;
  int chromID;
  int *filteredReadCountsByType;
  int isSorted;
  int startBase;
  int endBase;
  int windowStartBase;
  int windowEndBase;
  int maxReads;
  int minMapQual;
  int minBaseQual;
  int minFlank;
  int trimReadFlank;
  int verbosity;
  int minGoodBases;
  int trimOverlapping;
  int trimAdapter;
  int trimSoftClipped;
  __pyx_t_13htslibWrapper_cAlignedRead *lastRead;
  PyObject *sample;
  struct __pyx_obj_7cwindow_ReadArray *reads;
  struct __pyx_obj_7cwindow_ReadArray *badReads;
  struct __pyx_obj_7cwindow_ReadArray *brokenMates;
};


/* "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;
};



/* "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 *);
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  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;


/* "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;


/* "cwindow.pxd":13
 * ###################################################################################################
 * 
 * cdef class ReadArray:             # <<<<<<<<<<<<<<
 *     cdef cAlignedRead** array
 *     cdef cAlignedRead** windowStart
 */

struct __pyx_vtabstruct_7cwindow_ReadArray {
  int (*getSize)(struct __pyx_obj_7cwindow_ReadArray *);
  void (*append)(struct __pyx_obj_7cwindow_ReadArray *, __pyx_t_13htslibWrapper_cAlignedRead *);
  void (*setWindowPointers)(struct __pyx_obj_7cwindow_ReadArray *, int, int);
  void (*setWindowPointersBasedOnMatePos)(struct __pyx_obj_7cwindow_ReadArray *, int, int);
  int (*getLengthOfLongestRead)(struct __pyx_obj_7cwindow_ReadArray *);
  int (*countReadsCoveringRegion)(struct __pyx_obj_7cwindow_ReadArray *, int, int);
};
static struct __pyx_vtabstruct_7cwindow_ReadArray *__pyx_vtabptr_7cwindow_ReadArray;


/* "cwindow.pxd":29
 * ###################################################################################################
 * 
 * cdef class bamReadBuffer:             # <<<<<<<<<<<<<<
 *     cdef char* chrom
 *     cdef int chromID
 */

struct __pyx_vtabstruct_7cwindow_bamReadBuffer {
  void (*setWindowPointers)(struct __pyx_obj_7cwindow_bamReadBuffer *, int, int, int, int, char *, int);
  void (*recompressReadsInCurrentWindow)(struct __pyx_obj_7cwindow_bamReadBuffer *, int, int, char *, int, int);
  void (*addReadToBuffer)(struct __pyx_obj_7cwindow_bamReadBuffer *, __pyx_t_13htslibWrapper_cAlignedRead *);
  int (*countImproperPairs)(struct __pyx_obj_7cwindow_bamReadBuffer *);
  int (*countAlignmentGaps)(struct __pyx_obj_7cwindow_bamReadBuffer *);
  void (*sortReads)(struct __pyx_obj_7cwindow_bamReadBuffer *);
  void (*sortBrokenMates)(struct __pyx_obj_7cwindow_bamReadBuffer *);
  void (*logFilterSummary)(struct __pyx_obj_7cwindow_bamReadBuffer *);
  int (*countReadsCoveringRegion)(struct __pyx_obj_7cwindow_bamReadBuffer *, int, int);
};
static struct __pyx_vtabstruct_7cwindow_bamReadBuffer *__pyx_vtabptr_7cwindow_bamReadBuffer;


/* "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;

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/* py_abs.proto */
#if CYTHON_USE_PYLONG_INTERNALS
static PyObject *__Pyx_PyLong_AbsNeg(PyObject *num);
#define __Pyx_PyNumber_Absolute(x)\
    ((likely(PyLong_CheckExact(x))) ?\
         (likely(Py_SIZE(x) >= 0) ? (Py_INCREF(x), (x)) : __Pyx_PyLong_AbsNeg(x)) :\
         PyNumber_Absolute(x))
#else
#define __Pyx_PyNumber_Absolute(x)  PyNumber_Absolute(x)
#endif

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

/* 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);

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

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

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

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

/* 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 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);

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


/* Module declarations from 'cython' */

/* 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 'fastafile' */
static PyTypeObject *__pyx_ptype_9fastafile_FastaIndex = 0;
static PyTypeObject *__pyx_ptype_9fastafile_FastaFile = 0;

/* Module declarations from 'cwindow' */
static PyTypeObject *__pyx_ptype_7cwindow_ReadArray = 0;
static PyTypeObject *__pyx_ptype_7cwindow_bamReadBuffer = 0;

/* 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 'assembler' */
static int __pyx_v_9assembler_REF;
static int __pyx_v_9assembler_READ;
static int __pyx_v_9assembler_REF_AND_READ;
static __pyx_t_9assembler_Path *__pyx_f_9assembler_createPath(int); /*proto*/
static void __pyx_f_9assembler_destroyPath(__pyx_t_9assembler_Path *); /*proto*/
static void __pyx_f_9assembler_addNodeToPath(__pyx_t_9assembler_Path *, __pyx_t_9assembler_Node *, double); /*proto*/
static __pyx_t_9assembler_Node *__pyx_f_9assembler_createNode(char *, int, int, int, double); /*proto*/
static void *__pyx_f_9assembler_destroyNode(__pyx_t_9assembler_Node *); /*proto*/
static CYTHON_INLINE int __pyx_f_9assembler_Node_Equal(__pyx_t_9assembler_Node *, __pyx_t_9assembler_Node *); /*proto*/
static CYTHON_INLINE void __pyx_f_9assembler_Node_AddEdge(__pyx_t_9assembler_Node *, __pyx_t_9assembler_Edge *); /*proto*/
static CYTHON_INLINE int __pyx_f_9assembler_nodePosComp(void const *, void const *); /*proto*/
static CYTHON_INLINE unsigned int __pyx_f_9assembler_hashKmer(char *, int); /*proto*/
static __pyx_t_9assembler_PathStack *__pyx_f_9assembler_createPathStack(int); /*proto*/
static void __pyx_f_9assembler_destroyPathStack(__pyx_t_9assembler_PathStack *); /*proto*/
static int __pyx_f_9assembler_PathStack_IsEmpty(__pyx_t_9assembler_PathStack *); /*proto*/
static int __pyx_f_9assembler_PathStack_IsFull(__pyx_t_9assembler_PathStack *); /*proto*/
static void __pyx_f_9assembler_PathStack_Push(__pyx_t_9assembler_PathStack *, __pyx_t_9assembler_Path *); /*proto*/
static __pyx_t_9assembler_Path *__pyx_f_9assembler_PathStack_Pop(__pyx_t_9assembler_PathStack *); /*proto*/
static __pyx_t_9assembler_NodeStack *__pyx_f_9assembler_createNodeStack(int); /*proto*/
static void __pyx_f_9assembler_destroyNodeStack(__pyx_t_9assembler_NodeStack *); /*proto*/
static int __pyx_f_9assembler_NodeStack_IsEmpty(__pyx_t_9assembler_NodeStack *); /*proto*/
static int __pyx_f_9assembler_NodeStack_IsFull(__pyx_t_9assembler_NodeStack *); /*proto*/
static void __pyx_f_9assembler_NodeStack_Push(__pyx_t_9assembler_NodeStack *, __pyx_t_9assembler_Node *); /*proto*/
static __pyx_t_9assembler_Node *__pyx_f_9assembler_NodeStack_Pop(__pyx_t_9assembler_NodeStack *); /*proto*/
static __pyx_t_9assembler_Edge *__pyx_f_9assembler_createEdge(__pyx_t_9assembler_Node *, __pyx_t_9assembler_Node *, double); /*proto*/
static void __pyx_f_9assembler_destroyEdge(__pyx_t_9assembler_Edge *); /*proto*/
static int __pyx_f_9assembler_EdgeStack_IsEmpty(__pyx_t_9assembler_EdgeStack *); /*proto*/
static int __pyx_f_9assembler_EdgeStack_IsFull(__pyx_t_9assembler_EdgeStack *); /*proto*/
static __pyx_t_9assembler_NodeDict *__pyx_f_9assembler_createNodeDict(int); /*proto*/
static void __pyx_f_9assembler_destroyNodeDict(__pyx_t_9assembler_NodeDict *); /*proto*/
static int __pyx_f_9assembler_NodeDict_FindOrInsert(__pyx_t_9assembler_NodeDict *, __pyx_t_9assembler_Node **, int, __pyx_t_9assembler_Node **); /*proto*/
static __pyx_t_9assembler_DeBruijnGraph *__pyx_f_9assembler_createDeBruijnGraph(int, int); /*proto*/
static void __pyx_f_9assembler_destroyDeBruijnGraph(__pyx_t_9assembler_DeBruijnGraph *); /*proto*/
static int __pyx_f_9assembler_DeBruijnGraph_InsertOrUpdateNode(__pyx_t_9assembler_DeBruijnGraph *, __pyx_t_9assembler_Node **); /*proto*/
static void __pyx_f_9assembler_DeBruijnGraph_AddEdge(__pyx_t_9assembler_DeBruijnGraph *, __pyx_t_9assembler_Node *, __pyx_t_9assembler_Node *, double); /*proto*/
static int __pyx_f_9assembler_dfsVisit(__pyx_t_9assembler_Node *, double); /*proto*/
static int __pyx_f_9assembler_detectCyclesInGraph_Recursive(__pyx_t_9assembler_DeBruijnGraph *, double); /*proto*/
static int __pyx_f_9assembler_checkPathForCycles(__pyx_t_9assembler_Path *); /*proto*/
static __pyx_t_9assembler_PathStack *__pyx_f_9assembler_getVariantPathsThroughGraphFromNode(__pyx_t_9assembler_DeBruijnGraph *, __pyx_t_9assembler_Path *, double); /*proto*/
static PyObject *__pyx_f_9assembler_findBubblesInGraph(__pyx_t_9assembler_DeBruijnGraph *, double, char *, char *, int, int, int, int, int); /*proto*/
static struct __pyx_obj_7variant_Variant *__pyx_f_9assembler_extractVarFromBubblePath(__pyx_t_9assembler_DeBruijnGraph *, __pyx_t_9assembler_Path *, char *, char *, int, int, int); /*proto*/
static void __pyx_f_9assembler_loadReferenceIntoGraph(__pyx_t_9assembler_DeBruijnGraph *, char *, int, int); /*proto*/
static void __pyx_f_9assembler_loadReadIntoGraph(__pyx_t_13htslibWrapper_cAlignedRead *, __pyx_t_9assembler_DeBruijnGraph *, int, int); /*proto*/
static void __pyx_f_9assembler_loadBAMDataIntoGraph(__pyx_t_9assembler_DeBruijnGraph *, PyObject *, int, int, int, int); /*proto*/
#define __Pyx_MODULE_NAME "assembler"
extern int __pyx_module_is_main_assembler;
int __pyx_module_is_main_assembler = 0;

/* Implementation of 'assembler' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_StandardError;
static const char __pyx_k_Log[] = "Log";
static const char __pyx_k_info[] = "info";
static const char __pyx_k_main[] = "__main__";
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_heapq[] = "heapq";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_logger[] = "logger";
static const char __pyx_k_logging[] = "logging";
static const char __pyx_k_warning[] = "warning";
static const char __pyx_k_minReads[] = "minReads";
static const char __pyx_k_noCycles[] = "noCycles";
static const char __pyx_k_Null_Node[] = "Null Node";
static const char __pyx_k_Null_path[] = "Null path";
static const char __pyx_k_getLogger[] = "getLogger";
static const char __pyx_k_verbosity[] = "verbosity";
static const char __pyx_k_minMapQual[] = "minMapQual";
static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
static const char __pyx_k_collections[] = "collections";
static const char __pyx_k_defaultdict[] = "defaultdict";
static const char __pyx_k_minBaseQual[] = "minBaseQual";
static const char __pyx_k_StandardError[] = "StandardError";
static const char __pyx_k_assembleBadReads[] = "assembleBadReads";
static const char __pyx_k_assemblerKmerSize[] = "assemblerKmerSize";
static const char __pyx_k_assemblyRegionSize[] = "assemblyRegionSize";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_assembleBrokenPairs[] = "assembleBrokenPairs";
static const char __pyx_k_Assembling_region_s_s_s[] = "Assembling region %s:%s-%s";
static const char __pyx_k_Could_not_allocate_node[] = "Could not allocate node";
static const char __pyx_k_Could_not_allocate_path[] = "Could not allocate path";
static const char __pyx_k_Logging_path_of_s_nodes[] = "Logging path of %s nodes";
static const char __pyx_k_Error_Could_not_NodeDict[] = "Error. Could not NodeDict";
static const char __pyx_k_Could_not_re_allocate_bucket[] = "Could not re-allocate bucket";
static const char __pyx_k_Error_Could_not_allocate_edge[] = "Error. Could not allocate edge";
static const char __pyx_k_Could_not_assemble_region_s_s_s[] = "Could not assemble region %s:%s-%s without cycles. Max k-mer size tried = %s";
static const char __pyx_k_Could_not_re_allocate_EdgeStack[] = "Could not re-allocate EdgeStack";
static const char __pyx_k_Could_not_re_allocate_NodeStack[] = "Could not re-allocate NodeStack";
static const char __pyx_k_Could_not_re_allocate_PathStack[] = "Could not re-allocate PathStack";
static const char __pyx_k_Cython_module_used_to_interface[] = "\nCython module used to interface to assembler routines.\n";
static const char __pyx_k_Node_struct_cannot_have_4_edges[] = "Node struct cannot have > 4 edges. Now we have %s. This will cause problems";
static const char __pyx_k_Could_not_allocate_hash_table_bu[] = "Could not allocate hash table bucket with size %s";
static const char __pyx_k_Could_not_allocate_memory_for_De[] = "Could not allocate memory for DeBruijnGraph";
static const char __pyx_k_Could_not_allocate_memory_for_ch[] = "Could not allocate memory for charReadSeq of size %s";
static const char __pyx_k_Could_not_allocate_memory_for_st[] = "Could not allocate memory for string of size %s";
static const char __pyx_k_Error_Could_not_NodeDict_bucketS[] = "Error. Could not NodeDict.bucketSize of size %s";
static const char __pyx_k_Error_Could_not_NodeDict_buckets[] = "Error. Could not NodeDict.buckets of size %s";
static const char __pyx_k_Error_Could_not_allocate_edge_st[] = "Error. Could not allocate edge stack with capacity %s";
static const char __pyx_k_Error_Could_not_allocate_node_st[] = "Error. Could not allocate node stack with capacity %s";
static const char __pyx_k_Error_Could_not_allocate_path_st[] = "Error. Could not allocate path stack with capacity %s";
static const char __pyx_k_Found_complex_variation_that_Pla[] = "Found complex variation that Platypus can't deal with yet at %s:%s-%s";
static const char __pyx_k_Found_cycles_in_region_s_s_s_wit[] = "Found cycles in region %s:%s-%s with kmer size %s. Trying again with kmer size %s";
static const char __pyx_k_Platypus_assembler_found_candida[] = "Platypus assembler found candidate variant of size %s. %s:%s-%s %s --> %s";
static const char __pyx_k_Pos_s_Seq_s_RefSeq_c_Colours_s_N[] = "Pos = %s. Seq = %s. RefSeq = %c. Colours = %s. Node weight = %s";
static const char __pyx_k_nNodes_s_nFilledBuckets_s_mean_e[] = "nNodes = %s. nFilledBuckets = %s. mean entries/bucket = %s";
static const char __pyx_k_Error_Could_not_allocate_edge_st_2[] = "Error. Could not allocate edge stack elements with capacity %s";
static const char __pyx_k_Error_Could_not_allocate_node_st_2[] = "Error. Could not allocate node stack elements with capacity %s";
static const char __pyx_k_Error_Could_not_allocate_path_st_2[] = "Error. Could not allocate path stack elements with capacity %s";
static PyObject *__pyx_kp_s_Assembling_region_s_s_s;
static PyObject *__pyx_kp_s_Could_not_allocate_hash_table_bu;
static PyObject *__pyx_kp_s_Could_not_allocate_memory_for_De;
static PyObject *__pyx_kp_s_Could_not_allocate_memory_for_ch;
static PyObject *__pyx_kp_s_Could_not_allocate_memory_for_st;
static PyObject *__pyx_kp_s_Could_not_allocate_node;
static PyObject *__pyx_kp_s_Could_not_allocate_path;
static PyObject *__pyx_kp_s_Could_not_assemble_region_s_s_s;
static PyObject *__pyx_kp_s_Could_not_re_allocate_EdgeStack;
static PyObject *__pyx_kp_s_Could_not_re_allocate_NodeStack;
static PyObject *__pyx_kp_s_Could_not_re_allocate_PathStack;
static PyObject *__pyx_kp_s_Could_not_re_allocate_bucket;
static PyObject *__pyx_kp_s_Error_Could_not_NodeDict;
static PyObject *__pyx_kp_s_Error_Could_not_NodeDict_bucketS;
static PyObject *__pyx_kp_s_Error_Could_not_NodeDict_buckets;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_edge;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_edge_st;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_edge_st_2;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_node_st;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_node_st_2;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_path_st;
static PyObject *__pyx_kp_s_Error_Could_not_allocate_path_st_2;
static PyObject *__pyx_kp_s_Found_complex_variation_that_Pla;
static PyObject *__pyx_kp_s_Found_cycles_in_region_s_s_s_wit;
static PyObject *__pyx_n_s_Log;
static PyObject *__pyx_kp_s_Logging_path_of_s_nodes;
static PyObject *__pyx_kp_s_Node_struct_cannot_have_4_edges;
static PyObject *__pyx_kp_s_Null_Node;
static PyObject *__pyx_kp_s_Null_path;
static PyObject *__pyx_kp_s_Platypus_assembler_found_candida;
static PyObject *__pyx_kp_s_Pos_s_Seq_s_RefSeq_c_Colours_s_N;
static PyObject *__pyx_n_s_StandardError;
static PyObject *__pyx_n_s_assembleBadReads;
static PyObject *__pyx_n_s_assembleBrokenPairs;
static PyObject *__pyx_n_s_assemblerKmerSize;
static PyObject *__pyx_n_s_assemblyRegionSize;
static PyObject *__pyx_n_s_cline_in_traceback;
static PyObject *__pyx_n_s_collections;
static PyObject *__pyx_n_s_debug;
static PyObject *__pyx_n_s_defaultdict;
static PyObject *__pyx_n_s_error;
static PyObject *__pyx_n_s_getLogger;
static PyObject *__pyx_n_s_heapq;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_info;
static PyObject *__pyx_n_s_logger;
static PyObject *__pyx_n_s_logging;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_minBaseQual;
static PyObject *__pyx_n_s_minMapQual;
static PyObject *__pyx_n_s_minReads;
static PyObject *__pyx_kp_s_nNodes_s_nFilledBuckets_s_mean_e;
static PyObject *__pyx_n_s_name;
static PyObject *__pyx_n_s_noCycles;
static PyObject *__pyx_n_s_pyx_vtable;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_verbosity;
static PyObject *__pyx_n_s_warning;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_100;
static PyObject *__pyx_tuple_;
/* Late includes */

/* "assembler.pyx":128
 * ###################################################################################################
 * 
 * cdef Path* createPath(int initialSize):             # <<<<<<<<<<<<<<
 *     """
 *     Create and return a Path struct.
 */

static __pyx_t_9assembler_Path *__pyx_f_9assembler_createPath(int __pyx_v_initialSize) {
  __pyx_t_9assembler_Path *__pyx_v_thePath;
  __pyx_t_9assembler_Path *__pyx_r;
  __Pyx_RefNannyDeclarations
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  PyObject *__pyx_t_3 = NULL;
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 * cdef void destroyDeBruijnGraph(DeBruijnGraph* theGraph):             # <<<<<<<<<<<<<<
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 * 
 * cdef int DeBruijnGraph_InsertOrUpdateNode(DeBruijnGraph* theGraph, Node** theNode):             # <<<<<<<<<<<<<<
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/* "assembler.pyx":801
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 * cdef void DeBruijnGraph_AddEdge(DeBruijnGraph* theGraph, Node* startNode, Node* endNode, double weight):             # <<<<<<<<<<<<<<
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/* "assembler.pyx":831
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 *         # Ignore low-weight edges that are only in reads
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 */
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        /* "assembler.pyx":854
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 *     cdef int nEdgesThisNode = 0
 *     cdef int i = 0
 */
  __pyx_v_theEdge = NULL;

  /* "assembler.pyx":1039
 *     cdef Node* newEnd = NULL
 *     cdef Edge* theEdge = NULL
 *     cdef int nEdgesThisNode = 0             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int j = 0
 */
  __pyx_v_nEdgesThisNode = 0;

  /* "assembler.pyx":1040
 *     cdef Edge* theEdge = NULL
 *     cdef int nEdgesThisNode = 0
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef int j = 0
 *     cdef int hasCycle = 0
 */
  __pyx_v_i = 0;

  /* "assembler.pyx":1041
 *     cdef int nEdgesThisNode = 0
 *     cdef int i = 0
 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef int hasCycle = 0
 * 
 */
  __pyx_v_j = 0;

  /* "assembler.pyx":1042
 *     cdef int i = 0
 *     cdef int j = 0
 *     cdef int hasCycle = 0             # <<<<<<<<<<<<<<
 * 
 *     PathStack_Push(thePathStack, thePath)
 */
  __pyx_v_hasCycle = 0;

  /* "assembler.pyx":1044
 *     cdef int hasCycle = 0
 * 
 *     PathStack_Push(thePathStack, thePath)             # <<<<<<<<<<<<<<
 * 
 *     while not PathStack_IsEmpty(thePathStack):
 */
  __pyx_f_9assembler_PathStack_Push(__pyx_v_thePathStack, __pyx_v_thePath);

  /* "assembler.pyx":1046
 *     PathStack_Push(thePathStack, thePath)
 * 
 *     while not PathStack_IsEmpty(thePathStack):             # <<<<<<<<<<<<<<
 * 
 *         pathSoFar = PathStack_Pop(thePathStack)
 */
  while (1) {
    __pyx_t_1 = ((!(__pyx_f_9assembler_PathStack_IsEmpty(__pyx_v_thePathStack) != 0)) != 0);
    if (!__pyx_t_1) break;

    /* "assembler.pyx":1048
 *     while not PathStack_IsEmpty(thePathStack):
 * 
 *         pathSoFar = PathStack_Pop(thePathStack)             # <<<<<<<<<<<<<<
 *         endSoFar = pathSoFar.nodes.elements[pathSoFar.nNodes-1]
 * 
 */
    __pyx_v_pathSoFar = __pyx_f_9assembler_PathStack_Pop(__pyx_v_thePathStack);

    /* "assembler.pyx":1049
 * 
 *         pathSoFar = PathStack_Pop(thePathStack)
 *         endSoFar = pathSoFar.nodes.elements[pathSoFar.nNodes-1]             # <<<<<<<<<<<<<<
 * 
 *         # TODO: Replace with maxHaplotypes??
 */
    __pyx_v_endSoFar = (__pyx_v_pathSoFar->nodes->elements[(__pyx_v_pathSoFar->nNodes - 1)]);

    /* "assembler.pyx":1052
 * 
 *         # TODO: Replace with maxHaplotypes??
 *         if thePathStack.top + 1 > 20 or finishedPaths.top + 1 > 20:             # <<<<<<<<<<<<<<
 *             #logger.info("Too many paths %s (%s) from this node. Giving up" %(thePathStack.top, finishedPaths.top))
 *             destroyPath(pathSoFar)
 */
    __pyx_t_2 = (((__pyx_v_thePathStack->top + 1) > 20) != 0);
    if (!__pyx_t_2) {
    } else {
      __pyx_t_1 = __pyx_t_2;
      goto __pyx_L6_bool_binop_done;
    }
    __pyx_t_2 = (((__pyx_v_finishedPaths->top + 1) > 20) != 0);
    __pyx_t_1 = __pyx_t_2;
    __pyx_L6_bool_binop_done:;
    if (__pyx_t_1) {

      /* "assembler.pyx":1054
 *         if thePathStack.top + 1 > 20 or finishedPaths.top + 1 > 20:
 *             #logger.info("Too many paths %s (%s) from this node. Giving up" %(thePathStack.top, finishedPaths.top))
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 *             destroyPathStack(thePathStack)
 *             destroyPathStack(finishedPaths)
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);

      /* "assembler.pyx":1055
 *             #logger.info("Too many paths %s (%s) from this node. Giving up" %(thePathStack.top, finishedPaths.top))
 *             destroyPath(pathSoFar)
 *             destroyPathStack(thePathStack)             # <<<<<<<<<<<<<<
 *             destroyPathStack(finishedPaths)
 *             return NULL
 */
      __pyx_f_9assembler_destroyPathStack(__pyx_v_thePathStack);

      /* "assembler.pyx":1056
 *             destroyPath(pathSoFar)
 *             destroyPathStack(thePathStack)
 *             destroyPathStack(finishedPaths)             # <<<<<<<<<<<<<<
 *             return NULL
 * 
 */
      __pyx_f_9assembler_destroyPathStack(__pyx_v_finishedPaths);

      /* "assembler.pyx":1057
 *             destroyPathStack(thePathStack)
 *             destroyPathStack(finishedPaths)
 *             return NULL             # <<<<<<<<<<<<<<
 * 
 *         # At the moment, don't allow any cycles.
 */
      __pyx_r = NULL;
      goto __pyx_L0;

      /* "assembler.pyx":1052
 * 
 *         # TODO: Replace with maxHaplotypes??
 *         if thePathStack.top + 1 > 20 or finishedPaths.top + 1 > 20:             # <<<<<<<<<<<<<<
 *             #logger.info("Too many paths %s (%s) from this node. Giving up" %(thePathStack.top, finishedPaths.top))
 *             destroyPath(pathSoFar)
 */
    }

    /* "assembler.pyx":1060
 * 
 *         # At the moment, don't allow any cycles.
 *         hasCycle = checkPathForCycles(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         if hasCycle:
 */
    __pyx_v_hasCycle = __pyx_f_9assembler_checkPathForCycles(__pyx_v_pathSoFar);

    /* "assembler.pyx":1062
 *         hasCycle = checkPathForCycles(pathSoFar)
 * 
 *         if hasCycle:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
    __pyx_t_1 = (__pyx_v_hasCycle != 0);
    if (__pyx_t_1) {

      /* "assembler.pyx":1063
 * 
 *         if hasCycle:
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # Got back to ref, this path is done with. This is a bubble.
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);

      /* "assembler.pyx":1062
 *         hasCycle = checkPathForCycles(pathSoFar)
 * 
 *         if hasCycle:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
      goto __pyx_L8;
    }

    /* "assembler.pyx":1066
 * 
 *         # Got back to ref, this path is done with. This is a bubble.
 *         elif endSoFar.colours == REF_AND_READ:             # <<<<<<<<<<<<<<
 *             pathSoFar.isBubble = 1
 *             PathStack_Push(finishedPaths, pathSoFar)
 */
    __pyx_t_1 = ((__pyx_v_endSoFar->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
    if (__pyx_t_1) {

      /* "assembler.pyx":1067
 *         # Got back to ref, this path is done with. This is a bubble.
 *         elif endSoFar.colours == REF_AND_READ:
 *             pathSoFar.isBubble = 1             # <<<<<<<<<<<<<<
 *             PathStack_Push(finishedPaths, pathSoFar)
 * 
 */
      __pyx_v_pathSoFar->isBubble = 1;

      /* "assembler.pyx":1068
 *         elif endSoFar.colours == REF_AND_READ:
 *             pathSoFar.isBubble = 1
 *             PathStack_Push(finishedPaths, pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # No reads here. Not quite sure how this could happen. Went from ref and read to only
 */
      __pyx_f_9assembler_PathStack_Push(__pyx_v_finishedPaths, __pyx_v_pathSoFar);

      /* "assembler.pyx":1066
 * 
 *         # Got back to ref, this path is done with. This is a bubble.
 *         elif endSoFar.colours == REF_AND_READ:             # <<<<<<<<<<<<<<
 *             pathSoFar.isBubble = 1
 *             PathStack_Push(finishedPaths, pathSoFar)
 */
      goto __pyx_L8;
    }

    /* "assembler.pyx":1072
 *         # No reads here. Not quite sure how this could happen. Went from ref and read to only
 *         # ref.
 *         elif endSoFar.colours == REF:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
    __pyx_t_1 = ((__pyx_v_endSoFar->colours == __pyx_v_9assembler_REF) != 0);
    if (__pyx_t_1) {

      /* "assembler.pyx":1073
 *         # ref.
 *         elif endSoFar.colours == REF:
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # Keep extending path
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);

      /* "assembler.pyx":1072
 *         # No reads here. Not quite sure how this could happen. Went from ref and read to only
 *         # ref.
 *         elif endSoFar.colours == REF:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
      goto __pyx_L8;
    }

    /* "assembler.pyx":1091
 * 
 *                 #else:
 *             nEdgesThisNode = endSoFar.nEdges             # <<<<<<<<<<<<<<
 * 
 *             for i in range(nEdgesThisNode):
 */
    /*else*/ {
      __pyx_t_3 = __pyx_v_endSoFar->nEdges;
      __pyx_v_nEdgesThisNode = __pyx_t_3;

      /* "assembler.pyx":1093
 *             nEdgesThisNode = endSoFar.nEdges
 * 
 *             for i in range(nEdgesThisNode):             # <<<<<<<<<<<<<<
 *                 theEdge = endSoFar.edges[i]
 *                 newEnd = theEdge.endNode
 */
      __pyx_t_3 = __pyx_v_nEdgesThisNode;
      __pyx_t_4 = __pyx_t_3;
      for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
        __pyx_v_i = __pyx_t_5;

        /* "assembler.pyx":1094
 * 
 *             for i in range(nEdgesThisNode):
 *                 theEdge = endSoFar.edges[i]             # <<<<<<<<<<<<<<
 *                 newEnd = theEdge.endNode
 * 
 */
        __pyx_v_theEdge = (__pyx_v_endSoFar->edges[__pyx_v_i]);

        /* "assembler.pyx":1095
 *             for i in range(nEdgesThisNode):
 *                 theEdge = endSoFar.edges[i]
 *                 newEnd = theEdge.endNode             # <<<<<<<<<<<<<<
 * 
 *                 if theEdge.weight >= minWeight or newEnd.colours == REF_AND_READ or newEnd.colours == REF:
 */
        __pyx_t_6 = __pyx_v_theEdge->endNode;
        __pyx_v_newEnd = __pyx_t_6;

        /* "assembler.pyx":1097
 *                 newEnd = theEdge.endNode
 * 
 *                 if theEdge.weight >= minWeight or newEnd.colours == REF_AND_READ or newEnd.colours == REF:             # <<<<<<<<<<<<<<
 *                     newPath = createPath(theGraph.kmerSize)
 * 
 */
        __pyx_t_2 = ((__pyx_v_theEdge->weight >= __pyx_v_minWeight) != 0);
        if (!__pyx_t_2) {
        } else {
          __pyx_t_1 = __pyx_t_2;
          goto __pyx_L12_bool_binop_done;
        }
        __pyx_t_2 = ((__pyx_v_newEnd->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
        if (!__pyx_t_2) {
        } else {
          __pyx_t_1 = __pyx_t_2;
          goto __pyx_L12_bool_binop_done;
        }
        __pyx_t_2 = ((__pyx_v_newEnd->colours == __pyx_v_9assembler_REF) != 0);
        __pyx_t_1 = __pyx_t_2;
        __pyx_L12_bool_binop_done:;
        if (__pyx_t_1) {

          /* "assembler.pyx":1098
 * 
 *                 if theEdge.weight >= minWeight or newEnd.colours == REF_AND_READ or newEnd.colours == REF:
 *                     newPath = createPath(theGraph.kmerSize)             # <<<<<<<<<<<<<<
 * 
 *                     # Copy old path
 */
          __pyx_v_newPath = __pyx_f_9assembler_createPath(__pyx_v_theGraph->kmerSize);

          /* "assembler.pyx":1101
 * 
 *                     # Copy old path
 *                     for j in range(pathSoFar.nNodes):             # <<<<<<<<<<<<<<
 *                         addNodeToPath(newPath, pathSoFar.nodes.elements[j], 0.0)
 * 
 */
          __pyx_t_7 = __pyx_v_pathSoFar->nNodes;
          __pyx_t_8 = __pyx_t_7;
          for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
            __pyx_v_j = __pyx_t_9;

            /* "assembler.pyx":1102
 *                     # Copy old path
 *                     for j in range(pathSoFar.nNodes):
 *                         addNodeToPath(newPath, pathSoFar.nodes.elements[j], 0.0)             # <<<<<<<<<<<<<<
 * 
 *                     # Weight for this path is weight of existing path + weight of new edge
 */
            __pyx_f_9assembler_addNodeToPath(__pyx_v_newPath, (__pyx_v_pathSoFar->nodes->elements[__pyx_v_j]), 0.0);
          }

          /* "assembler.pyx":1105
 * 
 *                     # Weight for this path is weight of existing path + weight of new edge
 *                     newPath.weight = pathSoFar.weight             # <<<<<<<<<<<<<<
 *                     addNodeToPath(newPath, newEnd, theEdge.weight)
 *                     PathStack_Push(thePathStack, newPath)
 */
          __pyx_t_10 = __pyx_v_pathSoFar->weight;
          __pyx_v_newPath->weight = __pyx_t_10;

          /* "assembler.pyx":1106
 *                     # Weight for this path is weight of existing path + weight of new edge
 *                     newPath.weight = pathSoFar.weight
 *                     addNodeToPath(newPath, newEnd, theEdge.weight)             # <<<<<<<<<<<<<<
 *                     PathStack_Push(thePathStack, newPath)
 * 
 */
          __pyx_f_9assembler_addNodeToPath(__pyx_v_newPath, __pyx_v_newEnd, __pyx_v_theEdge->weight);

          /* "assembler.pyx":1107
 *                     newPath.weight = pathSoFar.weight
 *                     addNodeToPath(newPath, newEnd, theEdge.weight)
 *                     PathStack_Push(thePathStack, newPath)             # <<<<<<<<<<<<<<
 * 
 *             destroyPath(pathSoFar)
 */
          __pyx_f_9assembler_PathStack_Push(__pyx_v_thePathStack, __pyx_v_newPath);

          /* "assembler.pyx":1097
 *                 newEnd = theEdge.endNode
 * 
 *                 if theEdge.weight >= minWeight or newEnd.colours == REF_AND_READ or newEnd.colours == REF:             # <<<<<<<<<<<<<<
 *                     newPath = createPath(theGraph.kmerSize)
 * 
 */
        }
      }

      /* "assembler.pyx":1109
 *                     PathStack_Push(thePathStack, newPath)
 * 
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *     destroyPathStack(thePathStack)
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);
    }
    __pyx_L8:;
  }

  /* "assembler.pyx":1111
 *             destroyPath(pathSoFar)
 * 
 *     destroyPathStack(thePathStack)             # <<<<<<<<<<<<<<
 *     return finishedPaths
 * 
 */
  __pyx_f_9assembler_destroyPathStack(__pyx_v_thePathStack);

  /* "assembler.pyx":1112
 * 
 *     destroyPathStack(thePathStack)
 *     return finishedPaths             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = __pyx_v_finishedPaths;
  goto __pyx_L0;

  /* "assembler.pyx":1027
 * ###################################################################################################
 * 
 * cdef PathStack* getVariantPathsThroughGraphFromNode(DeBruijnGraph* theGraph, Path* thePath, double minWeight):             # <<<<<<<<<<<<<<
 *     """
 *     Check all valid paths through the graph starting at the last node in "thePath". If any path
 */

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

/* "assembler.pyx":1116
 * ###################################################################################################
 * 
 * cdef list findBubblesInGraph(DeBruijnGraph* theGraph, double minWeight, char* refSeq, char* chrom, int refStart, int refEnd, int assemStart, int assemEnd, int verbosity):             # <<<<<<<<<<<<<<
 *     """
 *     Find and return all bubbles in the graph.
 */

static PyObject *__pyx_f_9assembler_findBubblesInGraph(__pyx_t_9assembler_DeBruijnGraph *__pyx_v_theGraph, double __pyx_v_minWeight, char *__pyx_v_refSeq, char *__pyx_v_chrom, int __pyx_v_refStart, int __pyx_v_refEnd, int __pyx_v_assemStart, int __pyx_v_assemEnd, int __pyx_v_verbosity) {
  int __pyx_v_nNodes;
  int __pyx_v_nEdgesThisNode;
  int __pyx_v_nBubblePaths;
  CYTHON_UNUSED int __pyx_v_nNodesThisPath;
  int __pyx_v_i;
  int __pyx_v_j;
  __pyx_t_9assembler_Edge *__pyx_v_theEdge;
  __pyx_t_9assembler_Node **__pyx_v_allNodes;
  __pyx_t_9assembler_Node *__pyx_v_theNode;
  __pyx_t_9assembler_PathStack *__pyx_v_bubblePathsThisNode;
  __pyx_t_9assembler_Path *__pyx_v_thePath;
  __pyx_t_9assembler_Path *__pyx_v_theBubblePath;
  PyObject *__pyx_v_variants = 0;
  struct __pyx_obj_7variant_Variant *__pyx_v_theVar = 0;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __pyx_t_9assembler_Node **__pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  int __pyx_t_8;
  int __pyx_t_9;
  int __pyx_t_10;
  int __pyx_t_11;
  int __pyx_t_12;
  int __pyx_t_13;
  int __pyx_t_14;
  __Pyx_RefNannySetupContext("findBubblesInGraph", 0);

  /* "assembler.pyx":1125
 *     4) Keep a stack of the current path
 *     """
 *     cdef int nNodes = theGraph.allNodes.top + 1             # <<<<<<<<<<<<<<
 *     cdef int nEdgesThisNode = 0
 *     cdef int nBubblePaths = 0
 */
  __pyx_v_nNodes = (__pyx_v_theGraph->allNodes->top + 1);

  /* "assembler.pyx":1126
 *     """
 *     cdef int nNodes = theGraph.allNodes.top + 1
 *     cdef int nEdgesThisNode = 0             # <<<<<<<<<<<<<<
 *     cdef int nBubblePaths = 0
 *     cdef int nNodesThisPath = 0
 */
  __pyx_v_nEdgesThisNode = 0;

  /* "assembler.pyx":1127
 *     cdef int nNodes = theGraph.allNodes.top + 1
 *     cdef int nEdgesThisNode = 0
 *     cdef int nBubblePaths = 0             # <<<<<<<<<<<<<<
 *     cdef int nNodesThisPath = 0
 *     cdef int i = 0
 */
  __pyx_v_nBubblePaths = 0;

  /* "assembler.pyx":1128
 *     cdef int nEdgesThisNode = 0
 *     cdef int nBubblePaths = 0
 *     cdef int nNodesThisPath = 0             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int j = 0
 */
  __pyx_v_nNodesThisPath = 0;

  /* "assembler.pyx":1129
 *     cdef int nBubblePaths = 0
 *     cdef int nNodesThisPath = 0
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef int j = 0
 *     cdef Edge* theEdge = NULL
 */
  __pyx_v_i = 0;

  /* "assembler.pyx":1130
 *     cdef int nNodesThisPath = 0
 *     cdef int i = 0
 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef Edge* theEdge = NULL
 *     cdef Node** allNodes = theGraph.allNodes.elements
 */
  __pyx_v_j = 0;

  /* "assembler.pyx":1131
 *     cdef int i = 0
 *     cdef int j = 0
 *     cdef Edge* theEdge = NULL             # <<<<<<<<<<<<<<
 *     cdef Node** allNodes = theGraph.allNodes.elements
 *     cdef Node* theNode = NULL
 */
  __pyx_v_theEdge = NULL;

  /* "assembler.pyx":1132
 *     cdef int j = 0
 *     cdef Edge* theEdge = NULL
 *     cdef Node** allNodes = theGraph.allNodes.elements             # <<<<<<<<<<<<<<
 *     cdef Node* theNode = NULL
 *     cdef PathStack* bubblePathsThisNode = NULL
 */
  __pyx_t_1 = __pyx_v_theGraph->allNodes->elements;
  __pyx_v_allNodes = __pyx_t_1;

  /* "assembler.pyx":1133
 *     cdef Edge* theEdge = NULL
 *     cdef Node** allNodes = theGraph.allNodes.elements
 *     cdef Node* theNode = NULL             # <<<<<<<<<<<<<<
 *     cdef PathStack* bubblePathsThisNode = NULL
 *     cdef Path* thePath = NULL
 */
  __pyx_v_theNode = NULL;

  /* "assembler.pyx":1134
 *     cdef Node** allNodes = theGraph.allNodes.elements
 *     cdef Node* theNode = NULL
 *     cdef PathStack* bubblePathsThisNode = NULL             # <<<<<<<<<<<<<<
 *     cdef Path* thePath = NULL
 *     cdef Path* theBubblePath = NULL
 */
  __pyx_v_bubblePathsThisNode = NULL;

  /* "assembler.pyx":1135
 *     cdef Node* theNode = NULL
 *     cdef PathStack* bubblePathsThisNode = NULL
 *     cdef Path* thePath = NULL             # <<<<<<<<<<<<<<
 *     cdef Path* theBubblePath = NULL
 *     cdef list variants = []
 */
  __pyx_v_thePath = NULL;

  /* "assembler.pyx":1136
 *     cdef PathStack* bubblePathsThisNode = NULL
 *     cdef Path* thePath = NULL
 *     cdef Path* theBubblePath = NULL             # <<<<<<<<<<<<<<
 *     cdef list variants = []
 *     cdef Variant theVar
 */
  __pyx_v_theBubblePath = NULL;

  /* "assembler.pyx":1137
 *     cdef Path* thePath = NULL
 *     cdef Path* theBubblePath = NULL
 *     cdef list variants = []             # <<<<<<<<<<<<<<
 *     cdef Variant theVar
 * 
 */
  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1137, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_v_variants = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "assembler.pyx":1140
 *     cdef Variant theVar
 * 
 *     for i in range(nNodes):             # <<<<<<<<<<<<<<
 *         theNode = allNodes[i]
 * 
 */
  __pyx_t_3 = __pyx_v_nNodes;
  __pyx_t_4 = __pyx_t_3;
  for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
    __pyx_v_i = __pyx_t_5;

    /* "assembler.pyx":1141
 * 
 *     for i in range(nNodes):
 *         theNode = allNodes[i]             # <<<<<<<<<<<<<<
 * 
 *         # First node which is ref only
 */
    __pyx_v_theNode = (__pyx_v_allNodes[__pyx_v_i]);

    /* "assembler.pyx":1144
 * 
 *         # First node which is ref only
 *         if theNode.colours == REF_AND_READ and theNode.position >= assemStart and theNode.position < assemEnd:             # <<<<<<<<<<<<<<
 *             nEdgesThisNode = theNode.nEdges
 * 
 */
    __pyx_t_7 = ((__pyx_v_theNode->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
    if (__pyx_t_7) {
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 *             if theSeq[j] == 'N':             # <<<<<<<<<<<<<<
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 */
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 *         if thisMinQual >= minQual and NsInKmer == 0:             # <<<<<<<<<<<<<<
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 *             tempStartNode.colours = READ             # <<<<<<<<<<<<<<
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 *             tempStartNode.weight = thisMinQual
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 */
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 *             tempStartNode.position = - 1
 *             tempStartNode.weight = thisMinQual             # <<<<<<<<<<<<<<
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 *             tempEndNode.sequence = theSeq + i + 1
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 * 
 *             tempEndNode.sequence = theSeq + i + 1             # <<<<<<<<<<<<<<
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 * 
 *             tempEndNode.sequence = theSeq + i + 1
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 *             tempEndNode.colours = READ
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 *             tempEndNode.colours = READ             # <<<<<<<<<<<<<<
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 *     """
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/* "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 */
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}

/* "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 */
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}

/* "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:
 */
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  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 */
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/* "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:
 */
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  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;
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/* "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;
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}

/* "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 */
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}

/* "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:
 */
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  /* "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 */
}

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#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

/* 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;
}

/* 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

/* 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

/* 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
}

/* 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

/* 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));
}

/* py_abs */
#if CYTHON_USE_PYLONG_INTERNALS
static PyObject *__Pyx_PyLong_AbsNeg(PyObject *n) {
    if (likely(Py_SIZE(n) == -1)) {
        return PyLong_FromLong(((PyLongObject*)n)->ob_digit[0]);
    }
#if CYTHON_COMPILING_IN_CPYTHON
    {
        PyObject *copy = _PyLong_Copy((PyLongObject*)n);
        if (likely(copy)) {
            Py_SIZE(copy) = -(Py_SIZE(copy));
        }
        return copy;
    }
#else
    return PyNumber_Negative(n);
#endif
}
#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;
}

/* 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;
}

/* ImportFrom */
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
    PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
    if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
        PyErr_Format(PyExc_ImportError,
        #if PY_MAJOR_VERSION < 3
            "cannot import name %.230s", PyString_AS_STRING(name));
        #else
            "cannot import name %S", name);
        #endif
    }
    return value;
}

/* CLineInTraceback */
#ifndef CYTHON_CLINE_IN_TRACEBACK
static int __Pyx_CLineForTraceback(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);
}

/* 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);
    }
}

/* 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_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 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

/* 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 */
