/* 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)
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    #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
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#else
  #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef __Pyx_PyAsyncMethodsStruct
    typedef struct {
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        unaryfunc am_aiter;
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    } __Pyx_PyAsyncMethodsStruct;
#endif

#if defined(WIN32) || defined(MS_WINDOWS)
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#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__calign
#define __PYX_HAVE_API__calign
/* 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"
#include "align.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:
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    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/calign.pyx",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "cython/htslibWrapper.pxd",
};

/* "calign.pyx":30
 * cdef int mask = (1 << 2*hash_nucs) - 1
 * 
 * ctypedef long long size_t             # <<<<<<<<<<<<<<
 * cdef double mLTOT = -0.23025850929940459    # Minus log ten over ten
 * 
 */
typedef PY_LONG_LONG __pyx_t_6calign_size_t;

/*--- Type declarations ---*/
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_13htslibWrapper_ReadIterator;
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;
};

/* "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;
};



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

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


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

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

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  #define __Pyx_GIVEREF(r)
  #define __Pyx_XINCREF(r) Py_XINCREF(r)
  #define __Pyx_XDECREF(r) Py_XDECREF(r)
  #define __Pyx_XGOTREF(r)
  #define __Pyx_XGIVEREF(r)
#endif
#define __Pyx_XDECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_XDECREF(tmp);\
    } while (0)
#define __Pyx_DECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_DECREF(tmp);\
    } while (0)
#define __Pyx_CLEAR(r)    do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r)   do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)

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

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

/* 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);

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

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

/* 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);

/* None.proto */
static CYTHON_INLINE long __Pyx_pow_long(long, long);

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

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

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

/* 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);

/* PyObjectSetAttrStr.proto */
#if CYTHON_USE_TYPE_SLOTS
#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL)
static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value);
#else
#define __Pyx_PyObject_DelAttrStr(o,n)   PyObject_DelAttr(o,n)
#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
#endif

/* VoidPtrExport.proto */
static int __Pyx_ExportVoidPtr(PyObject *name, void *p, const char *sig);

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

/* Module declarations from 'cerrormodel' */

/* Module declarations from 'calign' */
static int __pyx_v_6calign_hash_nucs;
static int __pyx_v_6calign_hash_size;
static int __pyx_v_6calign_max_sequence_length;
static int __pyx_v_6calign_mask;
static double __pyx_v_6calign_mLTOT;
static CYTHON_INLINE unsigned int __pyx_f_6calign_my_hash(char *); /*proto*/
static CYTHON_INLINE unsigned int __pyx_f_6calign_my_hash_update(char, int); /*proto*/
#define __Pyx_MODULE_NAME "calign"
extern int __pyx_module_is_main_calign;
int __pyx_module_is_main_calign = 0;

/* Implementation of 'calign' */
static PyObject *__pyx_builtin_range;
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_range[] = "range";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_logging[] = "logging";
static const char __pyx_k_pyx_capi[] = "__pyx_capi__";
static const char __pyx_k_hash_nucs[] = "hash_nucs";
static const char __pyx_k_hash_size[] = "hash_size";
static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
static const char __pyx_k_htslibWrapper[] = "htslibWrapper";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_max_sequence_length[] = "max_sequence_length";
static const char __pyx_k_Cython_module_containing_glue_c[] = "\nCython module containing glue code for the alignment routines used in\nPlatypus.\n";
static PyObject *__pyx_n_s_cline_in_traceback;
static PyObject *__pyx_n_s_hash_nucs;
static PyObject *__pyx_n_s_hash_size;
static PyObject *__pyx_n_s_htslibWrapper;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_logging;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_max_sequence_length;
static PyObject *__pyx_n_s_name;
static PyObject *__pyx_n_s_pyx_capi;
static PyObject *__pyx_n_s_pyx_vtable;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_test;
/* Late includes */

/* "calign.pyx":61
 * ###################################################################################################
 * 
 * cdef inline unsigned int my_hash(char* seq) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Encodes first hash_nucs nucleotides (A,C,G,T or a,c,g,t) into an integer
 */

static CYTHON_INLINE unsigned int __pyx_f_6calign_my_hash(char *__pyx_v_seq) {
  int __pyx_v_i;
  int __pyx_v_c;
  unsigned int __pyx_v_h;
  unsigned int __pyx_r;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;

  /* "calign.pyx":66
 *     """
 *     cdef int i, c
 *     cdef unsigned int h = 0             # <<<<<<<<<<<<<<
 * 
 *     for i in range(hash_nucs):
 */
  __pyx_v_h = 0;

  /* "calign.pyx":68
 *     cdef unsigned int h = 0
 * 
 *     for i in range(hash_nucs):             # <<<<<<<<<<<<<<
 *         c = seq[i] & 7   # a,A->1  c,C->3  g,G->7  t,T->4
 * 
 */
  __pyx_t_1 = __pyx_v_6calign_hash_nucs;
  __pyx_t_2 = __pyx_t_1;
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_i = __pyx_t_3;

    /* "calign.pyx":69
 * 
 *     for i in range(hash_nucs):
 *         c = seq[i] & 7   # a,A->1  c,C->3  g,G->7  t,T->4             # <<<<<<<<<<<<<<
 * 
 *         if c == 7:
 */
    __pyx_v_c = ((__pyx_v_seq[__pyx_v_i]) & 7);

    /* "calign.pyx":71
 *         c = seq[i] & 7   # a,A->1  c,C->3  g,G->7  t,T->4
 * 
 *         if c == 7:             # <<<<<<<<<<<<<<
 *             c = 2
 * 
 */
    __pyx_t_4 = ((__pyx_v_c == 7) != 0);
    if (__pyx_t_4) {

      /* "calign.pyx":72
 * 
 *         if c == 7:
 *             c = 2             # <<<<<<<<<<<<<<
 * 
 *         h = (h << 2) + <unsigned int>(c & 3)
 */
      __pyx_v_c = 2;

      /* "calign.pyx":71
 *         c = seq[i] & 7   # a,A->1  c,C->3  g,G->7  t,T->4
 * 
 *         if c == 7:             # <<<<<<<<<<<<<<
 *             c = 2
 * 
 */
    }

    /* "calign.pyx":74
 *             c = 2
 * 
 *         h = (h << 2) + <unsigned int>(c & 3)             # <<<<<<<<<<<<<<
 * 
 *     return h
 */
    __pyx_v_h = ((__pyx_v_h << 2) + ((unsigned int)(__pyx_v_c & 3)));
  }

  /* "calign.pyx":76
 *         h = (h << 2) + <unsigned int>(c & 3)
 * 
 *     return h             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = __pyx_v_h;
  goto __pyx_L0;

  /* "calign.pyx":61
 * ###################################################################################################
 * 
 * cdef inline unsigned int my_hash(char* seq) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Encodes first hash_nucs nucleotides (A,C,G,T or a,c,g,t) into an integer
 */

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

/* "calign.pyx":80
 * ###################################################################################################
 * 
 * cdef inline unsigned int my_hash_update(char character, int oldVal) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Incrementally update hash value with one new character
 */

static CYTHON_INLINE unsigned int __pyx_f_6calign_my_hash_update(char __pyx_v_character, int __pyx_v_oldVal) {
  int __pyx_v_c;
  unsigned int __pyx_r;
  int __pyx_t_1;

  /* "calign.pyx":85
 *     """
 *     global mask
 *     cdef int c = character & 7   # a,A->1  c,C->3  g,G->7  t,T->4             # <<<<<<<<<<<<<<
 * 
 *     if c == 7:
 */
  __pyx_v_c = (__pyx_v_character & 7);

  /* "calign.pyx":87
 *     cdef int c = character & 7   # a,A->1  c,C->3  g,G->7  t,T->4
 * 
 *     if c == 7:             # <<<<<<<<<<<<<<
 *         c = 2
 * 
 */
  __pyx_t_1 = ((__pyx_v_c == 7) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":88
 * 
 *     if c == 7:
 *         c = 2             # <<<<<<<<<<<<<<
 * 
 *     return ((oldVal << 2) & mask) + <unsigned int>(c & 3)
 */
    __pyx_v_c = 2;

    /* "calign.pyx":87
 *     cdef int c = character & 7   # a,A->1  c,C->3  g,G->7  t,T->4
 * 
 *     if c == 7:             # <<<<<<<<<<<<<<
 *         c = 2
 * 
 */
  }

  /* "calign.pyx":90
 *         c = 2
 * 
 *     return ((oldVal << 2) & mask) + <unsigned int>(c & 3)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = (((__pyx_v_oldVal << 2) & __pyx_v_6calign_mask) + ((unsigned int)(__pyx_v_c & 3)));
  goto __pyx_L0;

  /* "calign.pyx":80
 * ###################################################################################################
 * 
 * cdef inline unsigned int my_hash_update(char character, int oldVal) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Incrementally update hash value with one new character
 */

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

/* "calign.pyx":94
 * ###################################################################################################
 * 
 * cdef void hash_sequence_multihit(char* sequence, int sequenceLength, short** hash_table, short** next_array) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Builds a hash table of the byte sequence, allowing multiple hits
 */

static void __pyx_f_6calign_hash_sequence_multihit(char *__pyx_v_sequence, int __pyx_v_sequenceLength, short **__pyx_v_hash_table, short **__pyx_v_next_array) {
  int __pyx_v_next_empty;
  int __pyx_v_hidx;
  int __pyx_v_i;
  int __pyx_v_j;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;

  /* "calign.pyx":98
 *     Builds a hash table of the byte sequence, allowing multiple hits
 *     """
 *     hash_table[0] = <short*>(calloc(hash_size, sizeof(short)))             # <<<<<<<<<<<<<<
 *     next_array[0] = <short*>(calloc(hash_size, sizeof(short)))
 * 
 */
  (__pyx_v_hash_table[0]) = ((short *)calloc(__pyx_v_6calign_hash_size, (sizeof(short))));

  /* "calign.pyx":99
 *     """
 *     hash_table[0] = <short*>(calloc(hash_size, sizeof(short)))
 *     next_array[0] = <short*>(calloc(hash_size, sizeof(short)))             # <<<<<<<<<<<<<<
 * 
 *     if sequenceLength < hash_nucs:
 */
  (__pyx_v_next_array[0]) = ((short *)calloc(__pyx_v_6calign_hash_size, (sizeof(short))));

  /* "calign.pyx":101
 *     next_array[0] = <short*>(calloc(hash_size, sizeof(short)))
 * 
 *     if sequenceLength < hash_nucs:             # <<<<<<<<<<<<<<
 *         return
 * 
 */
  __pyx_t_1 = ((__pyx_v_sequenceLength < __pyx_v_6calign_hash_nucs) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":102
 * 
 *     if sequenceLength < hash_nucs:
 *         return             # <<<<<<<<<<<<<<
 * 
 *     cdef int next_empty = 1
 */
    goto __pyx_L0;

    /* "calign.pyx":101
 *     next_array[0] = <short*>(calloc(hash_size, sizeof(short)))
 * 
 *     if sequenceLength < hash_nucs:             # <<<<<<<<<<<<<<
 *         return
 * 
 */
  }

  /* "calign.pyx":104
 *         return
 * 
 *     cdef int next_empty = 1             # <<<<<<<<<<<<<<
 *     cdef int hidx
 *     cdef int i
 */
  __pyx_v_next_empty = 1;

  /* "calign.pyx":109
 *     cdef int j
 * 
 *     for i in range(sequenceLength - hash_nucs):             # <<<<<<<<<<<<<<
 *         hidx = my_hash(sequence + i)
 * 
 */
  __pyx_t_2 = (__pyx_v_sequenceLength - __pyx_v_6calign_hash_nucs);
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "calign.pyx":110
 * 
 *     for i in range(sequenceLength - hash_nucs):
 *         hidx = my_hash(sequence + i)             # <<<<<<<<<<<<<<
 * 
 *         # add position i into hash table under hash hidx
 */
    __pyx_v_hidx = __pyx_f_6calign_my_hash((__pyx_v_sequence + __pyx_v_i));

    /* "calign.pyx":115
 *         #*position[next_empty] = i
 *         # invariant: next_empty == i+1; therefore the position array is not necessary
 *         if hash_table[0][hidx] == 0:             # <<<<<<<<<<<<<<
 *             hash_table[0][hidx] = next_empty
 *         else:
 */
    __pyx_t_1 = ((((__pyx_v_hash_table[0])[__pyx_v_hidx]) == 0) != 0);
    if (__pyx_t_1) {

      /* "calign.pyx":116
 *         # invariant: next_empty == i+1; therefore the position array is not necessary
 *         if hash_table[0][hidx] == 0:
 *             hash_table[0][hidx] = next_empty             # <<<<<<<<<<<<<<
 *         else:
 *             # find the end of the list
 */
      ((__pyx_v_hash_table[0])[__pyx_v_hidx]) = __pyx_v_next_empty;

      /* "calign.pyx":115
 *         #*position[next_empty] = i
 *         # invariant: next_empty == i+1; therefore the position array is not necessary
 *         if hash_table[0][hidx] == 0:             # <<<<<<<<<<<<<<
 *             hash_table[0][hidx] = next_empty
 *         else:
 */
      goto __pyx_L6;
    }

    /* "calign.pyx":119
 *         else:
 *             # find the end of the list
 *             j = hash_table[0][hidx]             # <<<<<<<<<<<<<<
 *             while next_array[0][j] != 0:
 *                 j = next_array[0][j]
 */
    /*else*/ {
      __pyx_v_j = ((__pyx_v_hash_table[0])[__pyx_v_hidx]);

      /* "calign.pyx":120
 *             # find the end of the list
 *             j = hash_table[0][hidx]
 *             while next_array[0][j] != 0:             # <<<<<<<<<<<<<<
 *                 j = next_array[0][j]
 *             next_array[0][j] = next_empty
 */
      while (1) {
        __pyx_t_1 = ((((__pyx_v_next_array[0])[__pyx_v_j]) != 0) != 0);
        if (!__pyx_t_1) break;

        /* "calign.pyx":121
 *             j = hash_table[0][hidx]
 *             while next_array[0][j] != 0:
 *                 j = next_array[0][j]             # <<<<<<<<<<<<<<
 *             next_array[0][j] = next_empty
 *         # point to next empty location
 */
        __pyx_v_j = ((__pyx_v_next_array[0])[__pyx_v_j]);
      }

      /* "calign.pyx":122
 *             while next_array[0][j] != 0:
 *                 j = next_array[0][j]
 *             next_array[0][j] = next_empty             # <<<<<<<<<<<<<<
 *         # point to next empty location
 *         next_empty += 1
 */
      ((__pyx_v_next_array[0])[__pyx_v_j]) = __pyx_v_next_empty;
    }
    __pyx_L6:;

    /* "calign.pyx":124
 *             next_array[0][j] = next_empty
 *         # point to next empty location
 *         next_empty += 1             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
    __pyx_v_next_empty = (__pyx_v_next_empty + 1);
  }

  /* "calign.pyx":94
 * ###################################################################################################
 * 
 * cdef void hash_sequence_multihit(char* sequence, int sequenceLength, short** hash_table, short** next_array) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Builds a hash table of the byte sequence, allowing multiple hits
 */

  /* function exit code */
  __pyx_L0:;
}

/* "calign.pyx":128
 * ###################################################################################################
 * 
 * cdef short* hash_sequence(char* sequence, int sequenceLength) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Returns a hash of the byte sequence
 */

static short *__pyx_f_6calign_hash_sequence(char *__pyx_v_sequence, int __pyx_v_sequenceLength) {
  char *__pyx_v_seq;
  short *__pyx_v_h;
  int __pyx_v_i;
  unsigned int __pyx_v_hidx;
  short *__pyx_r;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;

  /* "calign.pyx":132
 *     Returns a hash of the byte sequence
 *     """
 *     cdef char* seq = sequence             # <<<<<<<<<<<<<<
 *     cdef short* h = <short*>(calloc(hash_size, sizeof(short)))
 *     cdef int i
 */
  __pyx_v_seq = __pyx_v_sequence;

  /* "calign.pyx":133
 *     """
 *     cdef char* seq = sequence
 *     cdef short* h = <short*>(calloc(hash_size, sizeof(short)))             # <<<<<<<<<<<<<<
 *     cdef int i
 *     cdef unsigned int hidx
 */
  __pyx_v_h = ((short *)calloc(__pyx_v_6calign_hash_size, (sizeof(short))));

  /* "calign.pyx":137
 *     cdef unsigned int hidx
 * 
 *     if sequenceLength < hash_nucs:             # <<<<<<<<<<<<<<
 *         return h
 * 
 */
  __pyx_t_1 = ((__pyx_v_sequenceLength < __pyx_v_6calign_hash_nucs) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":138
 * 
 *     if sequenceLength < hash_nucs:
 *         return h             # <<<<<<<<<<<<<<
 * 
 *     for i in range(sequenceLength - hash_nucs):
 */
    __pyx_r = __pyx_v_h;
    goto __pyx_L0;

    /* "calign.pyx":137
 *     cdef unsigned int hidx
 * 
 *     if sequenceLength < hash_nucs:             # <<<<<<<<<<<<<<
 *         return h
 * 
 */
  }

  /* "calign.pyx":140
 *         return h
 * 
 *     for i in range(sequenceLength - hash_nucs):             # <<<<<<<<<<<<<<
 *         if i == 0:
 *             hidx = my_hash(seq + i)
 */
  __pyx_t_2 = (__pyx_v_sequenceLength - __pyx_v_6calign_hash_nucs);
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "calign.pyx":141
 * 
 *     for i in range(sequenceLength - hash_nucs):
 *         if i == 0:             # <<<<<<<<<<<<<<
 *             hidx = my_hash(seq + i)
 *         else:
 */
    __pyx_t_1 = ((__pyx_v_i == 0) != 0);
    if (__pyx_t_1) {

      /* "calign.pyx":142
 *     for i in range(sequenceLength - hash_nucs):
 *         if i == 0:
 *             hidx = my_hash(seq + i)             # <<<<<<<<<<<<<<
 *         else:
 *             hidx = my_hash_update(seq[i + hash_nucs - 1], hidx)
 */
      __pyx_v_hidx = __pyx_f_6calign_my_hash((__pyx_v_seq + __pyx_v_i));

      /* "calign.pyx":141
 * 
 *     for i in range(sequenceLength - hash_nucs):
 *         if i == 0:             # <<<<<<<<<<<<<<
 *             hidx = my_hash(seq + i)
 *         else:
 */
      goto __pyx_L6;
    }

    /* "calign.pyx":144
 *             hidx = my_hash(seq + i)
 *         else:
 *             hidx = my_hash_update(seq[i + hash_nucs - 1], hidx)             # <<<<<<<<<<<<<<
 * 
 *         if h[hidx] != 0:
 */
    /*else*/ {
      __pyx_v_hidx = __pyx_f_6calign_my_hash_update((__pyx_v_seq[((__pyx_v_i + __pyx_v_6calign_hash_nucs) - 1)]), __pyx_v_hidx);
    }
    __pyx_L6:;

    /* "calign.pyx":146
 *             hidx = my_hash_update(seq[i + hash_nucs - 1], hidx)
 * 
 *         if h[hidx] != 0:             # <<<<<<<<<<<<<<
 *             h[hidx] = -1
 *         else:
 */
    __pyx_t_1 = (((__pyx_v_h[__pyx_v_hidx]) != 0) != 0);
    if (__pyx_t_1) {

      /* "calign.pyx":147
 * 
 *         if h[hidx] != 0:
 *             h[hidx] = -1             # <<<<<<<<<<<<<<
 *         else:
 *             h[hidx] = i + 1
 */
      (__pyx_v_h[__pyx_v_hidx]) = -1;

      /* "calign.pyx":146
 *             hidx = my_hash_update(seq[i + hash_nucs - 1], hidx)
 * 
 *         if h[hidx] != 0:             # <<<<<<<<<<<<<<
 *             h[hidx] = -1
 *         else:
 */
      goto __pyx_L7;
    }

    /* "calign.pyx":149
 *             h[hidx] = -1
 *         else:
 *             h[hidx] = i + 1             # <<<<<<<<<<<<<<
 * 
 *     return h
 */
    /*else*/ {
      (__pyx_v_h[__pyx_v_hidx]) = (__pyx_v_i + 1);
    }
    __pyx_L7:;
  }

  /* "calign.pyx":151
 *             h[hidx] = i + 1
 * 
 *     return h             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = __pyx_v_h;
  goto __pyx_L0;

  /* "calign.pyx":128
 * ###################################################################################################
 * 
 * cdef short* hash_sequence(char* sequence, int sequenceLength) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Returns a hash of the byte sequence
 */

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

/* "calign.pyx":155
 * ###################################################################################################
 * 
 * cdef void hashReadForMapping(cAlignedRead* read) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Hash the read, and store the hash for use in the mapReadToHaplotype
 */

static void __pyx_f_6calign_hashReadForMapping(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read) {
  int __pyx_v_i;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;

  /* "calign.pyx":161
 *     """
 *     cdef int i
 *     read.hash = <short*>(malloc( (read.rlen - hash_nucs)*sizeof(short) ))             # <<<<<<<<<<<<<<
 *     read.hash[0] = my_hash(read.seq)
 * 
 */
  __pyx_v_read->hash = ((short *)malloc(((__pyx_v_read->rlen - __pyx_v_6calign_hash_nucs) * (sizeof(short)))));

  /* "calign.pyx":162
 *     cdef int i
 *     read.hash = <short*>(malloc( (read.rlen - hash_nucs)*sizeof(short) ))
 *     read.hash[0] = my_hash(read.seq)             # <<<<<<<<<<<<<<
 * 
 *     for i in range(1, read.rlen - hash_nucs):
 */
  (__pyx_v_read->hash[0]) = __pyx_f_6calign_my_hash(__pyx_v_read->seq);

  /* "calign.pyx":164
 *     read.hash[0] = my_hash(read.seq)
 * 
 *     for i in range(1, read.rlen - hash_nucs):             # <<<<<<<<<<<<<<
 *         read.hash[i] = my_hash_update(read.seq[i + hash_nucs - 1], read.hash[i - 1])
 * 
 */
  __pyx_t_1 = (__pyx_v_read->rlen - __pyx_v_6calign_hash_nucs);
  __pyx_t_2 = __pyx_t_1;
  for (__pyx_t_3 = 1; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_i = __pyx_t_3;

    /* "calign.pyx":165
 * 
 *     for i in range(1, read.rlen - hash_nucs):
 *         read.hash[i] = my_hash_update(read.seq[i + hash_nucs - 1], read.hash[i - 1])             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
    (__pyx_v_read->hash[__pyx_v_i]) = __pyx_f_6calign_my_hash_update((__pyx_v_read->seq[((__pyx_v_i + __pyx_v_6calign_hash_nucs) - 1)]), (__pyx_v_read->hash[(__pyx_v_i - 1)]));
  }

  /* "calign.pyx":155
 * ###################################################################################################
 * 
 * cdef void hashReadForMapping(cAlignedRead* read) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Hash the read, and store the hash for use in the mapReadToHaplotype
 */

  /* function exit code */
}

/* "calign.pyx":170
 * 
 * # remove 'nogil' when debugging (also in calign.pxd)
 * cdef int mapAndAlignReadToHaplotype(char* read, char* quals, int readStart, int hapStart, int readLen, int hapLen, short* haplotypeHash, short* haplotypeNextArray, short* readHash, char* haplotype, int gapExtend, int nucprior, char* localGapOpen, int* mapCounts, int mapCountsLen, int hapFlank, int doCalculateFlankScore) nogil:             # <<<<<<<<<<<<<<
 * 
 * 
 */

static int __pyx_f_6calign_mapAndAlignReadToHaplotype(char *__pyx_v_read, char *__pyx_v_quals, int __pyx_v_readStart, int __pyx_v_hapStart, int __pyx_v_readLen, int __pyx_v_hapLen, short *__pyx_v_haplotypeHash, short *__pyx_v_haplotypeNextArray, short *__pyx_v_readHash, char *__pyx_v_haplotype, int __pyx_v_gapExtend, int __pyx_v_nucprior, char *__pyx_v_localGapOpen, int *__pyx_v_mapCounts, int __pyx_v_mapCountsLen, int __pyx_v_hapFlank, int __pyx_v_doCalculateFlankScore) {
  int __pyx_v_maxcount;
  int __pyx_v_i;
  int __pyx_v_pos;
  int __pyx_v_hapIdx;
  int __pyx_v_bestMappingPosition;
  int __pyx_v_hapLenForAlignment;
  int __pyx_v_indexOfReadIntoHap;
  int __pyx_v_readStartInHap;
  int __pyx_v_bestScore;
  int __pyx_v_alignScore;
  char *__pyx_v_aln1;
  char *__pyx_v_aln2;
  int __pyx_v_firstpos;
  int __pyx_r;
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  long __pyx_t_7;
  long __pyx_t_8;
  long __pyx_t_9;

  /* "calign.pyx":179
 *     """
 * 
 *     if readLen < hash_nucs:             # <<<<<<<<<<<<<<
 *         return 0 # Don't even bother trying to align really short reads
 * 
 */
  __pyx_t_1 = ((__pyx_v_readLen < __pyx_v_6calign_hash_nucs) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":180
 * 
 *     if readLen < hash_nucs:
 *         return 0 # Don't even bother trying to align really short reads             # <<<<<<<<<<<<<<
 * 
 *     cdef int maxcount = 0
 */
    __pyx_r = 0;
    goto __pyx_L0;

    /* "calign.pyx":179
 *     """
 * 
 *     if readLen < hash_nucs:             # <<<<<<<<<<<<<<
 *         return 0 # Don't even bother trying to align really short reads
 * 
 */
  }

  /* "calign.pyx":182
 *         return 0 # Don't even bother trying to align really short reads
 * 
 *     cdef int maxcount = 0             # <<<<<<<<<<<<<<
 *     cdef int i = -1
 *     cdef int pos = -1
 */
  __pyx_v_maxcount = 0;

  /* "calign.pyx":183
 * 
 *     cdef int maxcount = 0
 *     cdef int i = -1             # <<<<<<<<<<<<<<
 *     cdef int pos = -1
 *     cdef int hapIdx = 0
 */
  __pyx_v_i = -1;

  /* "calign.pyx":184
 *     cdef int maxcount = 0
 *     cdef int i = -1
 *     cdef int pos = -1             # <<<<<<<<<<<<<<
 *     cdef int hapIdx = 0
 *     cdef int bestMappingPosition = -1
 */
  __pyx_v_pos = -1;

  /* "calign.pyx":185
 *     cdef int i = -1
 *     cdef int pos = -1
 *     cdef int hapIdx = 0             # <<<<<<<<<<<<<<
 *     cdef int bestMappingPosition = -1
 *     cdef int hapLenForAlignment = 0
 */
  __pyx_v_hapIdx = 0;

  /* "calign.pyx":186
 *     cdef int pos = -1
 *     cdef int hapIdx = 0
 *     cdef int bestMappingPosition = -1             # <<<<<<<<<<<<<<
 *     cdef int hapLenForAlignment = 0
 *     cdef int indexOfReadIntoHap = -1
 */
  __pyx_v_bestMappingPosition = -1;

  /* "calign.pyx":187
 *     cdef int hapIdx = 0
 *     cdef int bestMappingPosition = -1
 *     cdef int hapLenForAlignment = 0             # <<<<<<<<<<<<<<
 *     cdef int indexOfReadIntoHap = -1
 *     cdef int readStartInHap = -1
 */
  __pyx_v_hapLenForAlignment = 0;

  /* "calign.pyx":188
 *     cdef int bestMappingPosition = -1
 *     cdef int hapLenForAlignment = 0
 *     cdef int indexOfReadIntoHap = -1             # <<<<<<<<<<<<<<
 *     cdef int readStartInHap = -1
 *     cdef int bestScore = 1000000
 */
  __pyx_v_indexOfReadIntoHap = -1;

  /* "calign.pyx":189
 *     cdef int hapLenForAlignment = 0
 *     cdef int indexOfReadIntoHap = -1
 *     cdef int readStartInHap = -1             # <<<<<<<<<<<<<<
 *     cdef int bestScore = 1000000
 *     cdef int alignScore = 1000000
 */
  __pyx_v_readStartInHap = -1;

  /* "calign.pyx":190
 *     cdef int indexOfReadIntoHap = -1
 *     cdef int readStartInHap = -1
 *     cdef int bestScore = 1000000             # <<<<<<<<<<<<<<
 *     cdef int alignScore = 1000000
 *     cdef char* aln1 = NULL
 */
  __pyx_v_bestScore = 0xF4240;

  /* "calign.pyx":191
 *     cdef int readStartInHap = -1
 *     cdef int bestScore = 1000000
 *     cdef int alignScore = 1000000             # <<<<<<<<<<<<<<
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL
 */
  __pyx_v_alignScore = 0xF4240;

  /* "calign.pyx":192
 *     cdef int bestScore = 1000000
 *     cdef int alignScore = 1000000
 *     cdef char* aln1 = NULL             # <<<<<<<<<<<<<<
 *     cdef char* aln2 = NULL
 *     cdef int firstpos = 0
 */
  __pyx_v_aln1 = NULL;

  /* "calign.pyx":193
 *     cdef int alignScore = 1000000
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL             # <<<<<<<<<<<<<<
 *     cdef int firstpos = 0
 * 
 */
  __pyx_v_aln2 = NULL;

  /* "calign.pyx":194
 *     cdef char* aln1 = NULL
 *     cdef char* aln2 = NULL
 *     cdef int firstpos = 0             # <<<<<<<<<<<<<<
 * 
 *     if strncmp(read, haplotype + indexOfReadIntoHap, readLen) == 0:
 */
  __pyx_v_firstpos = 0;

  /* "calign.pyx":196
 *     cdef int firstpos = 0
 * 
 *     if strncmp(read, haplotype + indexOfReadIntoHap, readLen) == 0:             # <<<<<<<<<<<<<<
 *         return 0
 * 
 */
  __pyx_t_1 = ((strncmp(__pyx_v_read, (__pyx_v_haplotype + __pyx_v_indexOfReadIntoHap), __pyx_v_readLen) == 0) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":197
 * 
 *     if strncmp(read, haplotype + indexOfReadIntoHap, readLen) == 0:
 *         return 0             # <<<<<<<<<<<<<<
 * 
 *     if hapFlank > 0:
 */
    __pyx_r = 0;
    goto __pyx_L0;

    /* "calign.pyx":196
 *     cdef int firstpos = 0
 * 
 *     if strncmp(read, haplotype + indexOfReadIntoHap, readLen) == 0:             # <<<<<<<<<<<<<<
 *         return 0
 * 
 */
  }

  /* "calign.pyx":199
 *         return 0
 * 
 *     if hapFlank > 0:             # <<<<<<<<<<<<<<
 *         # avoid allocating memory if there's no flank; this also stops the aligner from doing the backtrace
 *         aln1 = <char*>malloc(sizeof(char) * (2 * readLen + 16))
 */
  __pyx_t_1 = ((__pyx_v_hapFlank > 0) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":201
 *     if hapFlank > 0:
 *         # avoid allocating memory if there's no flank; this also stops the aligner from doing the backtrace
 *         aln1 = <char*>malloc(sizeof(char) * (2 * readLen + 16))             # <<<<<<<<<<<<<<
 *         aln2 = <char*>malloc(sizeof(char) * (2 * readLen + 16))
 * 
 */
    __pyx_v_aln1 = ((char *)malloc(((sizeof(char)) * ((2 * __pyx_v_readLen) + 16))));

    /* "calign.pyx":202
 *         # avoid allocating memory if there's no flank; this also stops the aligner from doing the backtrace
 *         aln1 = <char*>malloc(sizeof(char) * (2 * readLen + 16))
 *         aln2 = <char*>malloc(sizeof(char) * (2 * readLen + 16))             # <<<<<<<<<<<<<<
 * 
 *     indexOfReadIntoHap = readStart - hapStart
 */
    __pyx_v_aln2 = ((char *)malloc(((sizeof(char)) * ((2 * __pyx_v_readLen) + 16))));

    /* "calign.pyx":199
 *         return 0
 * 
 *     if hapFlank > 0:             # <<<<<<<<<<<<<<
 *         # avoid allocating memory if there's no flank; this also stops the aligner from doing the backtrace
 *         aln1 = <char*>malloc(sizeof(char) * (2 * readLen + 16))
 */
  }

  /* "calign.pyx":204
 *         aln2 = <char*>malloc(sizeof(char) * (2 * readLen + 16))
 * 
 *     indexOfReadIntoHap = readStart - hapStart             # <<<<<<<<<<<<<<
 * 
 *     memset(mapCounts, 0, sizeof(int) * mapCountsLen) # Reset counts
 */
  __pyx_v_indexOfReadIntoHap = (__pyx_v_readStart - __pyx_v_hapStart);

  /* "calign.pyx":206
 *     indexOfReadIntoHap = readStart - hapStart
 * 
 *     memset(mapCounts, 0, sizeof(int) * mapCountsLen) # Reset counts             # <<<<<<<<<<<<<<
 * 
 *     # Do the mapping.
 */
  (void)(memset(__pyx_v_mapCounts, 0, ((sizeof(int)) * __pyx_v_mapCountsLen)));

  /* "calign.pyx":209
 * 
 *     # Do the mapping.
 *     for i in range(readLen - hash_nucs):             # <<<<<<<<<<<<<<
 *         hapIdx = haplotypeHash[readHash[i]]
 * 
 */
  __pyx_t_2 = (__pyx_v_readLen - __pyx_v_6calign_hash_nucs);
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "calign.pyx":210
 *     # Do the mapping.
 *     for i in range(readLen - hash_nucs):
 *         hapIdx = haplotypeHash[readHash[i]]             # <<<<<<<<<<<<<<
 * 
 *         while hapIdx != 0:
 */
    __pyx_v_hapIdx = (__pyx_v_haplotypeHash[(__pyx_v_readHash[__pyx_v_i])]);

    /* "calign.pyx":212
 *         hapIdx = haplotypeHash[readHash[i]]
 * 
 *         while hapIdx != 0:             # <<<<<<<<<<<<<<
 *             pos = hapIdx - i - 1 # account for index into read
 * 
 */
    while (1) {
      __pyx_t_1 = ((__pyx_v_hapIdx != 0) != 0);
      if (!__pyx_t_1) break;

      /* "calign.pyx":213
 * 
 *         while hapIdx != 0:
 *             pos = hapIdx - i - 1 # account for index into read             # <<<<<<<<<<<<<<
 * 
 *             mapCounts[pos + readLen] += 1
 */
      __pyx_v_pos = ((__pyx_v_hapIdx - __pyx_v_i) - 1);

      /* "calign.pyx":215
 *             pos = hapIdx - i - 1 # account for index into read
 * 
 *             mapCounts[pos + readLen] += 1             # <<<<<<<<<<<<<<
 * 
 *             if mapCounts[pos + readLen] > maxcount:
 */
      __pyx_t_5 = (__pyx_v_pos + __pyx_v_readLen);
      (__pyx_v_mapCounts[__pyx_t_5]) = ((__pyx_v_mapCounts[__pyx_t_5]) + 1);

      /* "calign.pyx":217
 *             mapCounts[pos + readLen] += 1
 * 
 *             if mapCounts[pos + readLen] > maxcount:             # <<<<<<<<<<<<<<
 *                 maxcount = mapCounts[pos + readLen]
 * 
 */
      __pyx_t_1 = (((__pyx_v_mapCounts[(__pyx_v_pos + __pyx_v_readLen)]) > __pyx_v_maxcount) != 0);
      if (__pyx_t_1) {

        /* "calign.pyx":218
 * 
 *             if mapCounts[pos + readLen] > maxcount:
 *                 maxcount = mapCounts[pos + readLen]             # <<<<<<<<<<<<<<
 * 
 *             hapIdx = haplotypeNextArray[hapIdx] # move to next hash hit
 */
        __pyx_v_maxcount = (__pyx_v_mapCounts[(__pyx_v_pos + __pyx_v_readLen)]);

        /* "calign.pyx":217
 *             mapCounts[pos + readLen] += 1
 * 
 *             if mapCounts[pos + readLen] > maxcount:             # <<<<<<<<<<<<<<
 *                 maxcount = mapCounts[pos + readLen]
 * 
 */
      }

      /* "calign.pyx":220
 *                 maxcount = mapCounts[pos + readLen]
 * 
 *             hapIdx = haplotypeNextArray[hapIdx] # move to next hash hit             # <<<<<<<<<<<<<<
 * 
 *     if maxcount > 0:
 */
      __pyx_v_hapIdx = (__pyx_v_haplotypeNextArray[__pyx_v_hapIdx]);
    }
  }

  /* "calign.pyx":222
 *             hapIdx = haplotypeNextArray[hapIdx] # move to next hash hit
 * 
 *     if maxcount > 0:             # <<<<<<<<<<<<<<
 *         for i in range(hapLen + readLen):
 *             if mapCounts[i] == maxcount:
 */
  __pyx_t_1 = ((__pyx_v_maxcount > 0) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":223
 * 
 *     if maxcount > 0:
 *         for i in range(hapLen + readLen):             # <<<<<<<<<<<<<<
 *             if mapCounts[i] == maxcount:
 *                 indexOfReadIntoHap = i - readLen
 */
    __pyx_t_2 = (__pyx_v_hapLen + __pyx_v_readLen);
    __pyx_t_3 = __pyx_t_2;
    for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
      __pyx_v_i = __pyx_t_4;

      /* "calign.pyx":224
 *     if maxcount > 0:
 *         for i in range(hapLen + readLen):
 *             if mapCounts[i] == maxcount:             # <<<<<<<<<<<<<<
 *                 indexOfReadIntoHap = i - readLen
 * 
 */
      __pyx_t_1 = (((__pyx_v_mapCounts[__pyx_v_i]) == __pyx_v_maxcount) != 0);
      if (__pyx_t_1) {

        /* "calign.pyx":225
 *         for i in range(hapLen + readLen):
 *             if mapCounts[i] == maxcount:
 *                 indexOfReadIntoHap = i - readLen             # <<<<<<<<<<<<<<
 * 
 *                 # Align read around this position. Make sure we can't go off the end.
 */
        __pyx_v_indexOfReadIntoHap = (__pyx_v_i - __pyx_v_readLen);

        /* "calign.pyx":228
 * 
 *                 # Align read around this position. Make sure we can't go off the end.
 *                 if indexOfReadIntoHap >= -readLen and (indexOfReadIntoHap + readLen + 15 < hapLen):             # <<<<<<<<<<<<<<
 *                     readStartInHap     = max(0, indexOfReadIntoHap - 8)
 *                     hapLenForAlignment = readLen + 15 # This is fixed by the alignment algorithm
 */
        __pyx_t_6 = ((__pyx_v_indexOfReadIntoHap >= (-__pyx_v_readLen)) != 0);
        if (__pyx_t_6) {
        } else {
          __pyx_t_1 = __pyx_t_6;
          goto __pyx_L16_bool_binop_done;
        }
        __pyx_t_6 = ((((__pyx_v_indexOfReadIntoHap + __pyx_v_readLen) + 15) < __pyx_v_hapLen) != 0);
        __pyx_t_1 = __pyx_t_6;
        __pyx_L16_bool_binop_done:;
        if (__pyx_t_1) {

          /* "calign.pyx":229
 *                 # Align read around this position. Make sure we can't go off the end.
 *                 if indexOfReadIntoHap >= -readLen and (indexOfReadIntoHap + readLen + 15 < hapLen):
 *                     readStartInHap     = max(0, indexOfReadIntoHap - 8)             # <<<<<<<<<<<<<<
 *                     hapLenForAlignment = readLen + 15 # This is fixed by the alignment algorithm
 * 
 */
          __pyx_t_7 = (__pyx_v_indexOfReadIntoHap - 8);
          __pyx_t_8 = 0;
          if (((__pyx_t_7 > __pyx_t_8) != 0)) {
            __pyx_t_9 = __pyx_t_7;
          } else {
            __pyx_t_9 = __pyx_t_8;
          }
          __pyx_v_readStartInHap = __pyx_t_9;

          /* "calign.pyx":230
 *                 if indexOfReadIntoHap >= -readLen and (indexOfReadIntoHap + readLen + 15 < hapLen):
 *                     readStartInHap     = max(0, indexOfReadIntoHap - 8)
 *                     hapLenForAlignment = readLen + 15 # This is fixed by the alignment algorithm             # <<<<<<<<<<<<<<
 * 
 *                     alignScore = fastAlignmentRoutine(haplotype + readStartInHap, read, quals, hapLenForAlignment, readLen,
 */
          __pyx_v_hapLenForAlignment = (__pyx_v_readLen + 15);

          /* "calign.pyx":232
 *                     hapLenForAlignment = readLen + 15 # This is fixed by the alignment algorithm
 * 
 *                     alignScore = fastAlignmentRoutine(haplotype + readStartInHap, read, quals, hapLenForAlignment, readLen,             # <<<<<<<<<<<<<<
 *                                                       gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 */
          __pyx_v_alignScore = fastAlignmentRoutine((__pyx_v_haplotype + __pyx_v_readStartInHap), __pyx_v_read, __pyx_v_quals, __pyx_v_hapLenForAlignment, __pyx_v_readLen, __pyx_v_gapExtend, __pyx_v_nucprior, (__pyx_v_localGapOpen + __pyx_v_readStartInHap), __pyx_v_aln1, __pyx_v_aln2, (&__pyx_v_firstpos));

          /* "calign.pyx":235
 *                                                       gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 *                     if doCalculateFlankScore == 1 and alignScore > 0 and hapFlank > 0:             # <<<<<<<<<<<<<<
 *                         alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,
 *                                                           firstpos + readStartInHap, aln1, aln2)
 */
          __pyx_t_6 = ((__pyx_v_doCalculateFlankScore == 1) != 0);
          if (__pyx_t_6) {
          } else {
            __pyx_t_1 = __pyx_t_6;
            goto __pyx_L19_bool_binop_done;
          }
          __pyx_t_6 = ((__pyx_v_alignScore > 0) != 0);
          if (__pyx_t_6) {
          } else {
            __pyx_t_1 = __pyx_t_6;
            goto __pyx_L19_bool_binop_done;
          }
          __pyx_t_6 = ((__pyx_v_hapFlank > 0) != 0);
          __pyx_t_1 = __pyx_t_6;
          __pyx_L19_bool_binop_done:;
          if (__pyx_t_1) {

            /* "calign.pyx":236
 * 
 *                     if doCalculateFlankScore == 1 and alignScore > 0 and hapFlank > 0:
 *                         alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,             # <<<<<<<<<<<<<<
 *                                                           firstpos + readStartInHap, aln1, aln2)
 * 
 */
            __pyx_v_alignScore = (__pyx_v_alignScore - calculateFlankScore(__pyx_v_hapLen, __pyx_v_hapFlank, __pyx_v_quals, __pyx_v_localGapOpen, __pyx_v_gapExtend, __pyx_v_nucprior, (__pyx_v_firstpos + __pyx_v_readStartInHap), __pyx_v_aln1, __pyx_v_aln2));

            /* "calign.pyx":235
 *                                                       gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 *                     if doCalculateFlankScore == 1 and alignScore > 0 and hapFlank > 0:             # <<<<<<<<<<<<<<
 *                         alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,
 *                                                           firstpos + readStartInHap, aln1, aln2)
 */
          }

          /* "calign.pyx":239
 *                                                           firstpos + readStartInHap, aln1, aln2)
 * 
 *                     if alignScore < bestScore:             # <<<<<<<<<<<<<<
 *                         bestScore           = alignScore
 *                         bestMappingPosition = indexOfReadIntoHap
 */
          __pyx_t_1 = ((__pyx_v_alignScore < __pyx_v_bestScore) != 0);
          if (__pyx_t_1) {

            /* "calign.pyx":240
 * 
 *                     if alignScore < bestScore:
 *                         bestScore           = alignScore             # <<<<<<<<<<<<<<
 *                         bestMappingPosition = indexOfReadIntoHap
 * 
 */
            __pyx_v_bestScore = __pyx_v_alignScore;

            /* "calign.pyx":241
 *                     if alignScore < bestScore:
 *                         bestScore           = alignScore
 *                         bestMappingPosition = indexOfReadIntoHap             # <<<<<<<<<<<<<<
 * 
 *                         if bestScore == 0:
 */
            __pyx_v_bestMappingPosition = __pyx_v_indexOfReadIntoHap;

            /* "calign.pyx":243
 *                         bestMappingPosition = indexOfReadIntoHap
 * 
 *                         if bestScore == 0:             # <<<<<<<<<<<<<<
 *                             if hapFlank > 0:
 *                                 free (aln1)
 */
            __pyx_t_1 = ((__pyx_v_bestScore == 0) != 0);
            if (__pyx_t_1) {

              /* "calign.pyx":244
 * 
 *                         if bestScore == 0:
 *                             if hapFlank > 0:             # <<<<<<<<<<<<<<
 *                                 free (aln1)
 *                                 free (aln2)
 */
              __pyx_t_1 = ((__pyx_v_hapFlank > 0) != 0);
              if (__pyx_t_1) {

                /* "calign.pyx":245
 *                         if bestScore == 0:
 *                             if hapFlank > 0:
 *                                 free (aln1)             # <<<<<<<<<<<<<<
 *                                 free (aln2)
 *                             return bestScore # Short-circuit this loop if we find an exact match
 */
                free(__pyx_v_aln1);

                /* "calign.pyx":246
 *                             if hapFlank > 0:
 *                                 free (aln1)
 *                                 free (aln2)             # <<<<<<<<<<<<<<
 *                             return bestScore # Short-circuit this loop if we find an exact match
 * 
 */
                free(__pyx_v_aln2);

                /* "calign.pyx":244
 * 
 *                         if bestScore == 0:
 *                             if hapFlank > 0:             # <<<<<<<<<<<<<<
 *                                 free (aln1)
 *                                 free (aln2)
 */
              }

              /* "calign.pyx":247
 *                                 free (aln1)
 *                                 free (aln2)
 *                             return bestScore # Short-circuit this loop if we find an exact match             # <<<<<<<<<<<<<<
 * 
 *     # Now try original mapping position. If the read is past the end of the haplotype then
 */
              __pyx_r = __pyx_v_bestScore;
              goto __pyx_L0;

              /* "calign.pyx":243
 *                         bestMappingPosition = indexOfReadIntoHap
 * 
 *                         if bestScore == 0:             # <<<<<<<<<<<<<<
 *                             if hapFlank > 0:
 *                                 free (aln1)
 */
            }

            /* "calign.pyx":239
 *                                                           firstpos + readStartInHap, aln1, aln2)
 * 
 *                     if alignScore < bestScore:             # <<<<<<<<<<<<<<
 *                         bestScore           = alignScore
 *                         bestMappingPosition = indexOfReadIntoHap
 */
          }

          /* "calign.pyx":228
 * 
 *                 # Align read around this position. Make sure we can't go off the end.
 *                 if indexOfReadIntoHap >= -readLen and (indexOfReadIntoHap + readLen + 15 < hapLen):             # <<<<<<<<<<<<<<
 *                     readStartInHap     = max(0, indexOfReadIntoHap - 8)
 *                     hapLenForAlignment = readLen + 15 # This is fixed by the alignment algorithm
 */
        }

        /* "calign.pyx":224
 *     if maxcount > 0:
 *         for i in range(hapLen + readLen):
 *             if mapCounts[i] == maxcount:             # <<<<<<<<<<<<<<
 *                 indexOfReadIntoHap = i - readLen
 * 
 */
      }
    }

    /* "calign.pyx":222
 *             hapIdx = haplotypeNextArray[hapIdx] # move to next hash hit
 * 
 *     if maxcount > 0:             # <<<<<<<<<<<<<<
 *         for i in range(hapLen + readLen):
 *             if mapCounts[i] == maxcount:
 */
  }

  /* "calign.pyx":252
 *     # don't allow the algorithm to align off the end of the haplotype. This will only happen in the case
 *     # of very large deletions.
 *     indexOfReadIntoHap = min(readStart - hapStart, hapLen - readLen - 15)             # <<<<<<<<<<<<<<
 * 
 *     # Only try this if the mapper hasn't already found this position
 */
  __pyx_t_9 = ((__pyx_v_hapLen - __pyx_v_readLen) - 15);
  __pyx_t_2 = (__pyx_v_readStart - __pyx_v_hapStart);
  if (((__pyx_t_9 < __pyx_t_2) != 0)) {
    __pyx_t_7 = __pyx_t_9;
  } else {
    __pyx_t_7 = __pyx_t_2;
  }
  __pyx_v_indexOfReadIntoHap = __pyx_t_7;

  /* "calign.pyx":255
 * 
 *     # Only try this if the mapper hasn't already found this position
 *     if indexOfReadIntoHap != bestMappingPosition:             # <<<<<<<<<<<<<<
 *         readStartInHap = max(0, indexOfReadIntoHap - 8)
 * 
 */
  __pyx_t_1 = ((__pyx_v_indexOfReadIntoHap != __pyx_v_bestMappingPosition) != 0);
  if (__pyx_t_1) {

    /* "calign.pyx":256
 *     # Only try this if the mapper hasn't already found this position
 *     if indexOfReadIntoHap != bestMappingPosition:
 *         readStartInHap = max(0, indexOfReadIntoHap - 8)             # <<<<<<<<<<<<<<
 * 
 *         alignScore = fastAlignmentRoutine(haplotype + readStartInHap, read, quals, readLen + 15, readLen,
 */
    __pyx_t_7 = (__pyx_v_indexOfReadIntoHap - 8);
    __pyx_t_9 = 0;
    if (((__pyx_t_7 > __pyx_t_9) != 0)) {
      __pyx_t_8 = __pyx_t_7;
    } else {
      __pyx_t_8 = __pyx_t_9;
    }
    __pyx_v_readStartInHap = __pyx_t_8;

    /* "calign.pyx":258
 *         readStartInHap = max(0, indexOfReadIntoHap - 8)
 * 
 *         alignScore = fastAlignmentRoutine(haplotype + readStartInHap, read, quals, readLen + 15, readLen,             # <<<<<<<<<<<<<<
 *                                           gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 */
    __pyx_v_alignScore = fastAlignmentRoutine((__pyx_v_haplotype + __pyx_v_readStartInHap), __pyx_v_read, __pyx_v_quals, (__pyx_v_readLen + 15), __pyx_v_readLen, __pyx_v_gapExtend, __pyx_v_nucprior, (__pyx_v_localGapOpen + __pyx_v_readStartInHap), __pyx_v_aln1, __pyx_v_aln2, (&__pyx_v_firstpos));

    /* "calign.pyx":261
 *                                           gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 *         if doCalculateFlankScore == 1 and alignScore > 0 and hapLen > 0:             # <<<<<<<<<<<<<<
 *             alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,
 *                                               firstpos + readStartInHap, aln1, aln2)
 */
    __pyx_t_6 = ((__pyx_v_doCalculateFlankScore == 1) != 0);
    if (__pyx_t_6) {
    } else {
      __pyx_t_1 = __pyx_t_6;
      goto __pyx_L27_bool_binop_done;
    }
    __pyx_t_6 = ((__pyx_v_alignScore > 0) != 0);
    if (__pyx_t_6) {
    } else {
      __pyx_t_1 = __pyx_t_6;
      goto __pyx_L27_bool_binop_done;
    }
    __pyx_t_6 = ((__pyx_v_hapLen > 0) != 0);
    __pyx_t_1 = __pyx_t_6;
    __pyx_L27_bool_binop_done:;
    if (__pyx_t_1) {

      /* "calign.pyx":262
 * 
 *         if doCalculateFlankScore == 1 and alignScore > 0 and hapLen > 0:
 *             alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,             # <<<<<<<<<<<<<<
 *                                               firstpos + readStartInHap, aln1, aln2)
 * 
 */
      __pyx_v_alignScore = (__pyx_v_alignScore - calculateFlankScore(__pyx_v_hapLen, __pyx_v_hapFlank, __pyx_v_quals, __pyx_v_localGapOpen, __pyx_v_gapExtend, __pyx_v_nucprior, (__pyx_v_firstpos + __pyx_v_readStartInHap), __pyx_v_aln1, __pyx_v_aln2));

      /* "calign.pyx":261
 *                                           gapExtend, nucprior, localGapOpen + readStartInHap, aln1, aln2, &firstpos)
 * 
 *         if doCalculateFlankScore == 1 and alignScore > 0 and hapLen > 0:             # <<<<<<<<<<<<<<
 *             alignScore -= calculateFlankScore(hapLen, hapFlank, quals, localGapOpen, gapExtend, nucprior,
 *                                               firstpos + readStartInHap, aln1, aln2)
 */
    }

    /* "calign.pyx":265
 *                                               firstpos + readStartInHap, aln1, aln2)
 * 
 *         if alignScore < bestScore:             # <<<<<<<<<<<<<<
 *             bestScore           = alignScore
 *             bestMappingPosition = indexOfReadIntoHap
 */
    __pyx_t_1 = ((__pyx_v_alignScore < __pyx_v_bestScore) != 0);
    if (__pyx_t_1) {

      /* "calign.pyx":266
 * 
 *         if alignScore < bestScore:
 *             bestScore           = alignScore             # <<<<<<<<<<<<<<
 *             bestMappingPosition = indexOfReadIntoHap
 * 
 */
      __pyx_v_bestScore = __pyx_v_alignScore;

      /* "calign.pyx":267
 *         if alignScore < bestScore:
 *             bestScore           = alignScore
 *             bestMappingPosition = indexOfReadIntoHap             # <<<<<<<<<<<<<<
 * 
 *     free(aln1)
 */
      __pyx_v_bestMappingPosition = __pyx_v_indexOfReadIntoHap;

      /* "calign.pyx":265
 *                                               firstpos + readStartInHap, aln1, aln2)
 * 
 *         if alignScore < bestScore:             # <<<<<<<<<<<<<<
 *             bestScore           = alignScore
 *             bestMappingPosition = indexOfReadIntoHap
 */
    }

    /* "calign.pyx":255
 * 
 *     # Only try this if the mapper hasn't already found this position
 *     if indexOfReadIntoHap != bestMappingPosition:             # <<<<<<<<<<<<<<
 *         readStartInHap = max(0, indexOfReadIntoHap - 8)
 * 
 */
  }

  /* "calign.pyx":269
 *             bestMappingPosition = indexOfReadIntoHap
 * 
 *     free(aln1)             # <<<<<<<<<<<<<<
 *     free(aln2)
 * 
 */
  free(__pyx_v_aln1);

  /* "calign.pyx":270
 * 
 *     free(aln1)
 *     free(aln2)             # <<<<<<<<<<<<<<
 * 
 *     return bestScore
 */
  free(__pyx_v_aln2);

  /* "calign.pyx":272
 *     free(aln2)
 * 
 *     return bestScore             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = __pyx_v_bestScore;
  goto __pyx_L0;

  /* "calign.pyx":170
 * 
 * # remove 'nogil' when debugging (also in calign.pxd)
 * cdef int mapAndAlignReadToHaplotype(char* read, char* quals, int readStart, int hapStart, int readLen, int hapLen, short* haplotypeHash, short* haplotypeNextArray, short* readHash, char* haplotype, int gapExtend, int nucprior, char* localGapOpen, int* mapCounts, int mapCountsLen, int hapFlank, int doCalculateFlankScore) nogil:             # <<<<<<<<<<<<<<
 * 
 * 
 */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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  /* "htslibWrapper.pxd":263
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 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
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 */
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 */

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/* "htslibWrapper.pxd":265
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/* "htslibWrapper.pxd":271
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            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;
}

/* 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

/* 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);
}

/* None */
static CYTHON_INLINE long __Pyx_pow_long(long b, long e) {
    long t = b;
    switch (e) {
        case 3:
            t *= b;
        CYTHON_FALLTHROUGH;
        case 2:
            t *= b;
        CYTHON_FALLTHROUGH;
        case 1:
            return t;
        case 0:
            return 1;
    }
    #if 1
    if (unlikely(e<0)) return 0;
    #endif
    t = 1;
    while (likely(e)) {
        t *= (b * (e&1)) | ((~e)&1);
        b *= b;
        e >>= 1;
    }
    return t;
}

/* 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;\
    }

/* 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;
}

/* 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);
    }
}

/* 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;
}

/* PyObjectSetAttrStr */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
    PyTypeObject* tp = Py_TYPE(obj);
    if (likely(tp->tp_setattro))
        return tp->tp_setattro(obj, attr_name, value);
#if PY_MAJOR_VERSION < 3
    if (likely(tp->tp_setattr))
        return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
#endif
    return PyObject_SetAttr(obj, attr_name, value);
}
#endif

/* VoidPtrExport */
static int __Pyx_ExportVoidPtr(PyObject *name, void *p, const char *sig) {
    PyObject *d;
    PyObject *cobj = 0;
    d = PyDict_GetItem(__pyx_d, __pyx_n_s_pyx_capi);
    Py_XINCREF(d);
    if (!d) {
        d = PyDict_New();
        if (!d)
            goto bad;
        if (__Pyx_PyObject_SetAttrStr(__pyx_m, __pyx_n_s_pyx_capi, d) < 0)
            goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000
    cobj = PyCapsule_New(p, sig, 0);
#else
    cobj = PyCObject_FromVoidPtrAndDesc(p, (void *)sig, 0);
#endif
    if (!cobj)
        goto bad;
    if (PyDict_SetItem(d, name, cobj) < 0)
        goto bad;
    Py_DECREF(cobj);
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(cobj);
    Py_XDECREF(d);
    return -1;
}

/* 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;
}

/* 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 */
