/* Generated by Cython 0.19.1 on Wed Jun 28 05:32:00 2017 */

#define PY_SSIZE_T_CLEAN
#ifndef CYTHON_USE_PYLONG_INTERNALS
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 0
#else
#include "pyconfig.h"
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 1
#else
#define CYTHON_USE_PYLONG_INTERNALS 0
#endif
#endif
#endif
#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 < 0x02040000
    #error Cython requires Python 2.4+.
#else
#include <stddef.h> /* For offsetof */
#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
#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_CPYTHON 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
#if PY_VERSION_HEX < 0x02050000
  typedef int Py_ssize_t;
  #define PY_SSIZE_T_MAX INT_MAX
  #define PY_SSIZE_T_MIN INT_MIN
  #define PY_FORMAT_SIZE_T ""
  #define CYTHON_FORMAT_SSIZE_T ""
  #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
  #define PyInt_AsSsize_t(o)   __Pyx_PyInt_AsInt(o)
  #define PyNumber_Index(o)    ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
                                (PyErr_Format(PyExc_TypeError, \
                                              "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
                                 (PyObject*)0))
  #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
                                  !PyComplex_Check(o))
  #define PyIndex_Check __Pyx_PyIndex_Check
  #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
  #define __PYX_BUILD_PY_SSIZE_T "i"
#else
  #define __PYX_BUILD_PY_SSIZE_T "n"
  #define CYTHON_FORMAT_SSIZE_T "z"
  #define __Pyx_PyIndex_Check PyIndex_Check
#endif
#if PY_VERSION_HEX < 0x02060000
  #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
  #define Py_TYPE(ob)   (((PyObject*)(ob))->ob_type)
  #define Py_SIZE(ob)   (((PyVarObject*)(ob))->ob_size)
  #define PyVarObject_HEAD_INIT(type, size) \
          PyObject_HEAD_INIT(type) size,
  #define PyType_Modified(t)
  typedef struct {
     void *buf;
     PyObject *obj;
     Py_ssize_t len;
     Py_ssize_t itemsize;
     int readonly;
     int ndim;
     char *format;
     Py_ssize_t *shape;
     Py_ssize_t *strides;
     Py_ssize_t *suboffsets;
     void *internal;
  } Py_buffer;
  #define PyBUF_SIMPLE 0
  #define PyBUF_WRITABLE 0x0001
  #define PyBUF_FORMAT 0x0004
  #define PyBUF_ND 0x0008
  #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
  #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
  #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
  #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
  #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
  #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
  #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
  typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
  typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#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, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#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)
#endif
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
  #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
  #define Py_TPFLAGS_CHECKTYPES 0
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX < 0x02060000
  #define Py_TPFLAGS_HAVE_VERSION_TAG 0
#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_READ(k, d, i)   PyUnicode_READ(k, d, i)
#else
  #define CYTHON_PEP393_ENABLED 0
  #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_READ(k, d, i)   ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#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
#endif
#if PY_VERSION_HEX < 0x02060000
  #define PyBytesObject                PyStringObject
  #define PyBytes_Type                 PyString_Type
  #define PyBytes_Check                PyString_Check
  #define PyBytes_CheckExact           PyString_CheckExact
  #define PyBytes_FromString           PyString_FromString
  #define PyBytes_FromStringAndSize    PyString_FromStringAndSize
  #define PyBytes_FromFormat           PyString_FromFormat
  #define PyBytes_DecodeEscape         PyString_DecodeEscape
  #define PyBytes_AsString             PyString_AsString
  #define PyBytes_AsStringAndSize      PyString_AsStringAndSize
  #define PyBytes_Size                 PyString_Size
  #define PyBytes_AS_STRING            PyString_AS_STRING
  #define PyBytes_GET_SIZE             PyString_GET_SIZE
  #define PyBytes_Repr                 PyString_Repr
  #define PyBytes_Concat               PyString_Concat
  #define PyBytes_ConcatAndDel         PyString_ConcatAndDel
#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_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
                                         PyString_Check(obj) || PyUnicode_Check(obj))
  #define __Pyx_PyBaseString_CheckExact(obj) (Py_TYPE(obj) == &PyBaseString_Type)
#endif
#if PY_VERSION_HEX < 0x02060000
  #define PySet_Check(obj)             PyObject_TypeCheck(obj, &PySet_Type)
  #define PyFrozenSet_Check(obj)       PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
#ifndef PySet_CheckExact
  #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#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
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBoolObject                 PyLongObject
#endif
#if PY_VERSION_HEX < 0x03020000
  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) || (PY_VERSION_HEX >= 0x03010300)
  #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
  #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
  #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
  #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
        (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
        (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
            (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
  #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
        (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
        (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
            (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
  #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
        (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
        (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
            (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#if PY_VERSION_HEX < 0x02050000
  #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),((char *)(n)))
  #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
  #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),((char *)(n)))
#else
  #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),(n))
  #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
  #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),(n))
#endif
#if PY_VERSION_HEX < 0x02050000
  #define __Pyx_NAMESTR(n) ((char *)(n))
  #define __Pyx_DOCSTR(n)  ((char *)(n))
#else
  #define __Pyx_NAMESTR(n) (n)
  #define __Pyx_DOCSTR(n)  (n)
#endif
#ifndef CYTHON_INLINE
  #if 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
#ifndef CYTHON_RESTRICT
  #if defined(__GNUC__)
    #define CYTHON_RESTRICT __restrict__
  #elif defined(_MSC_VER)
    #define CYTHON_RESTRICT __restrict
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_RESTRICT restrict
  #else
    #define CYTHON_RESTRICT
  #endif
#endif
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
  /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
   a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
   a quiet NaN. */
  float value;
  memset(&value, 0xFF, sizeof(value));
  return value;
}
#endif


#if PY_MAJOR_VERSION >= 3
  #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_TrueDivide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
#endif

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

#if defined(WIN32) || defined(MS_WINDOWS)
#define _USE_MATH_DEFINES
#endif
#include <math.h>
#define __PYX_HAVE__assembler
#define __PYX_HAVE_API__assembler
#include "string.h"
#include "stdio.h"
#include "pythread.h"
#include "stdlib.h"
#include "math.h"
#include "ctype.h"
#include "stdint.h"
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "htslib/sam.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */

#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
#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
typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/

#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
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
#define __Pyx_PyBytes_FromString        PyBytes_FromString
#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(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_PyObject_AsUString(s)    ((unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_FromUString(s)  __Pyx_PyObject_FromString((char*)s)
#define __Pyx_PyBytes_FromUString(s)   __Pyx_PyBytes_FromString((char*)s)
#define __Pyx_PyStr_FromUString(s)     __Pyx_PyStr_FromString((char*)s)
#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
#if PY_MAJOR_VERSION < 3
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
{
    const Py_UNICODE *u_end = u;
    while (*u_end++) ;
    return u_end - u - 1;
}
#else
#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
#endif
#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_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#if CYTHON_COMPILING_IN_CPYTHON
#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 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params() {
    PyObject* sys = NULL;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    sys = PyImport_ImportModule("sys");
    if (sys == NULL) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    if (default_encoding == NULL) goto bad;
    if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
        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 == NULL) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (ascii_chars_b == NULL || strncmp(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 '%s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
    }
    Py_XDECREF(sys);
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return 0;
bad:
    Py_XDECREF(sys);
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return -1;
}
#endif
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
#else
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params() {
    PyObject* sys = NULL;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (sys == NULL) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    if (default_encoding == NULL) goto bad;
    default_encoding_c = PyBytes_AS_STRING(default_encoding);
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
    strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
    Py_DECREF(sys);
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(sys);
    Py_XDECREF(default_encoding);
    return -1;
}
#endif
#endif


#ifdef __GNUC__
  /* Test for GCC > 2.95 */
  #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
    #define likely(x)   __builtin_expect(!!(x), 1)
    #define unlikely(x) __builtin_expect(!!(x), 0)
  #else /* __GNUC__ > 2 ... */
    #define likely(x)   (x)
    #define unlikely(x) (x)
  #endif /* __GNUC__ > 2 ... */
#else /* __GNUC__ */
  #define likely(x)   (x)
  #define unlikely(x) (x)
#endif /* __GNUC__ */

static PyObject *__pyx_m;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
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[] = {
  "assembler.pyx",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "htslibWrapper.pxd",
  "fastafile.pxd",
  "cwindow.pxd",
  "variant.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_7variant_VariantCandidateGenerator;
struct __pyx_obj_9fastafile_FastaFile;
struct __pyx_obj_7cwindow_ReadArray;
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_9fastafile_FastaIndex;
struct __pyx_obj_13htslibWrapper_ReadIterator;
struct __pyx_obj_7cwindow_bamReadBuffer;
struct __pyx_obj_7variant_Variant;
struct __pyx_t_13htslibWrapper_cAlignedRead;
typedef struct __pyx_t_13htslibWrapper_cAlignedRead __pyx_t_13htslibWrapper_cAlignedRead;
struct __pyx_opt_args_13htslibWrapper_7Samfile__open;

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

/* "htslibWrapper.pxd":211
 *     cdef _hasIndex(self)
 *     cdef void openBAMFile(self, mode)
 *     cpdef _open(self, mode, loadIndex=*)             # <<<<<<<<<<<<<<
 *     cdef char* getrname(self, int tid)
 *     cpdef ReadIterator fetch(self, const char *region)
 */
struct __pyx_opt_args_13htslibWrapper_7Samfile__open {
  int __pyx_n;
  PyObject *loadIndex;
};
struct __pyx_t_9assembler_Node;
typedef struct __pyx_t_9assembler_Node __pyx_t_9assembler_Node;
struct __pyx_t_9assembler_NodeStack;
typedef struct __pyx_t_9assembler_NodeStack __pyx_t_9assembler_NodeStack;
struct __pyx_t_9assembler_Edge;
typedef struct __pyx_t_9assembler_Edge __pyx_t_9assembler_Edge;
struct __pyx_t_9assembler_EdgeStack;
typedef struct __pyx_t_9assembler_EdgeStack __pyx_t_9assembler_EdgeStack;
struct __pyx_t_9assembler_NodeDict;
typedef struct __pyx_t_9assembler_NodeDict __pyx_t_9assembler_NodeDict;
struct __pyx_t_9assembler_Path;
typedef struct __pyx_t_9assembler_Path __pyx_t_9assembler_Path;
struct __pyx_t_9assembler_PathStack;
typedef struct __pyx_t_9assembler_PathStack __pyx_t_9assembler_PathStack;
struct __pyx_t_9assembler_DeBruijnGraph;
typedef struct __pyx_t_9assembler_DeBruijnGraph __pyx_t_9assembler_DeBruijnGraph;

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

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

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

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

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

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

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

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

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


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


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


/* "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;
};


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


/* "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;
};


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


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



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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

struct __pyx_vtabstruct_7variant_VariantCandidateGenerator {
  void (*addVariantToList)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_7variant_Variant *);
  void (*getSnpCandidatesFromReadSegment)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *, char *, char *, int, int, int, int, int);
  void (*getVariantCandidatesFromSingleRead)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *);
  void (*addCandidatesFromReads)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **);
  PyObject *(*getCandidates)(struct __pyx_obj_7variant_VariantCandidateGenerator *, int);
};
static struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtabptr_7variant_VariantCandidateGenerator;
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#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
    (((size) <= sizeof(Py_ssize_t)) ? \
    __Pyx_GetItemInt_Tuple_Fast(o, i, wraparound, boundscheck) : \
    __Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                     int is_list, int wraparound, int boundscheck);

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

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

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

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

static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);

static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);

static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);

static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);

static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);

static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);

static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);

static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);

static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);

static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);

static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);

static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);

static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);

static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);

static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);

static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);

static int __Pyx_check_binary_version(void);

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

#if !defined(__Pyx_PyIdentifier_FromString)
#if PY_MAJOR_VERSION < 3
  #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
#else
  #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
#endif
#endif

static PyObject *__Pyx_ImportModule(const char *name); /*proto*/

static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);  /*proto*/

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

typedef struct {
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} __Pyx_CodeObjectCacheEntry;
struct __Pyx_CodeObjectCache {
    int count;
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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);

static void __Pyx_AddTraceback(const char *funcname, int c_line,
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static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/


/* Module declarations from 'cython' */

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

/* 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 'libc.string' */

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

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

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from 'cpython' */

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

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

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

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

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

/* Implementation of 'assembler' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_StandardError;
static PyObject *__pyx_builtin_sorted;
static char __pyx_k_1[] = "Could not allocate path";
static char __pyx_k_3[] = "Null path";
static char __pyx_k_5[] = "Null Node";
static char __pyx_k_7[] = "Could not allocate node";
static char __pyx_k_9[] = "Node struct cannot have > 4 edges. Now we have %s. This will cause problems";
static char __pyx_k_10[] = "Error. Could not allocate path stack with capacity %s";
static char __pyx_k_11[] = "Error. Could not allocate path stack elements with capacity %s";
static char __pyx_k_12[] = "Could not re-allocate PathStack";
static char __pyx_k_14[] = "Error. Could not allocate node stack with capacity %s";
static char __pyx_k_15[] = "Error. Could not allocate node stack elements with capacity %s";
static char __pyx_k_16[] = "Could not re-allocate NodeStack";
static char __pyx_k_18[] = "Error. Could not allocate edge";
static char __pyx_k_20[] = "Error. Could not allocate edge stack with capacity %s";
static char __pyx_k_21[] = "Error. Could not allocate edge stack elements with capacity %s";
static char __pyx_k_22[] = "Could not re-allocate EdgeStack";
static char __pyx_k_23[] = "Error. Could not NodeDict";
static char __pyx_k_25[] = "Error. Could not NodeDict.buckets of size %s";
static char __pyx_k_26[] = "Error. Could not NodeDict.bucketSize of size %s";
static char __pyx_k_27[] = "Could not allocate hash table bucket with size %s";
static char __pyx_k_28[] = "Could not re-allocate bucket";
static char __pyx_k_29[] = "Could not allocate memory for DeBruijnGraph";
static char __pyx_k_31[] = "nNodes = %s. nFilledBuckets = %s. mean entries/bucket = %s";
static char __pyx_k_32[] = "Could not allocate memory for string of size %s";
static char __pyx_k_33[] = "Logging path of %s nodes";
static char __pyx_k_34[] = "Pos = %s. Seq = %s. RefSeq = %c. Colours = %s. Node weight = %s";
static char __pyx_k_35[] = "Found complex variation that Platypus can't deal with yet at %s:%s-%s";
static char __pyx_k_36[] = "Could not allocate memory for charReadSeq of size %s";
static char __pyx_k_37[] = "Platypus assembler found candidate variant of size %s. %s:%s-%s %s --> %s";
static char __pyx_k_38[] = "Assembling region %s:%s-%s";
static char __pyx_k_39[] = "Could not assemble region %s:%s-%s without cycles. Max k-mer size tried = %s";
static char __pyx_k_40[] = "Found cycles in region %s:%s-%s with kmer size %s. Trying again with kmer size %s";
static char __pyx_k_41[] = "\nCython module used to interface to assembler routines.\n";
static char __pyx_k__Log[] = "Log";
static char __pyx_k__info[] = "info";
static char __pyx_k__debug[] = "debug";
static char __pyx_k__error[] = "error";
static char __pyx_k__heapq[] = "heapq";
static char __pyx_k__range[] = "range";
static char __pyx_k__logger[] = "logger";
static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__logging[] = "logging";
static char __pyx_k__warning[] = "warning";
static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__minReads[] = "minReads";
static char __pyx_k__noCycles[] = "noCycles";
static char __pyx_k__getLogger[] = "getLogger";
static char __pyx_k__verbosity[] = "verbosity";
static char __pyx_k____import__[] = "__import__";
static char __pyx_k__minMapQual[] = "minMapQual";
static char __pyx_k__collections[] = "collections";
static char __pyx_k__defaultdict[] = "defaultdict";
static char __pyx_k__minBaseQual[] = "minBaseQual";
static char __pyx_k__StandardError[] = "StandardError";
static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__";
static char __pyx_k__assembleBadReads[] = "assembleBadReads";
static char __pyx_k__assemblerKmerSize[] = "assemblerKmerSize";
static char __pyx_k__assemblyRegionSize[] = "assemblyRegionSize";
static char __pyx_k__assembleBrokenPairs[] = "assembleBrokenPairs";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_10;
static PyObject *__pyx_kp_s_11;
static PyObject *__pyx_kp_s_12;
static PyObject *__pyx_kp_s_14;
static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_20;
static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_22;
static PyObject *__pyx_kp_s_23;
static PyObject *__pyx_kp_s_25;
static PyObject *__pyx_kp_s_26;
static PyObject *__pyx_kp_s_27;
static PyObject *__pyx_kp_s_28;
static PyObject *__pyx_kp_s_29;
static PyObject *__pyx_kp_s_3;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_32;
static PyObject *__pyx_kp_s_33;
static PyObject *__pyx_kp_s_34;
static PyObject *__pyx_kp_s_35;
static PyObject *__pyx_kp_s_36;
static PyObject *__pyx_kp_s_37;
static PyObject *__pyx_kp_s_38;
static PyObject *__pyx_kp_s_39;
static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__Log;
static PyObject *__pyx_n_s__StandardError;
static PyObject *__pyx_n_s____import__;
static PyObject *__pyx_n_s____main__;
static PyObject *__pyx_n_s____pyx_vtable__;
static PyObject *__pyx_n_s____test__;
static PyObject *__pyx_n_s__assembleBadReads;
static PyObject *__pyx_n_s__assembleBrokenPairs;
static PyObject *__pyx_n_s__assemblerKmerSize;
static PyObject *__pyx_n_s__assemblyRegionSize;
static PyObject *__pyx_n_s__collections;
static PyObject *__pyx_n_s__debug;
static PyObject *__pyx_n_s__defaultdict;
static PyObject *__pyx_n_s__error;
static PyObject *__pyx_n_s__getLogger;
static PyObject *__pyx_n_s__heapq;
static PyObject *__pyx_n_s__info;
static PyObject *__pyx_n_s__logger;
static PyObject *__pyx_n_s__logging;
static PyObject *__pyx_n_s__minBaseQual;
static PyObject *__pyx_n_s__minMapQual;
static PyObject *__pyx_n_s__minReads;
static PyObject *__pyx_n_s__noCycles;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__sorted;
static PyObject *__pyx_n_s__verbosity;
static PyObject *__pyx_n_s__warning;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_100;
static PyObject *__pyx_k_tuple_2;
static PyObject *__pyx_k_tuple_4;
static PyObject *__pyx_k_tuple_6;
static PyObject *__pyx_k_tuple_8;
static PyObject *__pyx_k_tuple_13;
static PyObject *__pyx_k_tuple_17;
static PyObject *__pyx_k_tuple_19;
static PyObject *__pyx_k_tuple_24;
static PyObject *__pyx_k_tuple_30;
static PyObject *__pyx_k_tuple_42;

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

static __pyx_t_9assembler_Path *__pyx_f_9assembler_createPath(int __pyx_v_initialSize) {
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  /* "assembler.pyx":132
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 * 
 *     if thePath == NULL:
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  /* "assembler.pyx":134
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 * 
 *     if thePath == NULL:             # <<<<<<<<<<<<<<
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 * 
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  __pyx_t_1 = ((__pyx_v_thePath == NULL) != 0);
  if (__pyx_t_1) {

    /* "assembler.pyx":135
 * 
 *     if thePath == NULL:
 *         logger.error("Could not allocate path")             # <<<<<<<<<<<<<<
 * 
 *     thePath.nodes = createNodeStack(initialSize)
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 * 
 *         newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
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 *         theNode[0] = newNode
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    /* "assembler.pyx":695
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 */
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    /* "assembler.pyx":696
 *         theDict.bucketSize[hashValue] = initialBucketSize
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    /* "assembler.pyx":700
 *     # Bucket is there. Check all elements in bucket for match.
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 *         for i in range(bucketSize):
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 *             # Found empty slot. Insert new element
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      /* "assembler.pyx":705
 * 
 *             # Found empty slot. Insert new element
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 */
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        /* "assembler.pyx":706
 *             # Found empty slot. Insert new element
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 *                 theDict.buckets[hashValue][i] = newNode
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 */
        __pyx_v_newNode = __pyx_f_9assembler_createNode((__pyx_v_theNode[0])->sequence, (__pyx_v_theNode[0])->colours, (__pyx_v_theNode[0])->position, (__pyx_v_theNode[0])->kmerSize, (__pyx_v_theNode[0])->weight);

        /* "assembler.pyx":707
 *             if theDict.buckets[hashValue][i] == NULL:
 *                 newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
 *                 theDict.buckets[hashValue][i] = newNode             # <<<<<<<<<<<<<<
 *                 theNode[0] = newNode
 *                 return 0
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        ((__pyx_v_theDict->buckets[__pyx_v_hashValue])[__pyx_v_i]) = __pyx_v_newNode;

        /* "assembler.pyx":708
 *                 newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
 *                 theDict.buckets[hashValue][i] = newNode
 *                 theNode[0] = newNode             # <<<<<<<<<<<<<<
 *                 return 0
 * 
 */
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        /* "assembler.pyx":709
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 *             # Check for match
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        /* "assembler.pyx":714
 *             else:
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        /* "assembler.pyx":715
 *                 # Match. Return this element.
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 *                 if theNode[0] == testNode or strncmp(theNode[0].sequence, testNode.sequence, keyLen) == 0:             # <<<<<<<<<<<<<<
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          /* "assembler.pyx":716
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 *                     return 1
 * 
 */
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          /* "assembler.pyx":717
 *                 if theNode[0] == testNode or strncmp(theNode[0].sequence, testNode.sequence, keyLen) == 0:
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 *                     return 1             # <<<<<<<<<<<<<<
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 *     # If we get here, then we found no empty slots, and no matches. So we need to
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        __pyx_L10:;
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  __pyx_L3:;

  /* "assembler.pyx":722
 *     # allocate more space in the relevant bucket and then insert the key/value pair
 *     # in the next available space..
 *     cdef int oldBucketSize = theDict.bucketSize[hashValue]             # <<<<<<<<<<<<<<
 *     cdef int newBucketSize = 2*oldBucketSize
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  /* "assembler.pyx":723
 *     # in the next available space..
 *     cdef int oldBucketSize = theDict.bucketSize[hashValue]
 *     cdef int newBucketSize = 2*oldBucketSize             # <<<<<<<<<<<<<<
 *     cdef Node** temp = <Node**>(realloc(theDict.buckets[hashValue], sizeof(Node*)*newBucketSize))
 * 
 */
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  /* "assembler.pyx":724
 *     cdef int oldBucketSize = theDict.bucketSize[hashValue]
 *     cdef int newBucketSize = 2*oldBucketSize
 *     cdef Node** temp = <Node**>(realloc(theDict.buckets[hashValue], sizeof(Node*)*newBucketSize))             # <<<<<<<<<<<<<<
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 *     if temp == NULL:
 */
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  /* "assembler.pyx":726
 *     cdef Node** temp = <Node**>(realloc(theDict.buckets[hashValue], sizeof(Node*)*newBucketSize))
 * 
 *     if temp == NULL:             # <<<<<<<<<<<<<<
 *         raise StandardError, "Could not re-allocate bucket"
 *     else:
 */
  __pyx_t_8 = ((__pyx_v_temp == NULL) != 0);
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    /* "assembler.pyx":727
 * 
 *     if temp == NULL:
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 *     else:
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    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_kp_s_28), 0, 0);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  /*else*/ {

    /* "assembler.pyx":730
 *     else:
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 *         for i in range(oldBucketSize, newBucketSize):             # <<<<<<<<<<<<<<
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 * 
 */
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      __pyx_v_i = __pyx_t_6;

      /* "assembler.pyx":731
 *         # Set new entries to NULL
 *         for i in range(oldBucketSize, newBucketSize):
 *             temp[i] = NULL             # <<<<<<<<<<<<<<
 * 
 *         newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
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      (__pyx_v_temp[__pyx_v_i]) = NULL;
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    /* "assembler.pyx":733
 *             temp[i] = NULL
 * 
 *         newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)             # <<<<<<<<<<<<<<
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 *         theDict.buckets[hashValue] = temp
 */
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    /* "assembler.pyx":734
 * 
 *         newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
 *         theDict.bucketSize[hashValue] = newBucketSize             # <<<<<<<<<<<<<<
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    /* "assembler.pyx":735
 *         newNode = createNode(theNode[0].sequence, theNode[0].colours, theNode[0].position, theNode[0].kmerSize, theNode[0].weight)
 *         theDict.bucketSize[hashValue] = newBucketSize
 *         theDict.buckets[hashValue] = temp             # <<<<<<<<<<<<<<
 *         theDict.buckets[hashValue][oldBucketSize] = newNode
 *         theNode[0] = newNode
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    /* "assembler.pyx":736
 *         theDict.bucketSize[hashValue] = newBucketSize
 *         theDict.buckets[hashValue] = temp
 *         theDict.buckets[hashValue][oldBucketSize] = newNode             # <<<<<<<<<<<<<<
 *         theNode[0] = newNode
 * 
 */
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 *         theDict.buckets[hashValue] = temp
 *         theDict.buckets[hashValue][oldBucketSize] = newNode
 *         theNode[0] = newNode             # <<<<<<<<<<<<<<
 * 
 *     return 0
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      /* "assembler.pyx":853
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/* "assembler.pyx":902
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    /* "assembler.pyx":918
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      /* "assembler.pyx":919
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 *     logger.debug("nNodes = %s. nFilledBuckets = %s. mean entries/bucket = %s" %(nNodes, nFilledBuckets, float(nEntriesThisBucket)/nFilledBuckets))             # <<<<<<<<<<<<<<
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 *     cdef int nEdgesThisNode = 0             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int j = 0
 */
  __pyx_v_nEdgesThisNode = 0;

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

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

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

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

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

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

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

    /* "assembler.pyx":1052
 * 
 *         # TODO: Replace with maxHaplotypes??
 *         if thePathStack.top + 1 > 20 or finishedPaths.top + 1 > 20:             # <<<<<<<<<<<<<<
 *             #logger.info("Too many paths %s (%s) from this node. Giving up" %(thePathStack.top, finishedPaths.top))
 *             destroyPath(pathSoFar)
 */
    __pyx_t_1 = (((__pyx_v_thePathStack->top + 1) > 20) != 0);
    if (!__pyx_t_1) {
      __pyx_t_2 = (((__pyx_v_finishedPaths->top + 1) > 20) != 0);
      __pyx_t_3 = __pyx_t_2;
    } else {
      __pyx_t_3 = __pyx_t_1;
    }
    if (__pyx_t_3) {

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

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

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

      /* "assembler.pyx":1057
 *             destroyPathStack(thePathStack)
 *             destroyPathStack(finishedPaths)
 *             return NULL             # <<<<<<<<<<<<<<
 * 
 *         # At the moment, don't allow any cycles.
 */
      __pyx_r = NULL;
      goto __pyx_L0;
      goto __pyx_L5;
    }
    __pyx_L5:;

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

    /* "assembler.pyx":1062
 *         hasCycle = checkPathForCycles(pathSoFar)
 * 
 *         if hasCycle:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
    __pyx_t_3 = (__pyx_v_hasCycle != 0);
    if (__pyx_t_3) {

      /* "assembler.pyx":1063
 * 
 *         if hasCycle:
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # Got back to ref, this path is done with. This is a bubble.
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);
      goto __pyx_L6;
    }

    /* "assembler.pyx":1066
 * 
 *         # Got back to ref, this path is done with. This is a bubble.
 *         elif endSoFar.colours == REF_AND_READ:             # <<<<<<<<<<<<<<
 *             pathSoFar.isBubble = 1
 *             PathStack_Push(finishedPaths, pathSoFar)
 */
    __pyx_t_3 = ((__pyx_v_endSoFar->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
    if (__pyx_t_3) {

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

      /* "assembler.pyx":1068
 *         elif endSoFar.colours == REF_AND_READ:
 *             pathSoFar.isBubble = 1
 *             PathStack_Push(finishedPaths, pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # No reads here. Not quite sure how this could happen. Went from ref and read to only
 */
      __pyx_f_9assembler_PathStack_Push(__pyx_v_finishedPaths, __pyx_v_pathSoFar);
      goto __pyx_L6;
    }

    /* "assembler.pyx":1072
 *         # No reads here. Not quite sure how this could happen. Went from ref and read to only
 *         # ref.
 *         elif endSoFar.colours == REF:             # <<<<<<<<<<<<<<
 *             destroyPath(pathSoFar)
 * 
 */
    __pyx_t_3 = ((__pyx_v_endSoFar->colours == __pyx_v_9assembler_REF) != 0);
    if (__pyx_t_3) {

      /* "assembler.pyx":1073
 *         # ref.
 *         elif endSoFar.colours == REF:
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *         # Keep extending path
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);
      goto __pyx_L6;
    }
    /*else*/ {

      /* "assembler.pyx":1091
 * 
 *                 #else:
 *             nEdgesThisNode = endSoFar.nEdges             # <<<<<<<<<<<<<<
 * 
 *             for i in range(nEdgesThisNode):
 */
      __pyx_t_4 = __pyx_v_endSoFar->nEdges;
      __pyx_v_nEdgesThisNode = __pyx_t_4;

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

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

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

        /* "assembler.pyx":1097
 *                 newEnd = theEdge.endNode
 * 
 *                 if theEdge.weight >= minWeight or newEnd.colours == REF_AND_READ or newEnd.colours == REF:             # <<<<<<<<<<<<<<
 *                     newPath = createPath(theGraph.kmerSize)
 * 
 */
        __pyx_t_3 = ((__pyx_v_theEdge->weight >= __pyx_v_minWeight) != 0);
        if (!__pyx_t_3) {
          __pyx_t_1 = ((__pyx_v_newEnd->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
          if (!__pyx_t_1) {
            __pyx_t_2 = ((__pyx_v_newEnd->colours == __pyx_v_9assembler_REF) != 0);
            __pyx_t_7 = __pyx_t_2;
          } else {
            __pyx_t_7 = __pyx_t_1;
          }
          __pyx_t_1 = __pyx_t_7;
        } else {
          __pyx_t_1 = __pyx_t_3;
        }
        if (__pyx_t_1) {

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

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

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

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

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

          /* "assembler.pyx":1107
 *                     newPath.weight = pathSoFar.weight
 *                     addNodeToPath(newPath, newEnd, theEdge.weight)
 *                     PathStack_Push(thePathStack, newPath)             # <<<<<<<<<<<<<<
 * 
 *             destroyPath(pathSoFar)
 */
          __pyx_f_9assembler_PathStack_Push(__pyx_v_thePathStack, __pyx_v_newPath);
          goto __pyx_L9;
        }
        __pyx_L9:;
      }

      /* "assembler.pyx":1109
 *                     PathStack_Push(thePathStack, newPath)
 * 
 *             destroyPath(pathSoFar)             # <<<<<<<<<<<<<<
 * 
 *     destroyPathStack(thePathStack)
 */
      __pyx_f_9assembler_destroyPath(__pyx_v_pathSoFar);
    }
    __pyx_L6:;
  }

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

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

  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  /* "assembler.pyx":1137
 *     cdef Path* thePath = NULL
 *     cdef Path* theBubblePath = NULL
 *     cdef list variants = []             # <<<<<<<<<<<<<<
 *     cdef Variant theVar
 * 
 */
  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_v_variants = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

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

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

    /* "assembler.pyx":1144
 * 
 *         # First node which is ref only
 *         if theNode.colours == REF_AND_READ and theNode.position >= assemStart and theNode.position < assemEnd:             # <<<<<<<<<<<<<<
 *             nEdgesThisNode = theNode.nEdges
 * 
 */
    __pyx_t_5 = ((__pyx_v_theNode->colours == __pyx_v_9assembler_REF_AND_READ) != 0);
    if (__pyx_t_5) {
      __pyx_t_6 = ((__pyx_v_theNode->position >= __pyx_v_assemStart) != 0);
      if (__pyx_t_6) {
        __pyx_t_7 = ((__pyx_v_theNode->position < __pyx_v_assemEnd) != 0);
        __pyx_t_8 = __pyx_t_7;
      } else {
        __pyx_t_8 = __pyx_t_6;
      }
      __pyx_t_6 = __pyx_t_8;
    } else {
      __pyx_t_6 = __pyx_t_5;
    }
    if (__pyx_t_6) {

      /* "assembler.pyx":1145
 *         # First node which is ref only
 *         if theNode.colours == REF_AND_READ and theNode.position >= assemStart and theNode.position < assemEnd:
 *             nEdgesThisNode = theNode.nEdges             # <<<<<<<<<<<<<<
 * 
 *             for j in range(nEdgesThisNode):
 */
      __pyx_t_9 = __pyx_v_theNode->nEdges;
      __pyx_v_nEdgesThisNode = __pyx_t_9;

      /* "assembler.pyx":1147
 *             nEdgesThisNode = theNode.nEdges
 * 
 *             for j in range(nEdgesThisNode):             # <<<<<<<<<<<<<<
 *                 #logger.debug("Node %s has %s edges" %(i, nEdgesThisNode))
 *                 theEdge = theNode.edges[j]
 */
      __pyx_t_9 = __pyx_v_nEdgesThisNode;
      for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
        __pyx_v_j = __pyx_t_10;

        /* "assembler.pyx":1149
 *             for j in range(nEdgesThisNode):
 *                 #logger.debug("Node %s has %s edges" %(i, nEdgesThisNode))
 *                 theEdge = theNode.edges[j]             # <<<<<<<<<<<<<<
 * 
 *                 # New kmer in reads. Start path using a depth-first
 */
        __pyx_v_theEdge = (__pyx_v_theNode->edges[__pyx_v_j]);

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 *                 # New kmer in reads. Start path using a depth-first
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 * 
 *     for i in range(seqLen):
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 *             newSeq[seqLen - i - 1] = 'T'
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 *             newSeq[seqLen - i - 1] = 'A'
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 *             newSeq[seqLen - i - 1] = 'A'
 *         elif theSeq[i] == 'C':
 *             newSeq[seqLen - i - 1] = 'G'             # <<<<<<<<<<<<<<
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 *             newSeq[seqLen - i - 1] = 'C'
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 *     newSeq[seqLen] = 0
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/* "assembler.pyx":1348
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static void __pyx_f_9assembler_loadReadIntoGraph(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead, __pyx_t_9assembler_DeBruijnGraph *__pyx_v_theGraph, int __pyx_v_minQual, int __pyx_v_kmerSize) {
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 *     cdef char* theQuals = theRead.qual
 *     cdef int length = theRead.rlen
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 *     """
 *     cdef char* theSeq = theRead.seq
 *     cdef char* theQuals = theRead.qual             # <<<<<<<<<<<<<<
 *     cdef int length = theRead.rlen
 *     cdef int startPos = theRead.pos
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 *     cdef char* theQuals = theRead.qual
 *     cdef int length = theRead.rlen             # <<<<<<<<<<<<<<
 *     cdef int startPos = theRead.pos
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 *     cdef int i = 0
 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef int thisMinQual = 100000000
 *     cdef int NsInKmer = 0
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 *     cdef int i = 0
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 *     cdef int thisMinQual = 100000000             # <<<<<<<<<<<<<<
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 *     cdef int j = 0
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 *     cdef int NsInKmer = 0             # <<<<<<<<<<<<<<
 *     cdef Node tempStartNode
 *     cdef Node tempEndNode
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 *     cdef Node tempEndNode
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 *     for i in range( (length-kmerSize) - 1):             # <<<<<<<<<<<<<<
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 *         NsInKmer = 0
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 * 
 *     for i in range( (length-kmerSize) - 1):
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 *         NsInKmer = 0
 * 
 */
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 * 
 *         for j in range(i, i+kmerSize+1):
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 *         for j in range(i, i+kmerSize+1):             # <<<<<<<<<<<<<<
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 *             thisMinQual = min(thisMinQual, theQuals[j])
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 *             thisMinQual = min(thisMinQual, theQuals[j])             # <<<<<<<<<<<<<<
 * 
 *             if theSeq[j] == 'N':
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 * 
 *             if theSeq[j] == 'N':             # <<<<<<<<<<<<<<
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 * 
 */
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        /* "assembler.pyx":1371
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 *             if theSeq[j] == 'N':
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 * 
 *         if thisMinQual >= minQual and NsInKmer == 0:             # <<<<<<<<<<<<<<
 * 
 *             tempStartNode.sequence = theSeq + i
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 *         if thisMinQual >= minQual and NsInKmer == 0:
 * 
 *             tempStartNode.sequence = theSeq + i             # <<<<<<<<<<<<<<
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 * 
 *             tempStartNode.sequence = theSeq + i
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 *             tempStartNode.colours = READ
 *             tempStartNode.position = - 1
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 *             tempStartNode.kmerSize = kmerSize
 *             tempStartNode.colours = READ             # <<<<<<<<<<<<<<
 *             tempStartNode.position = - 1
 *             tempStartNode.weight = thisMinQual
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 *             tempStartNode.kmerSize = kmerSize
 *             tempStartNode.colours = READ
 *             tempStartNode.position = - 1             # <<<<<<<<<<<<<<
 *             tempStartNode.weight = thisMinQual
 * 
 */
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 *             tempStartNode.colours = READ
 *             tempStartNode.position = - 1
 *             tempStartNode.weight = thisMinQual             # <<<<<<<<<<<<<<
 * 
 *             tempEndNode.sequence = theSeq + i + 1
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 *             tempStartNode.weight = thisMinQual
 * 
 *             tempEndNode.sequence = theSeq + i + 1             # <<<<<<<<<<<<<<
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 * 
 *             tempEndNode.sequence = theSeq + i + 1
 *             tempEndNode.kmerSize = kmerSize             # <<<<<<<<<<<<<<
 *             tempEndNode.colours = READ
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 *             tempEndNode.sequence = theSeq + i + 1
 *             tempEndNode.kmerSize = kmerSize
 *             tempEndNode.colours = READ             # <<<<<<<<<<<<<<
 *             tempEndNode.position = -1
 *             tempEndNode.weight = thisMinQual
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 *             tempEndNode.colours = READ
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 *             tempEndNode.weight = thisMinQual
 * 
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 *             tempEndNode.position = -1
 *             tempEndNode.weight = thisMinQual             # <<<<<<<<<<<<<<
 * 
 *             DeBruijnGraph_AddEdge(theGraph, &tempStartNode, &tempEndNode, thisMinQual)
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 *             tempEndNode.weight = thisMinQual
 * 
 *             DeBruijnGraph_AddEdge(theGraph, &tempStartNode, &tempEndNode, thisMinQual)             # <<<<<<<<<<<<<<
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 * ###################################################################################################
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/* "assembler.pyx":1391
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 * 
 * cdef void loadBAMDataIntoGraph(DeBruijnGraph* theGraph, list readBuffers, int assembleBadReads, int assembleBrokenPairs, int minQual, int kmerSize):             # <<<<<<<<<<<<<<
 *     """
 *     Load k-mers from the specified BAM file into the graph. K-mers containing
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static void __pyx_f_9assembler_loadBAMDataIntoGraph(__pyx_t_9assembler_DeBruijnGraph *__pyx_v_theGraph, PyObject *__pyx_v_readBuffers, int __pyx_v_assembleBadReads, int __pyx_v_assembleBrokenPairs, int __pyx_v_minQual, int __pyx_v_kmerSize) {
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/* "htslibWrapper.pxd":250
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static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":251
 * # And here are accessor functions for the bit-fields
 * cdef inline int Read_IsReverse(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:
 */
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/* "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) {
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  /* "htslibWrapper.pxd":254
 * 
 * cdef inline int Read_IsPaired(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":256
 *     return ( (theRead.bitFlag & BAM_FPAIRED) != 0)
 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FPROPER_PAIR) != 0)
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 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsProperPair(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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 * 
 * cdef inline int Read_IsProperPair(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":259
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 */

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

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  /* "htslibWrapper.pxd":263
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":265
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 * 
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 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":266
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":268
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":269
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":271
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 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
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 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":272
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
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/* "htslibWrapper.pxd":274
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 * 
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 */

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  /* "htslibWrapper.pxd":275
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
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 * 
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/* "htslibWrapper.pxd":277
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
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 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsSecondaryAlignment(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":278
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":280
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 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":281
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":283
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FREVERSE)
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 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_SetIsNotReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":284
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
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 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
 */
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/* "htslibWrapper.pxd":286
 *     theRead.bitFlag &= (~BAM_FREVERSE)
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
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 */

static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_SetIsReverse(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
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  /* "htslibWrapper.pxd":287
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
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 */
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/* "htslibWrapper.pxd":289
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 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
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 */

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":290
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
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 */
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/* "htslibWrapper.pxd":292
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 */

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  /* "htslibWrapper.pxd":293
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:
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 * 
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 */
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/* "htslibWrapper.pxd":295
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 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:
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bad:
    Py_XDECREF(ob);
    return NULL;
}

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

static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
    PyObject *empty_list = 0;
    PyObject *module = 0;
    PyObject *global_dict = 0;
    PyObject *empty_dict = 0;
    PyObject *list;
    #if PY_VERSION_HEX < 0x03030000
    PyObject *py_import;
    py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s____import__);
    if (!py_import)
        goto bad;
    #endif
    if (from_list)
        list = from_list;
    else {
        empty_list = PyList_New(0);
        if (!empty_list)
            goto bad;
        list = empty_list;
    }
    global_dict = PyModule_GetDict(__pyx_m);
    if (!global_dict)
        goto bad;
    empty_dict = PyDict_New();
    if (!empty_dict)
        goto bad;
    #if PY_VERSION_HEX >= 0x02050000
    {
        #if PY_MAJOR_VERSION >= 3
        if (level == -1) {
            if (strchr(__Pyx_MODULE_NAME, '.')) {
                #if PY_VERSION_HEX < 0x03030000
                PyObject *py_level = PyInt_FromLong(1);
                if (!py_level)
                    goto bad;
                module = PyObject_CallFunctionObjArgs(py_import,
                    name, global_dict, empty_dict, list, py_level, NULL);
                Py_DECREF(py_level);
                #else
                module = PyImport_ImportModuleLevelObject(
                    name, global_dict, empty_dict, list, 1);
                #endif
                if (!module) {
                    if (!PyErr_ExceptionMatches(PyExc_ImportError))
                        goto bad;
                    PyErr_Clear();
                }
            }
            level = 0; /* try absolute import on failure */
        }
        #endif
        if (!module) {
            #if PY_VERSION_HEX < 0x03030000
            PyObject *py_level = PyInt_FromLong(level);
            if (!py_level)
                goto bad;
            module = PyObject_CallFunctionObjArgs(py_import,
                name, global_dict, empty_dict, list, py_level, NULL);
            Py_DECREF(py_level);
            #else
            module = PyImport_ImportModuleLevelObject(
                name, global_dict, empty_dict, list, level);
            #endif
        }
    }
    #else
    if (level>0) {
        PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
        goto bad;
    }
    module = PyObject_CallFunctionObjArgs(py_import,
        name, global_dict, empty_dict, list, NULL);
    #endif
bad:
    #if PY_VERSION_HEX < 0x03030000
    Py_XDECREF(py_import);
    #endif
    Py_XDECREF(empty_list);
    Py_XDECREF(empty_dict);
    return module;
}

static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
    const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(unsigned char) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(unsigned char)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to unsigned char" :
                    "value too large to convert to unsigned char");
            }
            return (unsigned char)-1;
        }
        return (unsigned char)val;
    }
    return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
}

static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
    const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(unsigned short) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(unsigned short)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to unsigned short" :
                    "value too large to convert to unsigned short");
            }
            return (unsigned short)-1;
        }
        return (unsigned short)val;
    }
    return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
}

static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
    const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(unsigned int) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(unsigned int)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to unsigned int" :
                    "value too large to convert to unsigned int");
            }
            return (unsigned int)-1;
        }
        return (unsigned int)val;
    }
    return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
}

static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
    const char neg_one = (char)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(char) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(char)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to char" :
                    "value too large to convert to char");
            }
            return (char)-1;
        }
        return (char)val;
    }
    return (char)__Pyx_PyInt_AsLong(x);
}

static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
    const short neg_one = (short)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(short) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(short)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to short" :
                    "value too large to convert to short");
            }
            return (short)-1;
        }
        return (short)val;
    }
    return (short)__Pyx_PyInt_AsLong(x);
}

static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
    const int neg_one = (int)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(int) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(int)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to int" :
                    "value too large to convert to int");
            }
            return (int)-1;
        }
        return (int)val;
    }
    return (int)__Pyx_PyInt_AsLong(x);
}

static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
    const signed char neg_one = (signed char)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(signed char) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(signed char)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to signed char" :
                    "value too large to convert to signed char");
            }
            return (signed char)-1;
        }
        return (signed char)val;
    }
    return (signed char)__Pyx_PyInt_AsSignedLong(x);
}

static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
    const signed short neg_one = (signed short)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(signed short) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(signed short)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to signed short" :
                    "value too large to convert to signed short");
            }
            return (signed short)-1;
        }
        return (signed short)val;
    }
    return (signed short)__Pyx_PyInt_AsSignedLong(x);
}

static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
    const signed int neg_one = (signed int)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(signed int) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(signed int)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to signed int" :
                    "value too large to convert to signed int");
            }
            return (signed int)-1;
        }
        return (signed int)val;
    }
    return (signed int)__Pyx_PyInt_AsSignedLong(x);
}

static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
    const int neg_one = (int)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
    if (sizeof(int) < sizeof(long)) {
        long val = __Pyx_PyInt_AsLong(x);
        if (unlikely(val != (long)(int)val)) {
            if (!unlikely(val == -1 && PyErr_Occurred())) {
                PyErr_SetString(PyExc_OverflowError,
                    (is_unsigned && unlikely(val < 0)) ?
                    "can't convert negative value to int" :
                    "value too large to convert to int");
            }
            return (int)-1;
        }
        return (int)val;
    }
    return (int)__Pyx_PyInt_AsLong(x);
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
    const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to unsigned long");
            return (unsigned long)-1;
        }
        return (unsigned long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(unsigned long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (unsigned long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to unsigned long");
                return (unsigned long)-1;
            }
            return (unsigned long)PyLong_AsUnsignedLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(unsigned long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(unsigned long) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(unsigned long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (unsigned long)PyLong_AsLong(x);
        }
    } else {
        unsigned long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (unsigned long)-1;
        val = __Pyx_PyInt_AsUnsignedLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
    const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to unsigned PY_LONG_LONG");
            return (unsigned PY_LONG_LONG)-1;
        }
        return (unsigned PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to unsigned PY_LONG_LONG");
                return (unsigned PY_LONG_LONG)-1;
            }
            return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
        }
    } else {
        unsigned PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (unsigned PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
    const long neg_one = (long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to long");
            return (long)-1;
        }
        return (long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to long");
                return (long)-1;
            }
            return (long)PyLong_AsUnsignedLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(long) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (long)PyLong_AsLong(x);
        }
    } else {
        long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (long)-1;
        val = __Pyx_PyInt_AsLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
    const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to PY_LONG_LONG");
            return (PY_LONG_LONG)-1;
        }
        return (PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to PY_LONG_LONG");
                return (PY_LONG_LONG)-1;
            }
            return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (PY_LONG_LONG)PyLong_AsLongLong(x);
        }
    } else {
        PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
    const signed long neg_one = (signed long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to signed long");
            return (signed long)-1;
        }
        return (signed long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(signed long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (signed long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to signed long");
                return (signed long)-1;
            }
            return (signed long)PyLong_AsUnsignedLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(signed long)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(signed long) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(signed long) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (signed long)PyLong_AsLong(x);
        }
    } else {
        signed long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (signed long)-1;
        val = __Pyx_PyInt_AsSignedLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
#endif
#endif
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
    const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to signed PY_LONG_LONG");
            return (signed PY_LONG_LONG)-1;
        }
        return (signed PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return (signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to signed PY_LONG_LONG");
                return (signed PY_LONG_LONG)-1;
            }
            return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
        } else {
#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
#if CYTHON_USE_PYLONG_INTERNALS
            if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) {
                switch (Py_SIZE(x)) {
                    case  0: return 0;
                    case  1: return +(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                    case -1: return -(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0];
                }
            }
#endif
#endif
            return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
        }
    } else {
        signed PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (signed PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsSignedLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

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);
        #if PY_VERSION_HEX < 0x02050000
        return PyErr_Warn(NULL, message);
        #else
        return PyErr_WarnEx(NULL, message, 1);
        #endif
    }
    return 0;
}

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 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    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;
}

#ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
    PyObject *py_name = 0;
    PyObject *py_module = 0;
    py_name = __Pyx_PyIdentifier_FromString(name);
    if (!py_name)
        goto bad;
    py_module = PyImport_Import(py_name);
    Py_DECREF(py_name);
    return py_module;
bad:
    Py_XDECREF(py_name);
    return 0;
}
#endif

#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
    size_t size, int strict)
{
    PyObject *py_module = 0;
    PyObject *result = 0;
    PyObject *py_name = 0;
    char warning[200];
    Py_ssize_t basicsize;
#ifdef Py_LIMITED_API
    PyObject *py_basicsize;
#endif
    py_module = __Pyx_ImportModule(module_name);
    if (!py_module)
        goto bad;
    py_name = __Pyx_PyIdentifier_FromString(class_name);
    if (!py_name)
        goto bad;
    result = PyObject_GetAttr(py_module, py_name);
    Py_DECREF(py_name);
    py_name = 0;
    Py_DECREF(py_module);
    py_module = 0;
    if (!result)
        goto bad;
    if (!PyType_Check(result)) {
        PyErr_Format(PyExc_TypeError,
            "%s.%s is not a type object",
            module_name, class_name);
        goto bad;
    }
#ifndef Py_LIMITED_API
    basicsize = ((PyTypeObject *)result)->tp_basicsize;
#else
    py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
    if (!py_basicsize)
        goto bad;
    basicsize = PyLong_AsSsize_t(py_basicsize);
    Py_DECREF(py_basicsize);
    py_basicsize = 0;
    if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
        goto bad;
#endif
    if (!strict && (size_t)basicsize > size) {
        PyOS_snprintf(warning, sizeof(warning),
            "%s.%s size changed, may indicate binary incompatibility",
            module_name, class_name);
        #if PY_VERSION_HEX < 0x02050000
        if (PyErr_Warn(NULL, warning) < 0) goto bad;
        #else
        if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
        #endif
    }
    else if ((size_t)basicsize != size) {
        PyErr_Format(PyExc_ValueError,
            "%s.%s has the wrong size, try recompiling",
            module_name, class_name);
        goto bad;
    }
    return (PyTypeObject *)result;
bad:
    Py_XDECREF(py_module);
    Py_XDECREF(result);
    return NULL;
}
#endif

#ifndef __PYX_HAVE_RT_ImportVoidPtr
#define __PYX_HAVE_RT_ImportVoidPtr
static int __Pyx_ImportVoidPtr(PyObject *module, const char *name, void **p, const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
    if (!d)
        goto bad;
    cobj = PyDict_GetItemString(d, name);
    if (!cobj) {
        PyErr_Format(PyExc_ImportError,
            "%s does not export expected C variable %s",
                PyModule_GetName(module), name);
        goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0)
    if (!PyCapsule_IsValid(cobj, sig)) {
        PyErr_Format(PyExc_TypeError,
            "C variable %s.%s has wrong signature (expected %s, got %s)",
             PyModule_GetName(module), name, sig, PyCapsule_GetName(cobj));
        goto bad;
    }
    *p = PyCapsule_GetPointer(cobj, sig);
#else
    {const char *desc, *s1, *s2;
    desc = (const char *)PyCObject_GetDesc(cobj);
    if (!desc)
        goto bad;
    s1 = desc; s2 = sig;
    while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
    if (*s1 != *s2) {
        PyErr_Format(PyExc_TypeError,
            "C variable %s.%s has wrong signature (expected %s, got %s)",
             PyModule_GetName(module), name, sig, desc);
        goto bad;
    }
    *p = PyCObject_AsVoidPtr(cobj);}
#endif
    if (!(*p))
        goto bad;
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(d);
    return -1;
}
#endif

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) / 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, 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);
}

#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,            /*int argcount,*/
        0,            /*int kwonlyargcount,*/
        0,            /*int nlocals,*/
        0,            /*int stacksize,*/
        0,            /*int flags,*/
        __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,      /*int firstlineno,*/
        __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;
    PyObject *py_globals = 0;
    PyFrameObject *py_frame = 0;
    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_globals = PyModule_GetDict(__pyx_m);
    if (!py_globals) goto bad;
    py_frame = PyFrame_New(
        PyThreadState_GET(), /*PyThreadState *tstate,*/
        py_code,             /*PyCodeObject *code,*/
        py_globals,          /*PyObject *globals,*/
        0                    /*PyObject *locals*/
    );
    if (!py_frame) goto bad;
    py_frame->f_lineno = py_line;
    PyTraceBack_Here(py_frame);
bad:
    Py_XDECREF(py_code);
    Py_XDECREF(py_frame);
}

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  /* Python 3+ has unicode identifiers */
        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;
        ++t;
    }
    return 0;
}

static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
    return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
}
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
    Py_ssize_t ignore;
    return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE 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)) {
#if PY_VERSION_HEX < 0x03030000
        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 /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
        *length = PyBytes_GET_SIZE(defenc);
        return defenc_c;
#else /* PY_VERSION_HEX < 0x03030000 */
        if (PyUnicode_READY(o) == -1) return NULL;
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
        if (PyUnicode_IS_ASCII(o)) {
            *length = PyUnicode_GET_DATA_SIZE(o);
            return PyUnicode_AsUTF8(o);
        } else {
            PyUnicode_AsASCIIString(o);
            return NULL;
        }
#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
        return PyUnicode_AsUTF8AndSize(o, length);
#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
#endif /* PY_VERSION_HEX < 0x03030000 */
    } else
#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII  || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (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 PyObject* __Pyx_PyNumber_Int(PyObject* x) {
  PyNumberMethods *m;
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
  if (PyInt_Check(x) || PyLong_Check(x))
#else
  if (PyLong_Check(x))
#endif
    return Py_INCREF(x), x;
  m = Py_TYPE(x)->tp_as_number;
#if PY_MAJOR_VERSION < 3
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = PyNumber_Long(x);
  }
#else
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Long(x);
  }
#endif
  if (res) {
#if PY_MAJOR_VERSION < 3
    if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
    if (!PyLong_Check(res)) {
#endif
      PyErr_Format(PyExc_TypeError,
                   "__%s__ returned non-%s (type %.200s)",
                   name, name, Py_TYPE(res)->tp_name);
      Py_DECREF(res);
      return NULL;
    }
  }
  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 = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
   if (ival <= LONG_MAX)
       return PyInt_FromLong((long)ival);
   else {
       unsigned char *bytes = (unsigned char *) &ival;
       int one = 1; int little = (int)*(unsigned char*)&one;
       return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
   }
#else
   return PyInt_FromSize_t(ival);
#endif
}
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
   unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
   if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
       if ((val != (unsigned PY_LONG_LONG)-1) || !PyErr_Occurred())
           PyErr_SetString(PyExc_OverflowError,
                           "value too large to convert to size_t");
       return (size_t)-1;
   }
   return (size_t)val;
}


#endif /* Py_PYTHON_H */
