/* 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_Divide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(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__cwindow
#define __PYX_HAVE_API__cwindow
#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[] = {
  "cwindow.pyx",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "htslibWrapper.pxd",
  "fastafile.pxd",
};

/*--- Type declarations ---*/
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_t_13htslibWrapper_cAlignedRead;
typedef struct __pyx_t_13htslibWrapper_cAlignedRead __pyx_t_13htslibWrapper_cAlignedRead;
struct __pyx_opt_args_13htslibWrapper_7Samfile__open;

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

/* "htslibWrapper.pxd":211
 *     cdef _hasIndex(self)
 *     cdef void openBAMFile(self, mode)
 *     cpdef _open(self, mode, loadIndex=*)             # <<<<<<<<<<<<<<
 *     cdef char* getrname(self, int tid)
 *     cpdef ReadIterator fetch(self, const char *region)
 */
struct __pyx_opt_args_13htslibWrapper_7Samfile__open {
  int __pyx_n;
  PyObject *loadIndex;
};
struct __pyx_opt_args_7cwindow_bisectReadsLeft;
struct __pyx_opt_args_7cwindow_bisectReadsRight;

/* "cwindow.pyx":276
 * ###################################################################################################
 * 
 * cdef int bisectReadsLeft(cAlignedRead** reads, int testPos, int nReads, int testMatePos=0):             # <<<<<<<<<<<<<<
 *     """
 *     Specialisation of bisection algorithm for array of
 */
struct __pyx_opt_args_7cwindow_bisectReadsLeft {
  int __pyx_n;
  int testMatePos;
};

/* "cwindow.pyx":304
 * ###################################################################################################
 * 
 * cdef int bisectReadsRight(cAlignedRead** reads, int testPos, int nReads, int testMatePos=0):             # <<<<<<<<<<<<<<
 *     """
 *     Specialisation of bisection algorithm for array of
 */
struct __pyx_opt_args_7cwindow_bisectReadsRight {
  int __pyx_n;
  int testMatePos;
};

/* "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;
};



/* "cwindow.pyx":109
 * ###################################################################################################
 * 
 * cdef class ReadArray:             # <<<<<<<<<<<<<<
 *     """
 *     Simple structure to wrap a raw C array, with some bounds
 */

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.pyx":485
 * ###################################################################################################
 * 
 * cdef class bamReadBuffer(object):             # <<<<<<<<<<<<<<
 *     """
 *     Utility class for bufffering reads from a single BAM file, so we only make a single pass
 */

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;


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

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


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

struct __pyx_vtabstruct_13htslibWrapper_ReadIterator {
  __pyx_t_13htslibWrapper_cAlignedRead *(*get)(struct __pyx_obj_13htslibWrapper_ReadIterator *, int, char **);
  int (*cnext)(struct __pyx_obj_13htslibWrapper_ReadIterator *);
  char (*_getBase)(struct __pyx_obj_13htslibWrapper_ReadIterator *, uint8_t *, int);
};
static struct __pyx_vtabstruct_13htslibWrapper_ReadIterator *__pyx_vtabptr_13htslibWrapper_ReadIterator;
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/* Module declarations from 'cpython.version' */

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

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static CYTHON_INLINE int __pyx_f_7cwindow_readPosComp(void const *, void const *); /*proto*/
static int __pyx_f_7cwindow_readMatePosComp(void const *, void const *); /*proto*/
static int __pyx_f_7cwindow_bisectReadsLeft(__pyx_t_13htslibWrapper_cAlignedRead **, int, int, struct __pyx_opt_args_7cwindow_bisectReadsLeft *__pyx_optional_args); /*proto*/
static int __pyx_f_7cwindow_checkAndTrimRead(__pyx_t_13htslibWrapper_cAlignedRead *, __pyx_t_13htslibWrapper_cAlignedRead *, int, int *, int, int, int, int, int, int, int); /*proto*/
#define __Pyx_MODULE_NAME "cwindow"
int __pyx_module_is_main_cwindow = 0;

/* Implementation of 'cwindow' */
static PyObject *__pyx_builtin_StandardError;
static PyObject *__pyx_builtin_range;
static int __pyx_pf_7cwindow_9ReadArray___init__(struct __pyx_obj_7cwindow_ReadArray *__pyx_v_self, int __pyx_v_size); /* proto */
static void __pyx_pf_7cwindow_9ReadArray_2__dealloc__(struct __pyx_obj_7cwindow_ReadArray *__pyx_v_self); /* proto */
static int __pyx_pf_7cwindow_13bamReadBuffer___init__(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self, char *__pyx_v_chrom, int __pyx_v_start, int __pyx_v_end, PyObject *__pyx_v_options); /* proto */
static void __pyx_pf_7cwindow_13bamReadBuffer_2__dealloc__(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self); /* proto */
static PyObject *__pyx_tp_new_7cwindow_ReadArray(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_7cwindow_bamReadBuffer(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_1[] = "Could not allocate memory for ReadArray";
static char __pyx_k_2[] = "Could not re-allocate ReadArray";
static char __pyx_k_3[] = "Start pos = %s. End pos = %s. Read start pos = %s. end pos = %s";
static char __pyx_k_4[] = "There are %s reads here.";
static char __pyx_k_5[] = "This should never happen. Read start pointer > read end pointer!!";
static char __pyx_k_6[] = "filterReadsWithUnmappedMates";
static char __pyx_k_7[] = "filterReadsWithDistantMates";
static char __pyx_k_8[] = "filterReadPairsWithSmallInserts";
static char __pyx_k_9[] = "Sample %s has %s good reads";
static char __pyx_k_10[] = "Sample %s has %s bad reads";
static char __pyx_k_11[] = "Sample %s has %s broken mates";
static char __pyx_k_12[] = "N low map quality reads = %s";
static char __pyx_k_13[] = "N low qual reads = %s";
static char __pyx_k_14[] = "N un-mapped reads = %s";
static char __pyx_k_15[] = "N reads with unmapped mates = %s";
static char __pyx_k_16[] = "N reads with distant mates = %s";
static char __pyx_k_17[] = "N reads pairs with small inserts = %s";
static char __pyx_k_18[] = "N duplicate reads = %s";
static char __pyx_k_19[] = "Overlapping segments of read pairs were clipped";
static char __pyx_k_21[] = "Overlapping segments of read pairs were not clipped";
static char __pyx_k_23[] = "Overhanging bits of reads (poss. adapter sequences) were clipped";
static char __pyx_k_25[] = "Overhanging bits of reads (poss. adapter sequences) were not clipped";
static char __pyx_k_27[] = "Found null read";
static char __pyx_k_29[] = "\nFast cython implementation of some windowing functions.\n";
static char __pyx_k__Log[] = "Log";
static char __pyx_k__end[] = "end";
static char __pyx_k__info[] = "info";
static char __pyx_k__math[] = "math";
static char __pyx_k__rlen[] = "rlen";
static char __pyx_k__size[] = "size";
static char __pyx_k__chrom[] = "chrom";
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__start[] = "start";
static char __pyx_k__bisect[] = "bisect";
static char __pyx_k__logger[] = "logger";
static char __pyx_k__heappop[] = "heappop";
static char __pyx_k__logging[] = "logging";
static char __pyx_k__options[] = "options";
static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__heappush[] = "heappush";
static char __pyx_k__maxReads[] = "maxReads";
static char __pyx_k__minFlank[] = "minFlank";
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__bisect_left[] = "bisect_left";
static char __pyx_k__minBaseQual[] = "minBaseQual";
static char __pyx_k__trimAdapter[] = "trimAdapter";
static char __pyx_k__StandardError[] = "StandardError";
static char __pyx_k__trimReadFlank[] = "trimReadFlank";
static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__";
static char __pyx_k__trimOverlapping[] = "trimOverlapping";
static char __pyx_k__trimSoftClipped[] = "trimSoftClipped";
static char __pyx_k__filterDuplicates[] = "filterDuplicates";
static char __pyx_k__minGoodQualBases[] = "minGoodQualBases";
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_13;
static PyObject *__pyx_kp_s_14;
static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_kp_s_17;
static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_23;
static PyObject *__pyx_kp_s_25;
static PyObject *__pyx_kp_s_27;
static PyObject *__pyx_kp_s_3;
static PyObject *__pyx_kp_s_4;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_n_s_6;
static PyObject *__pyx_n_s_7;
static PyObject *__pyx_n_s_8;
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__bisect;
static PyObject *__pyx_n_s__bisect_left;
static PyObject *__pyx_n_s__chrom;
static PyObject *__pyx_n_s__debug;
static PyObject *__pyx_n_s__end;
static PyObject *__pyx_n_s__error;
static PyObject *__pyx_n_s__filterDuplicates;
static PyObject *__pyx_n_s__getLogger;
static PyObject *__pyx_n_s__heappop;
static PyObject *__pyx_n_s__heappush;
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__math;
static PyObject *__pyx_n_s__maxReads;
static PyObject *__pyx_n_s__minBaseQual;
static PyObject *__pyx_n_s__minFlank;
static PyObject *__pyx_n_s__minGoodQualBases;
static PyObject *__pyx_n_s__minMapQual;
static PyObject *__pyx_n_s__options;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__size;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__trimAdapter;
static PyObject *__pyx_n_s__trimOverlapping;
static PyObject *__pyx_n_s__trimReadFlank;
static PyObject *__pyx_n_s__trimSoftClipped;
static PyObject *__pyx_n_s__verbosity;
static PyObject *__pyx_int_0;
static PyObject *__pyx_k_tuple_20;
static PyObject *__pyx_k_tuple_22;
static PyObject *__pyx_k_tuple_24;
static PyObject *__pyx_k_tuple_26;
static PyObject *__pyx_k_tuple_28;
static PyObject *__pyx_k_tuple_30;

/* "cwindow.pyx":79
 * 
 * @cython.profile(False)
 * cdef inline int readPosComp(const void* x, const void* y) nogil:             # <<<<<<<<<<<<<<
 *     """
 *     Comparison function for use in qsort, to sort reads by their start positions and
 */

static CYTHON_INLINE int __pyx_f_7cwindow_readPosComp(void const *__pyx_v_x, void const *__pyx_v_y) {
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_readOne;
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_readTwo;
  int __pyx_r;

  /* "cwindow.pyx":84
 *     then end positions.
 *     """
 *     cdef cAlignedRead** readOne = <cAlignedRead**>(x)             # <<<<<<<<<<<<<<
 *     cdef cAlignedRead** readTwo = <cAlignedRead**>(y)
 * 
 */
  __pyx_v_readOne = ((__pyx_t_13htslibWrapper_cAlignedRead **)__pyx_v_x);

  /* "cwindow.pyx":85
 *     """
 *     cdef cAlignedRead** readOne = <cAlignedRead**>(x)
 *     cdef cAlignedRead** readTwo = <cAlignedRead**>(y)             # <<<<<<<<<<<<<<
 * 
 *     #if readOne[0].pos != readTwo[0].pos
 */
  __pyx_v_readTwo = ((__pyx_t_13htslibWrapper_cAlignedRead **)__pyx_v_y);

  /* "cwindow.pyx":88
 * 
 *     #if readOne[0].pos != readTwo[0].pos
 *     return readOne[0].pos - readTwo[0].pos             # <<<<<<<<<<<<<<
 *     #else:
 *     #    return readOne[0].end - readTwo[0].end
 */
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  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
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/* "cwindow.pyx":95
 * 
 * @cython.profile(False)
 * cdef int readMatePosComp(const void* x, const void* y):             # <<<<<<<<<<<<<<
 *     """
 *     Comparison function for use in qsort, to sort reads by their mate positions, as long as
 */

static int __pyx_f_7cwindow_readMatePosComp(void const *__pyx_v_x, void const *__pyx_v_y) {
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_readOne;
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_readTwo;
  int __pyx_r;
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  /* "cwindow.pyx":100
 *     the mates are on the same chromosome.
 *     """
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 *     cdef cAlignedRead** readTwo = <cAlignedRead**>(y)
 * 
 */
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  /* "cwindow.pyx":101
 *     """
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 *     cdef cAlignedRead** readTwo = <cAlignedRead**>(y)             # <<<<<<<<<<<<<<
 * 
 *     # Sorting is broken for reads with mates on different chromosomes
 */
  __pyx_v_readTwo = ((__pyx_t_13htslibWrapper_cAlignedRead **)__pyx_v_y);

  /* "cwindow.pyx":104
 * 
 *     # Sorting is broken for reads with mates on different chromosomes
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 * 
 */
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  /* "cwindow.pyx":105
 *     # Sorting is broken for reads with mates on different chromosomes
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 * ###################################################################################################
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/* "cwindow.pyx":114
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  /* "cwindow.pyx":120
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 *     Performs various quality checks on the read, and trims read (i.e. set q-scores to zero). Returns
 */

static int __pyx_f_7cwindow_checkAndTrimRead(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead, __pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theLastRead, int __pyx_v_minGoodQualBases, int *__pyx_v_filteredReadCountsByType, int __pyx_v_minMapQual, int __pyx_v_minBaseQual, CYTHON_UNUSED int __pyx_v_minFlank, int __pyx_v_trimOverlapping, int __pyx_v_trimAdapter, int __pyx_v_trimReadFlank, int __pyx_v_trimSoftClipped) {
  int __pyx_v_nQualsBelowMin;
  int __pyx_v_index;
  int __pyx_v_absIns;
  int __pyx_v_cigarIndex;
  CYTHON_UNUSED int __pyx_v_j;
  int __pyx_v_cigarOp;
  CYTHON_UNUSED int __pyx_v_cigarLen;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  short __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  long __pyx_t_8;
  long __pyx_t_9;
  short __pyx_t_10;
  int __pyx_t_11;
  __Pyx_RefNannySetupContext("checkAndTrimRead", 0);

  /* "cwindow.pyx":337
 *     true if read is ok, and false otherwise.
 *     """
 *     if Read_IsSecondaryAlignment(theRead):             # <<<<<<<<<<<<<<
 *         Read_SetQCFail(theRead)
 *         return False
 */
  __pyx_t_1 = (__pyx_f_13htslibWrapper_Read_IsSecondaryAlignment(__pyx_v_theRead) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":338
 *     """
 *     if Read_IsSecondaryAlignment(theRead):
 *         Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *         return False
 * 
 */
    __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

    /* "cwindow.pyx":339
 *     if Read_IsSecondaryAlignment(theRead):
 *         Read_SetQCFail(theRead)
 *         return False             # <<<<<<<<<<<<<<
 * 
 *     if theRead.mapq < minMapQual:
 */
    __pyx_r = 0;
    goto __pyx_L0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "cwindow.pyx":341
 *         return False
 * 
 *     if theRead.mapq < minMapQual:             # <<<<<<<<<<<<<<
 *         filteredReadCountsByType[LOW_MAP_QUAL] += 1
 *         Read_SetQCFail(theRead)
 */
  __pyx_t_1 = ((__pyx_v_theRead->mapq < __pyx_v_minMapQual) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":342
 * 
 *     if theRead.mapq < minMapQual:
 *         filteredReadCountsByType[LOW_MAP_QUAL] += 1             # <<<<<<<<<<<<<<
 *         Read_SetQCFail(theRead)
 *         return False
 */
    __pyx_t_2 = __pyx_v_7cwindow_LOW_MAP_QUAL;
    (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

    /* "cwindow.pyx":343
 *     if theRead.mapq < minMapQual:
 *         filteredReadCountsByType[LOW_MAP_QUAL] += 1
 *         Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *         return False
 * 
 */
    __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

    /* "cwindow.pyx":344
 *         filteredReadCountsByType[LOW_MAP_QUAL] += 1
 *         Read_SetQCFail(theRead)
 *         return False             # <<<<<<<<<<<<<<
 * 
 *     # Filter out low quality reads, i.e. those with < minGoodQualBases with Q scores >= 20
 */
    __pyx_r = 0;
    goto __pyx_L0;
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "cwindow.pyx":347
 * 
 *     # Filter out low quality reads, i.e. those with < minGoodQualBases with Q scores >= 20
 *     cdef int nQualsBelowMin = 0             # <<<<<<<<<<<<<<
 *     cdef int index = 0
 * 
 */
  __pyx_v_nQualsBelowMin = 0;

  /* "cwindow.pyx":348
 *     # Filter out low quality reads, i.e. those with < minGoodQualBases with Q scores >= 20
 *     cdef int nQualsBelowMin = 0
 *     cdef int index = 0             # <<<<<<<<<<<<<<
 * 
 *     for index from 0 <= index < theRead.rlen:
 */
  __pyx_v_index = 0;

  /* "cwindow.pyx":350
 *     cdef int index = 0
 * 
 *     for index from 0 <= index < theRead.rlen:             # <<<<<<<<<<<<<<
 *         if theRead.qual[index] < minBaseQual:
 *             nQualsBelowMin += 1
 */
  __pyx_t_3 = __pyx_v_theRead->rlen;
  for (__pyx_v_index = 0; __pyx_v_index < __pyx_t_3; __pyx_v_index++) {

    /* "cwindow.pyx":351
 * 
 *     for index from 0 <= index < theRead.rlen:
 *         if theRead.qual[index] < minBaseQual:             # <<<<<<<<<<<<<<
 *             nQualsBelowMin += 1
 * 
 */
    __pyx_t_1 = (((__pyx_v_theRead->qual[__pyx_v_index]) < __pyx_v_minBaseQual) != 0);
    if (__pyx_t_1) {

      /* "cwindow.pyx":352
 *     for index from 0 <= index < theRead.rlen:
 *         if theRead.qual[index] < minBaseQual:
 *             nQualsBelowMin += 1             # <<<<<<<<<<<<<<
 * 
 *     if theRead.rlen - nQualsBelowMin < minGoodQualBases:
 */
      __pyx_v_nQualsBelowMin = (__pyx_v_nQualsBelowMin + 1);
      goto __pyx_L7;
    }
    __pyx_L7:;
  }

  /* "cwindow.pyx":354
 *             nQualsBelowMin += 1
 * 
 *     if theRead.rlen - nQualsBelowMin < minGoodQualBases:             # <<<<<<<<<<<<<<
 *         filteredReadCountsByType[LOW_QUAL_BASES] += 1
 *         Read_SetQCFail(theRead)
 */
  __pyx_t_1 = (((__pyx_v_theRead->rlen - __pyx_v_nQualsBelowMin) < __pyx_v_minGoodQualBases) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":355
 * 
 *     if theRead.rlen - nQualsBelowMin < minGoodQualBases:
 *         filteredReadCountsByType[LOW_QUAL_BASES] += 1             # <<<<<<<<<<<<<<
 *         Read_SetQCFail(theRead)
 *         return False
 */
    __pyx_t_2 = __pyx_v_7cwindow_LOW_QUAL_BASES;
    (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

    /* "cwindow.pyx":356
 *     if theRead.rlen - nQualsBelowMin < minGoodQualBases:
 *         filteredReadCountsByType[LOW_QUAL_BASES] += 1
 *         Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *         return False
 * 
 */
    __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

    /* "cwindow.pyx":357
 *         filteredReadCountsByType[LOW_QUAL_BASES] += 1
 *         Read_SetQCFail(theRead)
 *         return False             # <<<<<<<<<<<<<<
 * 
 *     # Remove unmapped reads
 */
    __pyx_r = 0;
    goto __pyx_L0;
    goto __pyx_L8;
  }
  __pyx_L8:;

  /* "cwindow.pyx":360
 * 
 *     # Remove unmapped reads
 *     if Read_IsUnmapped(theRead):             # <<<<<<<<<<<<<<
 *         filteredReadCountsByType[UNMAPPED_READ] += 1
 *         Read_SetQCFail(theRead)
 */
  __pyx_t_1 = (__pyx_f_13htslibWrapper_Read_IsUnmapped(__pyx_v_theRead) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":361
 *     # Remove unmapped reads
 *     if Read_IsUnmapped(theRead):
 *         filteredReadCountsByType[UNMAPPED_READ] += 1             # <<<<<<<<<<<<<<
 *         Read_SetQCFail(theRead)
 *         return False
 */
    __pyx_t_2 = __pyx_v_7cwindow_UNMAPPED_READ;
    (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

    /* "cwindow.pyx":362
 *     if Read_IsUnmapped(theRead):
 *         filteredReadCountsByType[UNMAPPED_READ] += 1
 *         Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *         return False
 * 
 */
    __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

    /* "cwindow.pyx":363
 *         filteredReadCountsByType[UNMAPPED_READ] += 1
 *         Read_SetQCFail(theRead)
 *         return False             # <<<<<<<<<<<<<<
 * 
 *     # Remove broken pairs, i.e. pairs where the mate is mapped to a different chromosome or the
 */
    __pyx_r = 0;
    goto __pyx_L0;
    goto __pyx_L9;
  }
  __pyx_L9:;

  /* "cwindow.pyx":367
 *     # Remove broken pairs, i.e. pairs where the mate is mapped to a different chromosome or the
 *     # mate is unmapped
 *     if filteredReadCountsByType[MATE_UNMAPPED] != -1:             # <<<<<<<<<<<<<<
 * 
 *         if Read_IsPaired(theRead) and Read_MateIsUnmapped(theRead):
 */
  __pyx_t_1 = (((__pyx_v_filteredReadCountsByType[__pyx_v_7cwindow_MATE_UNMAPPED]) != -1) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":369
 *     if filteredReadCountsByType[MATE_UNMAPPED] != -1:
 * 
 *         if Read_IsPaired(theRead) and Read_MateIsUnmapped(theRead):             # <<<<<<<<<<<<<<
 *             filteredReadCountsByType[MATE_UNMAPPED] += 1
 *             return False
 */
    __pyx_t_1 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
    if (__pyx_t_1) {
      __pyx_t_4 = (__pyx_f_13htslibWrapper_Read_MateIsUnmapped(__pyx_v_theRead) != 0);
      __pyx_t_5 = __pyx_t_4;
    } else {
      __pyx_t_5 = __pyx_t_1;
    }
    if (__pyx_t_5) {

      /* "cwindow.pyx":370
 * 
 *         if Read_IsPaired(theRead) and Read_MateIsUnmapped(theRead):
 *             filteredReadCountsByType[MATE_UNMAPPED] += 1             # <<<<<<<<<<<<<<
 *             return False
 * 
 */
      __pyx_t_2 = __pyx_v_7cwindow_MATE_UNMAPPED;
      (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

      /* "cwindow.pyx":371
 *         if Read_IsPaired(theRead) and Read_MateIsUnmapped(theRead):
 *             filteredReadCountsByType[MATE_UNMAPPED] += 1
 *             return False             # <<<<<<<<<<<<<<
 * 
 *     if filteredReadCountsByType[MATE_DISTANT] != -1:
 */
      __pyx_r = 0;
      goto __pyx_L0;
      goto __pyx_L11;
    }
    __pyx_L11:;
    goto __pyx_L10;
  }
  __pyx_L10:;

  /* "cwindow.pyx":373
 *             return False
 * 
 *     if filteredReadCountsByType[MATE_DISTANT] != -1:             # <<<<<<<<<<<<<<
 * 
 *         if Read_IsPaired(theRead) and (theRead.chromID != theRead.mateChromID or (not Read_IsProperPair(theRead))):
 */
  __pyx_t_5 = (((__pyx_v_filteredReadCountsByType[__pyx_v_7cwindow_MATE_DISTANT]) != -1) != 0);
  if (__pyx_t_5) {

    /* "cwindow.pyx":375
 *     if filteredReadCountsByType[MATE_DISTANT] != -1:
 * 
 *         if Read_IsPaired(theRead) and (theRead.chromID != theRead.mateChromID or (not Read_IsProperPair(theRead))):             # <<<<<<<<<<<<<<
 *             filteredReadCountsByType[MATE_DISTANT] += 1
 *             return False
 */
    if ((__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0)) {
      __pyx_t_5 = (__pyx_v_theRead->chromID != __pyx_v_theRead->mateChromID);
      if (!__pyx_t_5) {
        __pyx_t_1 = (!(__pyx_f_13htslibWrapper_Read_IsProperPair(__pyx_v_theRead) != 0));
        __pyx_t_4 = __pyx_t_1;
      } else {
        __pyx_t_4 = __pyx_t_5;
      }
      __pyx_t_5 = __pyx_t_4;
    } else {
      __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
    }
    if (__pyx_t_5) {

      /* "cwindow.pyx":376
 * 
 *         if Read_IsPaired(theRead) and (theRead.chromID != theRead.mateChromID or (not Read_IsProperPair(theRead))):
 *             filteredReadCountsByType[MATE_DISTANT] += 1             # <<<<<<<<<<<<<<
 *             return False
 * 
 */
      __pyx_t_2 = __pyx_v_7cwindow_MATE_DISTANT;
      (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

      /* "cwindow.pyx":377
 *         if Read_IsPaired(theRead) and (theRead.chromID != theRead.mateChromID or (not Read_IsProperPair(theRead))):
 *             filteredReadCountsByType[MATE_DISTANT] += 1
 *             return False             # <<<<<<<<<<<<<<
 * 
 *     # If the insert size is < read length, then we almost certainly have adapter contamination, in which case we should
 */
      __pyx_r = 0;
      goto __pyx_L0;
      goto __pyx_L13;
    }
    __pyx_L13:;
    goto __pyx_L12;
  }
  __pyx_L12:;

  /* "cwindow.pyx":381
 *     # If the insert size is < read length, then we almost certainly have adapter contamination, in which case we should
 *     # skip these reads, as they may be mapped to the wrong location in the genome.
 *     if filteredReadCountsByType[SMALL_INSERT] != -1:             # <<<<<<<<<<<<<<
 * 
 *         if Read_IsPaired(theRead) and (theRead.insertSize != 0 and abs(theRead.insertSize) < theRead.rlen):
 */
  __pyx_t_5 = (((__pyx_v_filteredReadCountsByType[__pyx_v_7cwindow_SMALL_INSERT]) != -1) != 0);
  if (__pyx_t_5) {

    /* "cwindow.pyx":383
 *     if filteredReadCountsByType[SMALL_INSERT] != -1:
 * 
 *         if Read_IsPaired(theRead) and (theRead.insertSize != 0 and abs(theRead.insertSize) < theRead.rlen):             # <<<<<<<<<<<<<<
 *             filteredReadCountsByType[SMALL_INSERT] += 1
 *             Read_SetQCFail(theRead)
 */
    if ((__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0)) {
      __pyx_t_5 = (__pyx_v_theRead->insertSize != 0);
      if (__pyx_t_5) {
        __pyx_t_4 = (abs(__pyx_v_theRead->insertSize) < __pyx_v_theRead->rlen);
        __pyx_t_1 = __pyx_t_4;
      } else {
        __pyx_t_1 = __pyx_t_5;
      }
      __pyx_t_5 = __pyx_t_1;
    } else {
      __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
    }
    if (__pyx_t_5) {

      /* "cwindow.pyx":384
 * 
 *         if Read_IsPaired(theRead) and (theRead.insertSize != 0 and abs(theRead.insertSize) < theRead.rlen):
 *             filteredReadCountsByType[SMALL_INSERT] += 1             # <<<<<<<<<<<<<<
 *             Read_SetQCFail(theRead)
 *             return False
 */
      __pyx_t_2 = __pyx_v_7cwindow_SMALL_INSERT;
      (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

      /* "cwindow.pyx":385
 *         if Read_IsPaired(theRead) and (theRead.insertSize != 0 and abs(theRead.insertSize) < theRead.rlen):
 *             filteredReadCountsByType[SMALL_INSERT] += 1
 *             Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *             return False
 * 
 */
      __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

      /* "cwindow.pyx":386
 *             filteredReadCountsByType[SMALL_INSERT] += 1
 *             Read_SetQCFail(theRead)
 *             return False             # <<<<<<<<<<<<<<
 * 
 *     # Check if this read is actually a duplicate. TODO: store library tag and check.
 */
      __pyx_r = 0;
      goto __pyx_L0;
      goto __pyx_L15;
    }
    __pyx_L15:;
    goto __pyx_L14;
  }
  __pyx_L14:;

  /* "cwindow.pyx":389
 * 
 *     # Check if this read is actually a duplicate. TODO: store library tag and check.
 *     if filteredReadCountsByType[DUPLICATE] != -1:             # <<<<<<<<<<<<<<
 * 
 *         if Read_IsDuplicate(theRead):
 */
  __pyx_t_5 = (((__pyx_v_filteredReadCountsByType[__pyx_v_7cwindow_DUPLICATE]) != -1) != 0);
  if (__pyx_t_5) {

    /* "cwindow.pyx":391
 *     if filteredReadCountsByType[DUPLICATE] != -1:
 * 
 *         if Read_IsDuplicate(theRead):             # <<<<<<<<<<<<<<
 *             filteredReadCountsByType[DUPLICATE] += 1
 *             Read_SetQCFail(theRead)
 */
    __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsDuplicate(__pyx_v_theRead) != 0);
    if (__pyx_t_5) {

      /* "cwindow.pyx":392
 * 
 *         if Read_IsDuplicate(theRead):
 *             filteredReadCountsByType[DUPLICATE] += 1             # <<<<<<<<<<<<<<
 *             Read_SetQCFail(theRead)
 *             return False
 */
      __pyx_t_2 = __pyx_v_7cwindow_DUPLICATE;
      (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

      /* "cwindow.pyx":393
 *         if Read_IsDuplicate(theRead):
 *             filteredReadCountsByType[DUPLICATE] += 1
 *             Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *             return False
 *         elif theLastRead != NULL:
 */
      __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

      /* "cwindow.pyx":394
 *             filteredReadCountsByType[DUPLICATE] += 1
 *             Read_SetQCFail(theRead)
 *             return False             # <<<<<<<<<<<<<<
 *         elif theLastRead != NULL:
 *             if theRead.pos == theLastRead.pos and theRead.rlen == theLastRead.rlen:
 */
      __pyx_r = 0;
      goto __pyx_L0;
      goto __pyx_L17;
    }

    /* "cwindow.pyx":395
 *             Read_SetQCFail(theRead)
 *             return False
 *         elif theLastRead != NULL:             # <<<<<<<<<<<<<<
 *             if theRead.pos == theLastRead.pos and theRead.rlen == theLastRead.rlen:
 * 
 */
    __pyx_t_5 = ((__pyx_v_theLastRead != NULL) != 0);
    if (__pyx_t_5) {

      /* "cwindow.pyx":396
 *             return False
 *         elif theLastRead != NULL:
 *             if theRead.pos == theLastRead.pos and theRead.rlen == theLastRead.rlen:             # <<<<<<<<<<<<<<
 * 
 *                 # For paired reads, check mate's position
 */
      __pyx_t_5 = ((__pyx_v_theRead->pos == __pyx_v_theLastRead->pos) != 0);
      if (__pyx_t_5) {
        __pyx_t_1 = ((__pyx_v_theRead->rlen == __pyx_v_theLastRead->rlen) != 0);
        __pyx_t_4 = __pyx_t_1;
      } else {
        __pyx_t_4 = __pyx_t_5;
      }
      if (__pyx_t_4) {

        /* "cwindow.pyx":399
 * 
 *                 # For paired reads, check mate's position
 *                 if Read_IsPaired(theRead):             # <<<<<<<<<<<<<<
 * 
 *                     if theLastRead.matePos == theRead.matePos:
 */
        __pyx_t_4 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
        if (__pyx_t_4) {

          /* "cwindow.pyx":401
 *                 if Read_IsPaired(theRead):
 * 
 *                     if theLastRead.matePos == theRead.matePos:             # <<<<<<<<<<<<<<
 *                         filteredReadCountsByType[DUPLICATE] += 1
 *                         Read_SetQCFail(theRead)
 */
          __pyx_t_4 = ((__pyx_v_theLastRead->matePos == __pyx_v_theRead->matePos) != 0);
          if (__pyx_t_4) {

            /* "cwindow.pyx":402
 * 
 *                     if theLastRead.matePos == theRead.matePos:
 *                         filteredReadCountsByType[DUPLICATE] += 1             # <<<<<<<<<<<<<<
 *                         Read_SetQCFail(theRead)
 *                         return False
 */
            __pyx_t_2 = __pyx_v_7cwindow_DUPLICATE;
            (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

            /* "cwindow.pyx":403
 *                     if theLastRead.matePos == theRead.matePos:
 *                         filteredReadCountsByType[DUPLICATE] += 1
 *                         Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *                         return False
 * 
 */
            __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

            /* "cwindow.pyx":404
 *                         filteredReadCountsByType[DUPLICATE] += 1
 *                         Read_SetQCFail(theRead)
 *                         return False             # <<<<<<<<<<<<<<
 * 
 *                 # For single reads, just check pos and length of reads
 */
            __pyx_r = 0;
            goto __pyx_L0;
            goto __pyx_L20;
          }
          __pyx_L20:;
          goto __pyx_L19;
        }
        /*else*/ {

          /* "cwindow.pyx":408
 *                 # For single reads, just check pos and length of reads
 *                 else:
 *                     filteredReadCountsByType[DUPLICATE] += 1             # <<<<<<<<<<<<<<
 *                     Read_SetQCFail(theRead)
 *                     return False
 */
          __pyx_t_2 = __pyx_v_7cwindow_DUPLICATE;
          (__pyx_v_filteredReadCountsByType[__pyx_t_2]) = ((__pyx_v_filteredReadCountsByType[__pyx_t_2]) + 1);

          /* "cwindow.pyx":409
 *                 else:
 *                     filteredReadCountsByType[DUPLICATE] += 1
 *                     Read_SetQCFail(theRead)             # <<<<<<<<<<<<<<
 *                     return False
 * 
 */
          __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_v_theRead);

          /* "cwindow.pyx":410
 *                     filteredReadCountsByType[DUPLICATE] += 1
 *                     Read_SetQCFail(theRead)
 *                     return False             # <<<<<<<<<<<<<<
 * 
 *     ## Any read that gets passed here will be used, but low quality tails will be trimmed, and
 */
          __pyx_r = 0;
          goto __pyx_L0;
        }
        __pyx_L19:;
        goto __pyx_L18;
      }
      __pyx_L18:;
      goto __pyx_L17;
    }
    __pyx_L17:;
    goto __pyx_L16;
  }
  __pyx_L16:;

  /* "cwindow.pyx":416
 * 
 *     # Trim low-quality tails for forward reads
 *     if not Read_IsReverse(theRead):             # <<<<<<<<<<<<<<
 * 
 *         for index from 1 <= index <= theRead.rlen:
 */
  __pyx_t_4 = ((!(__pyx_f_13htslibWrapper_Read_IsReverse(__pyx_v_theRead) != 0)) != 0);
  if (__pyx_t_4) {

    /* "cwindow.pyx":418
 *     if not Read_IsReverse(theRead):
 * 
 *         for index from 1 <= index <= theRead.rlen:             # <<<<<<<<<<<<<<
 *             if index < trimReadFlank or theRead.qual[theRead.rlen - index] < 5:
 *                 theRead.qual[theRead.rlen - index] = 0
 */
    __pyx_t_3 = __pyx_v_theRead->rlen;
    for (__pyx_v_index = 1; __pyx_v_index <= __pyx_t_3; __pyx_v_index++) {

      /* "cwindow.pyx":419
 * 
 *         for index from 1 <= index <= theRead.rlen:
 *             if index < trimReadFlank or theRead.qual[theRead.rlen - index] < 5:             # <<<<<<<<<<<<<<
 *                 theRead.qual[theRead.rlen - index] = 0
 *             else:
 */
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      if (!__pyx_t_4) {
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      } else {
        __pyx_t_1 = __pyx_t_4;
      }
      if (__pyx_t_1) {

        /* "cwindow.pyx":420
 *         for index from 1 <= index <= theRead.rlen:
 *             if index < trimReadFlank or theRead.qual[theRead.rlen - index] < 5:
 *                 theRead.qual[theRead.rlen - index] = 0             # <<<<<<<<<<<<<<
 *             else:
 *                 break
 */
        (__pyx_v_theRead->qual[(__pyx_v_theRead->rlen - __pyx_v_index)]) = 0;
        goto __pyx_L24;
      }
      /*else*/ {

        /* "cwindow.pyx":422
 *                 theRead.qual[theRead.rlen - index] = 0
 *             else:
 *                 break             # <<<<<<<<<<<<<<
 *     # Trim low-quality tails for reverse reads
 *     else:
 */
        goto __pyx_L23_break;
      }
      __pyx_L24:;
    }
    __pyx_L23_break:;
    goto __pyx_L21;
  }
  /*else*/ {

    /* "cwindow.pyx":425
 *     # Trim low-quality tails for reverse reads
 *     else:
 *         for index from 0 <= index < theRead.rlen:             # <<<<<<<<<<<<<<
 * 
 *             if index < trimReadFlank or theRead.qual[index] < 5:
 */
    __pyx_t_3 = __pyx_v_theRead->rlen;
    for (__pyx_v_index = 0; __pyx_v_index < __pyx_t_3; __pyx_v_index++) {

      /* "cwindow.pyx":427
 *         for index from 0 <= index < theRead.rlen:
 * 
 *             if index < trimReadFlank or theRead.qual[index] < 5:             # <<<<<<<<<<<<<<
 *                 theRead.qual[index] = 0
 *             else:
 */
      __pyx_t_1 = ((__pyx_v_index < __pyx_v_trimReadFlank) != 0);
      if (!__pyx_t_1) {
        __pyx_t_4 = (((__pyx_v_theRead->qual[__pyx_v_index]) < 5) != 0);
        __pyx_t_5 = __pyx_t_4;
      } else {
        __pyx_t_5 = __pyx_t_1;
      }
      if (__pyx_t_5) {

        /* "cwindow.pyx":428
 * 
 *             if index < trimReadFlank or theRead.qual[index] < 5:
 *                 theRead.qual[index] = 0             # <<<<<<<<<<<<<<
 *             else:
 *                 break
 */
        (__pyx_v_theRead->qual[__pyx_v_index]) = 0;
        goto __pyx_L27;
      }
      /*else*/ {

        /* "cwindow.pyx":430
 *                 theRead.qual[index] = 0
 *             else:
 *                 break             # <<<<<<<<<<<<<<
 * 
 *     cdef int absIns = abs(theRead.insertSize)
 */
        goto __pyx_L26_break;
      }
      __pyx_L27:;
    }
    __pyx_L26_break:;
  }
  __pyx_L21:;

  /* "cwindow.pyx":432
 *                 break
 * 
 *     cdef int absIns = abs(theRead.insertSize)             # <<<<<<<<<<<<<<
 * 
 *     # Trim overlapping part of forward read, in pairs where the read length is greater than the insert size
 */
  __pyx_v_absIns = abs(__pyx_v_theRead->insertSize);

  /* "cwindow.pyx":438
 *     # remove duplicate information, which gives systematic errors when pcr errors have occured in library prep.
 * 
 *     if trimOverlapping == 1 and (Read_IsPaired(theRead) and absIns > 0 and (not Read_IsReverse(theRead)) and Read_MateIsReverse(theRead) and absIns < 2*theRead.rlen):             # <<<<<<<<<<<<<<
 *         for index from 1 <= index <= min(theRead.rlen, (2*theRead.rlen - theRead.insertSize) + 1):
 *             theRead.qual[theRead.rlen - index] = 0
 */
  __pyx_t_5 = (__pyx_v_trimOverlapping == 1);
  if (__pyx_t_5) {
    if ((__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0)) {
      __pyx_t_1 = (__pyx_v_absIns > 0);
      if (__pyx_t_1) {
        __pyx_t_4 = (!(__pyx_f_13htslibWrapper_Read_IsReverse(__pyx_v_theRead) != 0));
        if (__pyx_t_4) {
          if ((__pyx_f_13htslibWrapper_Read_MateIsReverse(__pyx_v_theRead) != 0)) {
            __pyx_t_6 = (__pyx_v_absIns < (2 * __pyx_v_theRead->rlen));
            __pyx_t_7 = __pyx_t_6;
          } else {
            __pyx_t_7 = (__pyx_f_13htslibWrapper_Read_MateIsReverse(__pyx_v_theRead) != 0);
          }
          __pyx_t_6 = __pyx_t_7;
        } else {
          __pyx_t_6 = __pyx_t_4;
        }
        __pyx_t_4 = __pyx_t_6;
      } else {
        __pyx_t_4 = __pyx_t_1;
      }
      __pyx_t_1 = __pyx_t_4;
    } else {
      __pyx_t_1 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
    }
    __pyx_t_4 = __pyx_t_1;
  } else {
    __pyx_t_4 = __pyx_t_5;
  }
  if (__pyx_t_4) {

    /* "cwindow.pyx":439
 * 
 *     if trimOverlapping == 1 and (Read_IsPaired(theRead) and absIns > 0 and (not Read_IsReverse(theRead)) and Read_MateIsReverse(theRead) and absIns < 2*theRead.rlen):
 *         for index from 1 <= index <= min(theRead.rlen, (2*theRead.rlen - theRead.insertSize) + 1):             # <<<<<<<<<<<<<<
 *             theRead.qual[theRead.rlen - index] = 0
 * 
 */
    __pyx_t_8 = (((2 * __pyx_v_theRead->rlen) - __pyx_v_theRead->insertSize) + 1);
    __pyx_t_3 = __pyx_v_theRead->rlen;
    if (((__pyx_t_8 < __pyx_t_3) != 0)) {
      __pyx_t_9 = __pyx_t_8;
    } else {
      __pyx_t_9 = __pyx_t_3;
    }
    __pyx_t_8 = __pyx_t_9;
    for (__pyx_v_index = 1; __pyx_v_index <= __pyx_t_8; __pyx_v_index++) {

      /* "cwindow.pyx":440
 *     if trimOverlapping == 1 and (Read_IsPaired(theRead) and absIns > 0 and (not Read_IsReverse(theRead)) and Read_MateIsReverse(theRead) and absIns < 2*theRead.rlen):
 *         for index from 1 <= index <= min(theRead.rlen, (2*theRead.rlen - theRead.insertSize) + 1):
 *             theRead.qual[theRead.rlen - index] = 0             # <<<<<<<<<<<<<<
 * 
 *     # Trim the end of any read where the insert size is < read length. If these have not been
 */
      (__pyx_v_theRead->qual[(__pyx_v_theRead->rlen - __pyx_v_index)]) = 0;
    }
    goto __pyx_L28;
  }
  __pyx_L28:;

  /* "cwindow.pyx":445
 *     # already filtered out then they need trimming, as adapter contamination will cause a
 *     # high FP rate otherwise.
 *     if trimAdapter == 1 and (Read_IsPaired(theRead) and absIns > 0 and absIns < theRead.rlen):             # <<<<<<<<<<<<<<
 * 
 *         if Read_IsReverse(theRead):
 */
  __pyx_t_4 = (__pyx_v_trimAdapter == 1);
  if (__pyx_t_4) {
    if ((__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0)) {
      __pyx_t_5 = (__pyx_v_absIns > 0);
      if (__pyx_t_5) {
        __pyx_t_1 = (__pyx_v_absIns < __pyx_v_theRead->rlen);
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        __pyx_t_6 = __pyx_t_5;
      }
      __pyx_t_5 = __pyx_t_6;
    } else {
      __pyx_t_5 = (__pyx_f_13htslibWrapper_Read_IsPaired(__pyx_v_theRead) != 0);
    }
    __pyx_t_6 = __pyx_t_5;
  } else {
    __pyx_t_6 = __pyx_t_4;
  }
  if (__pyx_t_6) {

    /* "cwindow.pyx":447
 *     if trimAdapter == 1 and (Read_IsPaired(theRead) and absIns > 0 and absIns < theRead.rlen):
 * 
 *         if Read_IsReverse(theRead):             # <<<<<<<<<<<<<<
 *             for index from 1 <= index < theRead.rlen - absIns + 1:
 *                 theRead.qual[theRead.rlen - index] = 0
 */
    __pyx_t_6 = (__pyx_f_13htslibWrapper_Read_IsReverse(__pyx_v_theRead) != 0);
    if (__pyx_t_6) {

      /* "cwindow.pyx":448
 * 
 *         if Read_IsReverse(theRead):
 *             for index from 1 <= index < theRead.rlen - absIns + 1:             # <<<<<<<<<<<<<<
 *                 theRead.qual[theRead.rlen - index] = 0
 *         else:
 */
      __pyx_t_8 = ((__pyx_v_theRead->rlen - __pyx_v_absIns) + 1);
      for (__pyx_v_index = 1; __pyx_v_index < __pyx_t_8; __pyx_v_index++) {

        /* "cwindow.pyx":449
 *         if Read_IsReverse(theRead):
 *             for index from 1 <= index < theRead.rlen - absIns + 1:
 *                 theRead.qual[theRead.rlen - index] = 0             # <<<<<<<<<<<<<<
 *         else:
 *             for index from absIns <= index < theRead.rlen:
 */
        (__pyx_v_theRead->qual[(__pyx_v_theRead->rlen - __pyx_v_index)]) = 0;
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      goto __pyx_L32;
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    /*else*/ {

      /* "cwindow.pyx":451
 *                 theRead.qual[theRead.rlen - index] = 0
 *         else:
 *             for index from absIns <= index < theRead.rlen:             # <<<<<<<<<<<<<<
 *                 theRead.qual[index] = 0
 * 
 */
      __pyx_t_3 = __pyx_v_theRead->rlen;
      for (__pyx_v_index = __pyx_v_absIns; __pyx_v_index < __pyx_t_3; __pyx_v_index++) {

        /* "cwindow.pyx":452
 *         else:
 *             for index from absIns <= index < theRead.rlen:
 *                 theRead.qual[index] = 0             # <<<<<<<<<<<<<<
 * 
 * 
 */
        (__pyx_v_theRead->qual[__pyx_v_index]) = 0;
      }
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    __pyx_L32:;
    goto __pyx_L31;
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  __pyx_L31:;

  /* "cwindow.pyx":457
 *     # Check for soft-clipping (present in BWA reads, for example, but not Stampy). Soft-clipped
 *     # sequences should be set to QUAL = 0, as they may include contamination by adapters etc.
 *     cdef int cigarIndex = 0             # <<<<<<<<<<<<<<
 *     cdef int j = 0
 *     cdef int cigarOp = -1
 */
  __pyx_v_cigarIndex = 0;

  /* "cwindow.pyx":458
 *     # sequences should be set to QUAL = 0, as they may include contamination by adapters etc.
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 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef int cigarOp = -1
 *     cdef int cigarLen = -1
 */
  __pyx_v_j = 0;

  /* "cwindow.pyx":459
 *     cdef int cigarIndex = 0
 *     cdef int j = 0
 *     cdef int cigarOp = -1             # <<<<<<<<<<<<<<
 *     cdef int cigarLen = -1
 * 
 */
  __pyx_v_cigarOp = -1;

  /* "cwindow.pyx":460
 *     cdef int j = 0
 *     cdef int cigarOp = -1
 *     cdef int cigarLen = -1             # <<<<<<<<<<<<<<
 * 
 *     if trimSoftClipped == 1:
 */
  __pyx_v_cigarLen = -1;

  /* "cwindow.pyx":462
 *     cdef int cigarLen = -1
 * 
 *     if trimSoftClipped == 1:             # <<<<<<<<<<<<<<
 *         index = 0
 * 
 */
  __pyx_t_6 = ((__pyx_v_trimSoftClipped == 1) != 0);
  if (__pyx_t_6) {

    /* "cwindow.pyx":463
 * 
 *     if trimSoftClipped == 1:
 *         index = 0             # <<<<<<<<<<<<<<
 * 
 *         for cigarIndex in range(theRead.cigarLen):
 */
    __pyx_v_index = 0;

    /* "cwindow.pyx":465
 *         index = 0
 * 
 *         for cigarIndex in range(theRead.cigarLen):             # <<<<<<<<<<<<<<
 * 
 *             cigarOp = theRead.cigarOps[2*cigarIndex]
 */
    __pyx_t_3 = __pyx_v_theRead->cigarLen;
    for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_3; __pyx_t_2+=1) {
      __pyx_v_cigarIndex = __pyx_t_2;

      /* "cwindow.pyx":467
 *         for cigarIndex in range(theRead.cigarLen):
 * 
 *             cigarOp = theRead.cigarOps[2*cigarIndex]             # <<<<<<<<<<<<<<
 *             cigarLen = theRead.cigarOps[2*cigarIndex + 1]
 * 
 */
      __pyx_v_cigarOp = (__pyx_v_theRead->cigarOps[(2 * __pyx_v_cigarIndex)]);

      /* "cwindow.pyx":468
 * 
 *             cigarOp = theRead.cigarOps[2*cigarIndex]
 *             cigarLen = theRead.cigarOps[2*cigarIndex + 1]             # <<<<<<<<<<<<<<
 * 
 *             # Skip good sequence. 0 is match. 1 is insertion.
 */
      __pyx_v_cigarLen = (__pyx_v_theRead->cigarOps[((2 * __pyx_v_cigarIndex) + 1)]);

      /* "cwindow.pyx":475
 * 
 *             # 4 is soft-clipping
 *             elif cigarOp == 4:             # <<<<<<<<<<<<<<
 *                 # Set quals to zero across all sequence flagged as soft-clipped
 *                 for j in range(theRead.cigarOps[2*cigarIndex + 1]):
 */
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        /* "cwindow.pyx":471
 * 
 *             # Skip good sequence. 0 is match. 1 is insertion.
 *             if cigarOp == 0 or cigarOp == 1:             # <<<<<<<<<<<<<<
 *                 index += theRead.cigarOps[2*cigarIndex + 1]
 * 
 */
        case 0:
        case 1:

        /* "cwindow.pyx":472
 *             # Skip good sequence. 0 is match. 1 is insertion.
 *             if cigarOp == 0 or cigarOp == 1:
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 * 
 *             # 4 is soft-clipping
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 * 
 *             # 4 is soft-clipping
 *             elif cigarOp == 4:             # <<<<<<<<<<<<<<
 *                 # Set quals to zero across all sequence flagged as soft-clipped
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 */
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        /* "cwindow.pyx":477
 *             elif cigarOp == 4:
 *                 # Set quals to zero across all sequence flagged as soft-clipped
 *                 for j in range(theRead.cigarOps[2*cigarIndex + 1]):             # <<<<<<<<<<<<<<
 *                     theRead.qual[index] = 0
 *                     index += 1
 */
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          /* "cwindow.pyx":478
 *                 # Set quals to zero across all sequence flagged as soft-clipped
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 *                     theRead.qual[index] = 0             # <<<<<<<<<<<<<<
 *                     index += 1
 * 
 */
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          /* "cwindow.pyx":479
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 *                     index += 1             # <<<<<<<<<<<<<<
 * 
 *     return True
 */
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    goto __pyx_L37;
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  __pyx_L37:;

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 *                     index += 1
 * 
 *     return True             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
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/* "cwindow.pyx":490
 *     through the data in each BAM in the loop through windows.
 *     """
 *     def __init__(self, char* chrom, int start, int end, options):             # <<<<<<<<<<<<<<
 *         """
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 *         cdef cAlignedRead** bStart = self.badReads.windowStart             # <<<<<<<<<<<<<<
 *         cdef cAlignedRead** bEnd = self.badReads.windowEnd
 * 
 */
  __pyx_t_1 = __pyx_v_self->badReads->windowStart;
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  /* "cwindow.pyx":633
 *         cdef cAlignedRead** end = self.reads.windowEnd
 *         cdef cAlignedRead** bStart = self.badReads.windowStart
 *         cdef cAlignedRead** bEnd = self.badReads.windowEnd             # <<<<<<<<<<<<<<
 * 
 *         cdef int nImproper = 0
 */
  __pyx_t_1 = __pyx_v_self->badReads->windowEnd;
  __pyx_v_bEnd = __pyx_t_1;

  /* "cwindow.pyx":635
 *         cdef cAlignedRead** bEnd = self.badReads.windowEnd
 * 
 *         cdef int nImproper = 0             # <<<<<<<<<<<<<<
 * 
 *         while start != end:
 */
  __pyx_v_nImproper = 0;

  /* "cwindow.pyx":637
 *         cdef int nImproper = 0
 * 
 *         while start != end:             # <<<<<<<<<<<<<<
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  while (1) {
    __pyx_t_2 = ((__pyx_v_start != __pyx_v_end) != 0);
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    /* "cwindow.pyx":638
 * 
 *         while start != end:
 *             if not Read_IsProperPair(start[0]):             # <<<<<<<<<<<<<<
 *                 nImproper += 1
 *             start += 1
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    __pyx_t_2 = ((!(__pyx_f_13htslibWrapper_Read_IsProperPair((__pyx_v_start[0])) != 0)) != 0);
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      /* "cwindow.pyx":639
 *         while start != end:
 *             if not Read_IsProperPair(start[0]):
 *                 nImproper += 1             # <<<<<<<<<<<<<<
 *             start += 1
 * 
 */
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    __pyx_L5:;

    /* "cwindow.pyx":640
 *             if not Read_IsProperPair(start[0]):
 *                 nImproper += 1
 *             start += 1             # <<<<<<<<<<<<<<
 * 
 *         while bStart != bEnd:
 */
    __pyx_v_start = (__pyx_v_start + 1);
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  /* "cwindow.pyx":642
 *             start += 1
 * 
 *         while bStart != bEnd:             # <<<<<<<<<<<<<<
 *             if not Read_IsProperPair(bStart[0]):
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    __pyx_t_2 = ((__pyx_v_bStart != __pyx_v_bEnd) != 0);
    if (!__pyx_t_2) break;

    /* "cwindow.pyx":643
 * 
 *         while bStart != bEnd:
 *             if not Read_IsProperPair(bStart[0]):             # <<<<<<<<<<<<<<
 *                 nImproper += 1
 *             bStart += 1
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    __pyx_t_2 = ((!(__pyx_f_13htslibWrapper_Read_IsProperPair((__pyx_v_bStart[0])) != 0)) != 0);
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      /* "cwindow.pyx":644
 *         while bStart != bEnd:
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 *                 nImproper += 1             # <<<<<<<<<<<<<<
 *             bStart += 1
 * 
 */
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 *             bStart += 1             # <<<<<<<<<<<<<<
 * 
 *         return nImproper
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  /* "cwindow.pyx":647
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 * 
 *         return nImproper             # <<<<<<<<<<<<<<
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 *     cdef int countReadsCoveringRegion(self, int start, int end):
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/* "cwindow.pyx":649
 *         return nImproper
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 *     cdef int countReadsCoveringRegion(self, int start, int end):             # <<<<<<<<<<<<<<
 *         """
 *         Return the number of 'good' reads covering this region.
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static int __pyx_f_7cwindow_13bamReadBuffer_countReadsCoveringRegion(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self, int __pyx_v_start, int __pyx_v_end) {
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 *         return self.reads.countReadsCoveringRegion(start, end)             # <<<<<<<<<<<<<<
 * 
 *     cdef void setWindowPointers(self, int start, int end, int refStart, int refEnd, char* refSeq, int qualBinSize):
 */
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/* "cwindow.pyx":655
 *         return self.reads.countReadsCoveringRegion(start, end)
 * 
 *     cdef void setWindowPointers(self, int start, int end, int refStart, int refEnd, char* refSeq, int qualBinSize):             # <<<<<<<<<<<<<<
 *         """
 *         Set the windowStart and windowEnd pointers to point to the first
 */

static void __pyx_f_7cwindow_13bamReadBuffer_setWindowPointers(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self, int __pyx_v_start, int __pyx_v_end, int __pyx_v_refStart, int __pyx_v_refEnd, char *__pyx_v_refSeq, int __pyx_v_qualBinSize) {
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_theStart;
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_theEnd;
  __Pyx_RefNannyDeclarations
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_t_1;
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 *         self.reads.setWindowPointers(start, end)             # <<<<<<<<<<<<<<
 *         self.badReads.setWindowPointers(start, end)
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 */
  ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->reads->__pyx_vtab)->setWindowPointers(__pyx_v_self->reads, __pyx_v_start, __pyx_v_end);

  /* "cwindow.pyx":661
 *         """
 *         self.reads.setWindowPointers(start, end)
 *         self.badReads.setWindowPointers(start, end)             # <<<<<<<<<<<<<<
 *         self.brokenMates.setWindowPointersBasedOnMatePos(start, end)
 * 
 */
  ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->badReads->__pyx_vtab)->setWindowPointers(__pyx_v_self->badReads, __pyx_v_start, __pyx_v_end);

  /* "cwindow.pyx":662
 *         self.reads.setWindowPointers(start, end)
 *         self.badReads.setWindowPointers(start, end)
 *         self.brokenMates.setWindowPointersBasedOnMatePos(start, end)             # <<<<<<<<<<<<<<
 * 
 *         cdef cAlignedRead** theStart = NULL
 */
  ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->brokenMates->__pyx_vtab)->setWindowPointersBasedOnMatePos(__pyx_v_self->brokenMates, __pyx_v_start, __pyx_v_end);

  /* "cwindow.pyx":664
 *         self.brokenMates.setWindowPointersBasedOnMatePos(start, end)
 * 
 *         cdef cAlignedRead** theStart = NULL             # <<<<<<<<<<<<<<
 *         cdef cAlignedRead** theEnd = NULL
 * 
 */
  __pyx_v_theStart = NULL;

  /* "cwindow.pyx":665
 * 
 *         cdef cAlignedRead** theStart = NULL
 *         cdef cAlignedRead** theEnd = NULL             # <<<<<<<<<<<<<<
 * 
 *         # If the reads in this window are compressed, then uncompress them
 */
  __pyx_v_theEnd = NULL;

  /* "cwindow.pyx":668
 * 
 *         # If the reads in this window are compressed, then uncompress them
 *         theStart = self.reads.windowStart             # <<<<<<<<<<<<<<
 *         theEnd = self.reads.windowEnd
 * 
 */
  __pyx_t_1 = __pyx_v_self->reads->windowStart;
  __pyx_v_theStart = __pyx_t_1;

  /* "cwindow.pyx":669
 *         # If the reads in this window are compressed, then uncompress them
 *         theStart = self.reads.windowStart
 *         theEnd = self.reads.windowEnd             # <<<<<<<<<<<<<<
 * 
 *         if theStart != theEnd and Read_IsCompressed(theStart[0]):
 */
  __pyx_t_1 = __pyx_v_self->reads->windowEnd;
  __pyx_v_theEnd = __pyx_t_1;

  /* "cwindow.pyx":671
 *         theEnd = self.reads.windowEnd
 * 
 *         if theStart != theEnd and Read_IsCompressed(theStart[0]):             # <<<<<<<<<<<<<<
 * 
 *             while theStart != theEnd:
 */
  __pyx_t_2 = (__pyx_v_theStart != __pyx_v_theEnd);
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    __pyx_t_3 = (__pyx_f_13htslibWrapper_Read_IsCompressed((__pyx_v_theStart[0])) != 0);
  } else {
    __pyx_t_3 = __pyx_t_2;
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  if (__pyx_t_3) {

    /* "cwindow.pyx":673
 *         if theStart != theEnd and Read_IsCompressed(theStart[0]):
 * 
 *             while theStart != theEnd:             # <<<<<<<<<<<<<<
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1
 */
    while (1) {
      __pyx_t_3 = ((__pyx_v_theStart != __pyx_v_theEnd) != 0);
      if (!__pyx_t_3) break;

      /* "cwindow.pyx":674
 * 
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)             # <<<<<<<<<<<<<<
 *                 theStart += 1
 * 
 */
      __pyx_f_13htslibWrapper_uncompressRead((__pyx_v_theStart[0]), __pyx_v_refSeq, __pyx_v_refStart, __pyx_v_refEnd, __pyx_v_qualBinSize);

      /* "cwindow.pyx":675
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1             # <<<<<<<<<<<<<<
 * 
 *             theStart = self.badReads.windowStart
 */
      __pyx_v_theStart = (__pyx_v_theStart + 1);
    }

    /* "cwindow.pyx":677
 *                 theStart += 1
 * 
 *             theStart = self.badReads.windowStart             # <<<<<<<<<<<<<<
 *             theEnd = self.badReads.windowEnd
 * 
 */
    __pyx_t_1 = __pyx_v_self->badReads->windowStart;
    __pyx_v_theStart = __pyx_t_1;

    /* "cwindow.pyx":678
 * 
 *             theStart = self.badReads.windowStart
 *             theEnd = self.badReads.windowEnd             # <<<<<<<<<<<<<<
 * 
 *             while theStart != theEnd:
 */
    __pyx_t_1 = __pyx_v_self->badReads->windowEnd;
    __pyx_v_theEnd = __pyx_t_1;

    /* "cwindow.pyx":680
 *             theEnd = self.badReads.windowEnd
 * 
 *             while theStart != theEnd:             # <<<<<<<<<<<<<<
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1
 */
    while (1) {
      __pyx_t_3 = ((__pyx_v_theStart != __pyx_v_theEnd) != 0);
      if (!__pyx_t_3) break;

      /* "cwindow.pyx":681
 * 
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)             # <<<<<<<<<<<<<<
 *                 theStart += 1
 * 
 */
      __pyx_f_13htslibWrapper_uncompressRead((__pyx_v_theStart[0]), __pyx_v_refSeq, __pyx_v_refStart, __pyx_v_refEnd, __pyx_v_qualBinSize);

      /* "cwindow.pyx":682
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1             # <<<<<<<<<<<<<<
 * 
 *             theStart = self.brokenMates.windowStart
 */
      __pyx_v_theStart = (__pyx_v_theStart + 1);
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    /* "cwindow.pyx":684
 *                 theStart += 1
 * 
 *             theStart = self.brokenMates.windowStart             # <<<<<<<<<<<<<<
 *             theEnd = self.brokenMates.windowEnd
 * 
 */
    __pyx_t_1 = __pyx_v_self->brokenMates->windowStart;
    __pyx_v_theStart = __pyx_t_1;

    /* "cwindow.pyx":685
 * 
 *             theStart = self.brokenMates.windowStart
 *             theEnd = self.brokenMates.windowEnd             # <<<<<<<<<<<<<<
 * 
 *             while theStart != theEnd:
 */
    __pyx_t_1 = __pyx_v_self->brokenMates->windowEnd;
    __pyx_v_theEnd = __pyx_t_1;

    /* "cwindow.pyx":687
 *             theEnd = self.brokenMates.windowEnd
 * 
 *             while theStart != theEnd:             # <<<<<<<<<<<<<<
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1
 */
    while (1) {
      __pyx_t_3 = ((__pyx_v_theStart != __pyx_v_theEnd) != 0);
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      /* "cwindow.pyx":688
 * 
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)             # <<<<<<<<<<<<<<
 *                 theStart += 1
 * 
 */
      __pyx_f_13htslibWrapper_uncompressRead((__pyx_v_theStart[0]), __pyx_v_refSeq, __pyx_v_refStart, __pyx_v_refEnd, __pyx_v_qualBinSize);

      /* "cwindow.pyx":689
 *             while theStart != theEnd:
 *                 uncompressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize)
 *                 theStart += 1             # <<<<<<<<<<<<<<
 * 
 *     cdef void recompressReadsInCurrentWindow(self, int refStart, int refEnd, char* refSeq, int qualBinSize, int compressReads):
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      __pyx_v_theStart = (__pyx_v_theStart + 1);
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/* "cwindow.pyx":691
 *                 theStart += 1
 * 
 *     cdef void recompressReadsInCurrentWindow(self, int refStart, int refEnd, char* refSeq, int qualBinSize, int compressReads):             # <<<<<<<<<<<<<<
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 *         Set the windowStart and windowEnd pointers to point to the first
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static void __pyx_f_7cwindow_13bamReadBuffer_recompressReadsInCurrentWindow(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self, int __pyx_v_refStart, int __pyx_v_refEnd, char *__pyx_v_refSeq, int __pyx_v_qualBinSize, int __pyx_v_compressReads) {
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  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_v_theEnd;
  __Pyx_RefNannyDeclarations
  __pyx_t_13htslibWrapper_cAlignedRead **__pyx_t_1;
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 *         and last+1 reads covering this window.
 *         """
 *         cdef cAlignedRead** theStart = NULL             # <<<<<<<<<<<<<<
 *         cdef cAlignedRead** theEnd = NULL
 * 
 */
  __pyx_v_theStart = NULL;

  /* "cwindow.pyx":697
 *         """
 *         cdef cAlignedRead** theStart = NULL
 *         cdef cAlignedRead** theEnd = NULL             # <<<<<<<<<<<<<<
 * 
 *         # If the reads in this window are compressed, then uncompress them
 */
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  /* "cwindow.pyx":700
 * 
 *         # If the reads in this window are compressed, then uncompress them
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 *         theEnd = self.reads.windowEnd
 * 
 */
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  /* "cwindow.pyx":701
 *         # If the reads in this window are compressed, then uncompress them
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 *         theEnd = self.reads.windowEnd             # <<<<<<<<<<<<<<
 * 
 *         while theStart != theEnd:
 */
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  /* "cwindow.pyx":703
 *         theEnd = self.reads.windowEnd
 * 
 *         while theStart != theEnd:             # <<<<<<<<<<<<<<
 * 
 *             # Compresss reads is required
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 * 
 *             # Compresss reads is required
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 * 
 */
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      /* "cwindow.pyx":707
 *             # Compresss reads is required
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 * 
 *             # Otherwise, just clear the hash
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 * 
 *             # Otherwise, just clear the hash
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 *                 theStart[0].hash = NULL
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      /* "cwindow.pyx":711
 *             # Otherwise, just clear the hash
 *             if theStart[0].hash != NULL:
 *                 free(theStart[0].hash)             # <<<<<<<<<<<<<<
 *                 theStart[0].hash = NULL
 * 
 */
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      /* "cwindow.pyx":712
 *             if theStart[0].hash != NULL:
 *                 free(theStart[0].hash)
 *                 theStart[0].hash = NULL             # <<<<<<<<<<<<<<
 * 
 *             theStart += 1
 */
      (__pyx_v_theStart[0])->hash = NULL;
      goto __pyx_L6;
    }
    __pyx_L6:;

    /* "cwindow.pyx":714
 *                 theStart[0].hash = NULL
 * 
 *             theStart += 1             # <<<<<<<<<<<<<<
 * 
 *         theStart = self.badReads.windowStart
 */
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  /* "cwindow.pyx":716
 *             theStart += 1
 * 
 *         theStart = self.badReads.windowStart             # <<<<<<<<<<<<<<
 *         theEnd = self.badReads.windowEnd
 * 
 */
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  __pyx_v_theStart = __pyx_t_1;

  /* "cwindow.pyx":717
 * 
 *         theStart = self.badReads.windowStart
 *         theEnd = self.badReads.windowEnd             # <<<<<<<<<<<<<<
 * 
 *         while theStart != theEnd:
 */
  __pyx_t_1 = __pyx_v_self->badReads->windowEnd;
  __pyx_v_theEnd = __pyx_t_1;

  /* "cwindow.pyx":719
 *         theEnd = self.badReads.windowEnd
 * 
 *         while theStart != theEnd:             # <<<<<<<<<<<<<<
 * 
 *             # Compresss reads is required
 */
  while (1) {
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    /* "cwindow.pyx":722
 * 
 *             # Compresss reads is required
 *             if compressReads:             # <<<<<<<<<<<<<<
 *                 compressRead(theStart[0], refSeq, refStart, refEnd, qualBinSize, 1)
 * 
 */
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      /* "cwindow.pyx":723
 *             # Compresss reads is required
 *             if compressReads:
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 * 
 *             # Otherwise, just clear the hash
 */
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    __pyx_L9:;

    /* "cwindow.pyx":726
 * 
 *             # Otherwise, just clear the hash
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 *                 free(theStart[0].hash)
 *                 theStart[0].hash = NULL
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      /* "cwindow.pyx":727
 *             # Otherwise, just clear the hash
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 *                 free(theStart[0].hash)             # <<<<<<<<<<<<<<
 *                 theStart[0].hash = NULL
 * 
 */
      free((__pyx_v_theStart[0])->hash);

      /* "cwindow.pyx":728
 *             if theStart[0].hash != NULL:
 *                 free(theStart[0].hash)
 *                 theStart[0].hash = NULL             # <<<<<<<<<<<<<<
 * 
 *             theStart += 1
 */
      (__pyx_v_theStart[0])->hash = NULL;
      goto __pyx_L10;
    }
    __pyx_L10:;

    /* "cwindow.pyx":730
 *                 theStart[0].hash = NULL
 * 
 *             theStart += 1             # <<<<<<<<<<<<<<
 * 
 *         theStart = self.brokenMates.windowStart
 */
    __pyx_v_theStart = (__pyx_v_theStart + 1);
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  /* "cwindow.pyx":732
 *             theStart += 1
 * 
 *         theStart = self.brokenMates.windowStart             # <<<<<<<<<<<<<<
 *         theEnd = self.brokenMates.windowEnd
 * 
 */
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  /* "cwindow.pyx":733
 * 
 *         theStart = self.brokenMates.windowStart
 *         theEnd = self.brokenMates.windowEnd             # <<<<<<<<<<<<<<
 * 
 *         while theStart != theEnd:
 */
  __pyx_t_1 = __pyx_v_self->brokenMates->windowEnd;
  __pyx_v_theEnd = __pyx_t_1;

  /* "cwindow.pyx":735
 *         theEnd = self.brokenMates.windowEnd
 * 
 *         while theStart != theEnd:             # <<<<<<<<<<<<<<
 * 
 *             # Compresss reads is required
 */
  while (1) {
    __pyx_t_2 = ((__pyx_v_theStart != __pyx_v_theEnd) != 0);
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 */
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      /* "cwindow.pyx":739
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 *             # Otherwise, just clear the hash
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      __pyx_f_13htslibWrapper_compressRead((__pyx_v_theStart[0]), __pyx_v_refSeq, __pyx_v_refStart, __pyx_v_refEnd, __pyx_v_qualBinSize, 1);
      goto __pyx_L13;
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    /* "cwindow.pyx":742
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 *             # Otherwise, just clear the hash
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 *                 free(theStart[0].hash)
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 */
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      /* "cwindow.pyx":743
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 *                 theStart[0].hash = NULL
 * 
 */
      free((__pyx_v_theStart[0])->hash);

      /* "cwindow.pyx":744
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 *             theStart += 1
 */
      (__pyx_v_theStart[0])->hash = NULL;
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    /* "cwindow.pyx":746
 *                 theStart[0].hash = NULL
 * 
 *             theStart += 1             # <<<<<<<<<<<<<<
 * 
 *     cdef void sortReads(self):
 */
    __pyx_v_theStart = (__pyx_v_theStart + 1);
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/* "cwindow.pyx":748
 *             theStart += 1
 * 
 *     cdef void sortReads(self):             # <<<<<<<<<<<<<<
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 *         Sort the contents of the reads array by position
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static void __pyx_f_7cwindow_13bamReadBuffer_sortReads(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("sortReads", 0);

  /* "cwindow.pyx":752
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 *         """
 *         if not self.isSorted:             # <<<<<<<<<<<<<<
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 */
  __pyx_t_1 = ((!(__pyx_v_self->isSorted != 0)) != 0);
  if (__pyx_t_1) {

    /* "cwindow.pyx":753
 *         """
 *         if not self.isSorted:
 *             if self.reads.getSize() > 0:             # <<<<<<<<<<<<<<
 *                 qsort(self.reads.array, self.reads.getSize(), sizeof(cAlignedRead**), readPosComp)
 * 
 */
    __pyx_t_1 = ((((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->reads->__pyx_vtab)->getSize(__pyx_v_self->reads) > 0) != 0);
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      /* "cwindow.pyx":754
 *         if not self.isSorted:
 *             if self.reads.getSize() > 0:
 *                 qsort(self.reads.array, self.reads.getSize(), sizeof(cAlignedRead**), readPosComp)             # <<<<<<<<<<<<<<
 * 
 *             if self.badReads.getSize() > 0:
 */
      qsort(__pyx_v_self->reads->array, ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->reads->__pyx_vtab)->getSize(__pyx_v_self->reads), (sizeof(__pyx_t_13htslibWrapper_cAlignedRead **)), __pyx_f_7cwindow_readPosComp);
      goto __pyx_L4;
    }
    __pyx_L4:;

    /* "cwindow.pyx":756
 *                 qsort(self.reads.array, self.reads.getSize(), sizeof(cAlignedRead**), readPosComp)
 * 
 *             if self.badReads.getSize() > 0:             # <<<<<<<<<<<<<<
 *                 qsort(self.badReads.array, self.badReads.getSize(), sizeof(cAlignedRead**), readPosComp)
 * 
 */
    __pyx_t_1 = ((((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->badReads->__pyx_vtab)->getSize(__pyx_v_self->badReads) > 0) != 0);
    if (__pyx_t_1) {

      /* "cwindow.pyx":757
 * 
 *             if self.badReads.getSize() > 0:
 *                 qsort(self.badReads.array, self.badReads.getSize(), sizeof(cAlignedRead**), readPosComp)             # <<<<<<<<<<<<<<
 * 
 *             self.isSorted = True
 */
      qsort(__pyx_v_self->badReads->array, ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->badReads->__pyx_vtab)->getSize(__pyx_v_self->badReads), (sizeof(__pyx_t_13htslibWrapper_cAlignedRead **)), __pyx_f_7cwindow_readPosComp);
      goto __pyx_L5;
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    __pyx_L5:;

    /* "cwindow.pyx":759
 *                 qsort(self.badReads.array, self.badReads.getSize(), sizeof(cAlignedRead**), readPosComp)
 * 
 *             self.isSorted = True             # <<<<<<<<<<<<<<
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 *     cdef void sortBrokenMates(self):
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/* "cwindow.pyx":761
 *             self.isSorted = True
 * 
 *     cdef void sortBrokenMates(self):             # <<<<<<<<<<<<<<
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static void __pyx_f_7cwindow_13bamReadBuffer_sortBrokenMates(struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
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  /* "cwindow.pyx":766
 *         mates.
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 * 
 * ###################################################################################################
 */
  qsort(__pyx_v_self->brokenMates->array, ((struct __pyx_vtabstruct_7cwindow_ReadArray *)__pyx_v_self->brokenMates->__pyx_vtab)->getSize(__pyx_v_self->brokenMates), (sizeof(__pyx_t_13htslibWrapper_cAlignedRead **)), __pyx_f_7cwindow_readMatePosComp);

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
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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) {
  int __pyx_r;

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

  __pyx_r = 0;
  __pyx_L0:;
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}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
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}

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

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

  /* "htslibWrapper.pxd":260
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)             # <<<<<<<<<<<<<<
 * 
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 */
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  __pyx_r = 0;
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}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":266
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 */
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}

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

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

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

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
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/* "htslibWrapper.pxd":274
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)
 * 
 */

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":278
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FSECONDARY) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 256) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
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}

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

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

  /* "htslibWrapper.pxd":287
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FREVERSE             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
 */
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  __pyx_r = 0;
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}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":290
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FQCFAIL             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 512);

}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":293
 * 
 * cdef inline void Read_SetCompressed(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FCOMPRESSED             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 2048);

}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

  /* "htslibWrapper.pxd":296
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag & (~2048));

}
static struct __pyx_vtabstruct_7cwindow_ReadArray __pyx_vtable_7cwindow_ReadArray;

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  PyObject *o;
  o = (*t->tp_alloc)(t, 0);
  if (unlikely(!o)) return 0;
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static void __pyx_tp_dealloc_7cwindow_ReadArray(PyObject *o) {
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    PyObject *etype, *eval, *etb;
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    __pyx_pw_7cwindow_9ReadArray_3__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_7cwindow_ReadArray[] = {
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_7cwindow_ReadArray = {
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  __Pyx_NAMESTR("cwindow.ReadArray"), /*tp_name*/
  sizeof(struct __pyx_obj_7cwindow_ReadArray), /*tp_basicsize*/
  0, /*tp_itemsize*/
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 * 
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 * cdef int UNMAPPED_READ=1
 * cdef int MATE_UNMAPPED=2
 */
  __pyx_v_7cwindow_LOW_QUAL_BASES = 0;

  /* "cwindow.pyx":41
 * 
 * cdef int LOW_QUAL_BASES=0
 * cdef int UNMAPPED_READ=1             # <<<<<<<<<<<<<<
 * cdef int MATE_UNMAPPED=2
 * cdef int MATE_DISTANT=3
 */
  __pyx_v_7cwindow_UNMAPPED_READ = 1;

  /* "cwindow.pyx":42
 * cdef int LOW_QUAL_BASES=0
 * cdef int UNMAPPED_READ=1
 * cdef int MATE_UNMAPPED=2             # <<<<<<<<<<<<<<
 * cdef int MATE_DISTANT=3
 * cdef int SMALL_INSERT=4
 */
  __pyx_v_7cwindow_MATE_UNMAPPED = 2;

  /* "cwindow.pyx":43
 * cdef int UNMAPPED_READ=1
 * cdef int MATE_UNMAPPED=2
 * cdef int MATE_DISTANT=3             # <<<<<<<<<<<<<<
 * cdef int SMALL_INSERT=4
 * cdef int DUPLICATE=5
 */
  __pyx_v_7cwindow_MATE_DISTANT = 3;

  /* "cwindow.pyx":44
 * cdef int MATE_UNMAPPED=2
 * cdef int MATE_DISTANT=3
 * cdef int SMALL_INSERT=4             # <<<<<<<<<<<<<<
 * cdef int DUPLICATE=5
 * cdef int LOW_MAP_QUAL=6
 */
  __pyx_v_7cwindow_SMALL_INSERT = 4;

  /* "cwindow.pyx":45
 * cdef int MATE_DISTANT=3
 * cdef int SMALL_INSERT=4
 * cdef int DUPLICATE=5             # <<<<<<<<<<<<<<
 * cdef int LOW_MAP_QUAL=6
 * 
 */
  __pyx_v_7cwindow_DUPLICATE = 5;

  /* "cwindow.pyx":46
 * cdef int SMALL_INSERT=4
 * cdef int DUPLICATE=5
 * cdef int LOW_MAP_QUAL=6             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_v_7cwindow_LOW_MAP_QUAL = 6;

  /* "cwindow.pyx":1
 * """             # <<<<<<<<<<<<<<
 * Fast cython implementation of some windowing functions.
 * """
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyDict_SetItem(__pyx_d, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  /* "htslibWrapper.pxd":295
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)
 * 
 */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  if (__pyx_m) {
    __Pyx_AddTraceback("init cwindow", __pyx_clineno, __pyx_lineno, __pyx_filename);
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/* Runtime support code */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
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end:
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static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
    PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
    if (unlikely(!result)) {
        PyErr_Format(PyExc_NameError,
#if PY_MAJOR_VERSION >= 3
            "name '%U' is not defined", name);
#else
            "name '%s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyThreadState *tstate = PyThreadState_GET();
    tmp_type = tstate->curexc_type;
    tmp_value = tstate->curexc_value;
    tmp_tb = tstate->curexc_traceback;
    tstate->curexc_type = type;
    tstate->curexc_value = value;
    tstate->curexc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
#else
    PyErr_Restore(type, value, tb);
#endif
}
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyThreadState *tstate = PyThreadState_GET();
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    *value = tstate->curexc_value;
    *tb = tstate->curexc_traceback;
    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
#else
    PyErr_Fetch(type, value, tb);
#endif
}

static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
    PyObject *old_exc, *old_val, *old_tb;
    PyObject *ctx;
    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
    #if PY_MAJOR_VERSION < 3
    ctx = PyString_FromString(name);
    #else
    ctx = PyUnicode_FromString(name);
    #endif
    __Pyx_ErrRestore(old_exc, old_val, old_tb);
    if (!ctx) {
        PyErr_WriteUnraisable(Py_None);
    } else {
        PyErr_WriteUnraisable(ctx);
        Py_DECREF(ctx);
    }
}

static void __Pyx_RaiseDoubleKeywordsError(
    const char* func_name,
    PyObject* kw_name)
{
    PyErr_Format(PyExc_TypeError,
        #if PY_MAJOR_VERSION >= 3
        "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
        #else
        "%s() got multiple values for keyword argument '%s'", func_name,
        PyString_AsString(kw_name));
        #endif
}

static int __Pyx_ParseOptionalKeywords(
    PyObject *kwds,
    PyObject **argnames[],
    PyObject *kwds2,
    PyObject *values[],
    Py_ssize_t num_pos_args,
    const char* function_name)
{
    PyObject *key = 0, *value = 0;
    Py_ssize_t pos = 0;
    PyObject*** name;
    PyObject*** first_kw_arg = argnames + num_pos_args;
    while (PyDict_Next(kwds, &pos, &key, &value)) {
        name = first_kw_arg;
        while (*name && (**name != key)) name++;
        if (*name) {
            values[name-argnames] = value;
            continue;
        }
        name = first_kw_arg;
        #if PY_MAJOR_VERSION < 3
        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
            while (*name) {
                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
                        && _PyString_Eq(**name, key)) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    if ((**argname == key) || (
                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
                             && _PyString_Eq(**argname, key))) {
                        goto arg_passed_twice;
                    }
                    argname++;
                }
            }
        } else
        #endif
        if (likely(PyUnicode_Check(key))) {
            while (*name) {
                int cmp = (**name == key) ? 0 :
                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                #endif
                    PyUnicode_Compare(**name, key);
                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                if (cmp == 0) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    int cmp = (**argname == key) ? 0 :
                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                    #endif
                        PyUnicode_Compare(**argname, key);
                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                    if (cmp == 0) goto arg_passed_twice;
                    argname++;
                }
            }
        } else
            goto invalid_keyword_type;
        if (kwds2) {
            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
        } else {
            goto invalid_keyword;
        }
    }
    return 0;
arg_passed_twice:
    __Pyx_RaiseDoubleKeywordsError(function_name, key);
    goto bad;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%s() got an unexpected keyword argument '%s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

static void __Pyx_RaiseArgtupleInvalid(
    const char* func_name,
    int exact,
    Py_ssize_t num_min,
    Py_ssize_t num_max,
    Py_ssize_t num_found)
{
    Py_ssize_t num_expected;
    const char *more_or_less;
    if (num_found < num_min) {
        num_expected = num_min;
        more_or_less = "at least";
    } else {
        num_expected = num_max;
        more_or_less = "at most";
    }
    if (exact) {
        more_or_less = "exactly";
    }
    PyErr_Format(PyExc_TypeError,
                 "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                 func_name, more_or_less, num_expected,
                 (num_expected == 1) ? "" : "s", num_found);
}

#if PY_MAJOR_VERSION < 3
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                        CYTHON_UNUSED PyObject *cause) {
    Py_XINCREF(type);
    if (!value || value == Py_None)
        value = NULL;
    else
        Py_INCREF(value);
    if (!tb || tb == Py_None)
        tb = NULL;
    else {
        Py_INCREF(tb);
        if (!PyTraceBack_Check(tb)) {
            PyErr_SetString(PyExc_TypeError,
                "raise: arg 3 must be a traceback or None");
            goto raise_error;
        }
    }
    #if PY_VERSION_HEX < 0x02050000
    if (PyClass_Check(type)) {
    #else
    if (PyType_Check(type)) {
    #endif
#if CYTHON_COMPILING_IN_PYPY
        if (!value) {
            Py_INCREF(Py_None);
            value = Py_None;
        }
#endif
        PyErr_NormalizeException(&type, &value, &tb);
    } else {
        if (value) {
            PyErr_SetString(PyExc_TypeError,
                "instance exception may not have a separate value");
            goto raise_error;
        }
        value = type;
        #if PY_VERSION_HEX < 0x02050000
        if (PyInstance_Check(type)) {
            type = (PyObject*) ((PyInstanceObject*)type)->in_class;
            Py_INCREF(type);
        } else {
            type = 0;
            PyErr_SetString(PyExc_TypeError,
                "raise: exception must be an old-style class or instance");
            goto raise_error;
        }
        #else
        type = (PyObject*) Py_TYPE(type);
        Py_INCREF(type);
        if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
            PyErr_SetString(PyExc_TypeError,
                "raise: exception class must be a subclass of BaseException");
            goto raise_error;
        }
        #endif
    }
    __Pyx_ErrRestore(type, value, tb);
    return;
raise_error:
    Py_XDECREF(value);
    Py_XDECREF(type);
    Py_XDECREF(tb);
    return;
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
    PyObject* owned_instance = NULL;
    if (tb == Py_None) {
        tb = 0;
    } else if (tb && !PyTraceBack_Check(tb)) {
        PyErr_SetString(PyExc_TypeError,
            "raise: arg 3 must be a traceback or None");
        goto bad;
    }
    if (value == Py_None)
        value = 0;
    if (PyExceptionInstance_Check(type)) {
        if (value) {
            PyErr_SetString(PyExc_TypeError,
                "instance exception may not have a separate value");
            goto bad;
        }
        value = type;
        type = (PyObject*) Py_TYPE(value);
    } else if (PyExceptionClass_Check(type)) {
        PyObject *args;
        if (!value)
            args = PyTuple_New(0);
        else if (PyTuple_Check(value)) {
            Py_INCREF(value);
            args = value;
        } else
            args = PyTuple_Pack(1, value);
        if (!args)
            goto bad;
        owned_instance = PyEval_CallObject(type, args);
        Py_DECREF(args);
        if (!owned_instance)
            goto bad;
        value = owned_instance;
        if (!PyExceptionInstance_Check(value)) {
            PyErr_Format(PyExc_TypeError,
                         "calling %R should have returned an instance of "
                         "BaseException, not %R",
                         type, Py_TYPE(value));
            goto bad;
        }
    } else {
        PyErr_SetString(PyExc_TypeError,
            "raise: exception class must be a subclass of BaseException");
        goto bad;
    }
#if PY_VERSION_HEX >= 0x03030000
    if (cause) {
#else
    if (cause && cause != Py_None) {
#endif
        PyObject *fixed_cause;
        if (cause == Py_None) {
            fixed_cause = NULL;
        } else if (PyExceptionClass_Check(cause)) {
            fixed_cause = PyObject_CallObject(cause, NULL);
            if (fixed_cause == NULL)
                goto bad;
        } else if (PyExceptionInstance_Check(cause)) {
            fixed_cause = cause;
            Py_INCREF(fixed_cause);
        } else {
            PyErr_SetString(PyExc_TypeError,
                            "exception causes must derive from "
                            "BaseException");
            goto bad;
        }
        PyException_SetCause(value, fixed_cause);
    }
    PyErr_SetObject(type, value);
    if (tb) {
        PyThreadState *tstate = PyThreadState_GET();
        PyObject* tmp_tb = tstate->curexc_traceback;
        if (tb != tmp_tb) {
            Py_INCREF(tb);
            tstate->curexc_traceback = tb;
            Py_XDECREF(tmp_tb);
        }
    }
bad:
    Py_XDECREF(owned_instance);
    return;
}
#endif

static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
    PyObject *result;
#if CYTHON_COMPILING_IN_CPYTHON
    result = PyDict_GetItem(__pyx_d, name);
    if (result) {
        Py_INCREF(result);
    } else {
#else
    result = PyObject_GetItem(__pyx_d, name);
    if (!result) {
        PyErr_Clear();
#endif
        result = __Pyx_GetBuiltinName(name);
    }
    return result;
}

static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    PyObject *ob = PyCapsule_New(vtable, 0, 0);
#else
    PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
#endif
    if (!ob)
        goto bad;
    if (PyDict_SetItem(dict, __pyx_n_s____pyx_vtable__, ob) < 0)
        goto bad;
    Py_DECREF(ob);
    return 0;
bad:
    Py_XDECREF(ob);
    return -1;
}

static void* __Pyx_GetVtable(PyObject *dict) {
    void* ptr;
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#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    ptr = PyCapsule_GetPointer(ob, 0);
#else
    ptr = PyCObject_AsVoidPtr(ob);
#endif
    if (!ptr && !PyErr_Occurred())
        PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
    Py_DECREF(ob);
    return ptr;
bad:
    Py_XDECREF(ob);
    return NULL;
}

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;
}

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

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 */
