/* Generated by Cython 0.19.1 on Wed Jun 28 05:40:04 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__platypusutils
#define __PYX_HAVE_API__platypusutils
#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[] = {
  "platypusutils.pyx",
  "fastafile.pxd",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
  "htslibWrapper.pxd",
  "variant.pxd",
  "cwindow.pxd",
  "chaplotype.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_7variant_VariantCandidateGenerator;
struct __pyx_obj_10chaplotype_Haplotype;
struct __pyx_obj_9fastafile_FastaFile;
struct __pyx_obj_7cwindow_ReadArray;
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_9fastafile_FastaIndex;
struct __pyx_obj_13htslibWrapper_ReadIterator;
struct __pyx_obj_7cwindow_bamReadBuffer;
struct __pyx_obj_7variant_Variant;
struct __pyx_t_13htslibWrapper_cAlignedRead;
typedef struct __pyx_t_13htslibWrapper_cAlignedRead __pyx_t_13htslibWrapper_cAlignedRead;
struct __pyx_opt_args_13htslibWrapper_7Samfile__open;

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

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

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

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


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


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


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


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


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


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


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


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



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

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


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

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


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

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


/* "chaplotype.pxd":14
 * 
 * @cython.final
 * cdef class Haplotype:             # <<<<<<<<<<<<<<
 *     cdef:
 *         bytes refName
 */

struct __pyx_vtabstruct_10chaplotype_Haplotype {
  double *(*alignReads)(struct __pyx_obj_10chaplotype_Haplotype *, int, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **, int);
  double (*alignSingleRead)(struct __pyx_obj_10chaplotype_Haplotype *, __pyx_t_13htslibWrapper_cAlignedRead *, int);
  char *(*getReferenceSequence)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args);
  char *(*getMutatedSequence)(struct __pyx_obj_10chaplotype_Haplotype *);
  char *(*getShortHaplotypeSequence)(struct __pyx_obj_10chaplotype_Haplotype *);
  PyObject *(*vcfINFO)(struct __pyx_obj_10chaplotype_Haplotype *);
  PyObject *(*getSequenceContext)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
  int (*homopolymerLengthForOneVariant)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *);
  PyObject *(*homopolymerLengths)(struct __pyx_obj_10chaplotype_Haplotype *);
  void (*annotateWithGapOpen)(struct __pyx_obj_10chaplotype_Haplotype *);
};
static struct __pyx_vtabstruct_10chaplotype_Haplotype *__pyx_vtabptr_10chaplotype_Haplotype;


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

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


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

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


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

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


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

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


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

struct __pyx_vtabstruct_7variant_VariantCandidateGenerator {
  void (*addVariantToList)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_7variant_Variant *);
  void (*getSnpCandidatesFromReadSegment)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *, char *, char *, int, int, int, int, int);
  void (*getVariantCandidatesFromSingleRead)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead *);
  void (*addCandidatesFromReads)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_13htslibWrapper_cAlignedRead **, __pyx_t_13htslibWrapper_cAlignedRead **);
  PyObject *(*getCandidates)(struct __pyx_obj_7variant_VariantCandidateGenerator *, int);
};
static struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtabptr_7variant_VariantCandidateGenerator;
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     (ob)->ob_type == &PyFrozenSet_Type)
#define PySet_New(iterable) \
    PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL)
#define Pyx_PyFrozenSet_New(iterable) \
    PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL)
#define PySet_Size(anyset) \
    PyObject_Size((anyset))
#define PySet_Contains(anyset, key) \
    PySequence_Contains((anyset), (key))
#define PySet_Pop(set) \
    PyObject_CallMethod(set, (char *)"pop", NULL)
static CYTHON_INLINE int PySet_Clear(PyObject *set) {
    PyObject *ret = PyObject_CallMethod(set, (char *)"clear", NULL);
    if (!ret) return -1;
    Py_DECREF(ret); return 0;
}
static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) {
    PyObject *ret = PyObject_CallMethod(set, (char *)"discard", (char *)"O", key);
    if (!ret) return -1;
    Py_DECREF(ret); return 0;
}
static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
    PyObject *ret = PyObject_CallMethod(set, (char *)"add", (char *)"O", key);
    if (!ret) return -1;
    Py_DECREF(ret); return 0;
}
#endif /* PyAnySet_CheckExact (<= Py2.4) */
#endif /* < Py2.5  */

#define __Pyx_GetItemInt(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
    (((size) <= sizeof(Py_ssize_t)) ? \
    __Pyx_GetItemInt_Fast(o, i, is_list, wraparound, boundscheck) : \
    __Pyx_GetItemInt_Generic(o, to_py_func(i)))
#define __Pyx_GetItemInt_List(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
    (((size) <= sizeof(Py_ssize_t)) ? \
    __Pyx_GetItemInt_List_Fast(o, i, wraparound, boundscheck) : \
    __Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func, is_list, wraparound, boundscheck) \
    (((size) <= sizeof(Py_ssize_t)) ? \
    __Pyx_GetItemInt_Tuple_Fast(o, i, wraparound, boundscheck) : \
    __Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                     int is_list, int wraparound, int boundscheck);

static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
        PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
        PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
        int has_cstart, int has_cstop, int wraparound);

#define __Pyx_PyNumber_Power2(a, b) PyNumber_Power(a, b, Py_None)

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

static CYTHON_INLINE unsigned long __Pyx_abs_long(long x) {
    if (unlikely(x == -LONG_MAX-1))
        return ((unsigned long)LONG_MAX) + 1U;
    return (unsigned long) labs(x);
}

static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);

static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);

static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);

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

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

#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
    PyObject *value;
    value = PyDict_GetItemWithError(d, key);
    if (unlikely(!value)) {
        if (!PyErr_Occurred()) {
            PyObject* args = PyTuple_Pack(1, key);
            if (likely(args))
                PyErr_SetObject(PyExc_KeyError, args);
            Py_XDECREF(args);
        }
        return NULL;
    }
    Py_INCREF(value);
    return value;
}
#else
    #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif

static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
    int result = PySequence_Contains(seq, item);
    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}

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

static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);

#if PY_MAJOR_VERSION >= 3
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d); /*proto*/
#else
#define __Pyx_PyDict_Values(d) PyDict_Values(d)
#endif

#define __Pyx_SetItemInt(o, i, v, size, to_py_func, is_list, wraparound, boundscheck) \
    (((size) <= sizeof(Py_ssize_t)) ? \
    __Pyx_SetItemInt_Fast(o, i, v, is_list, wraparound, boundscheck) : \
    __Pyx_SetItemInt_Generic(o, to_py_func(i), v))
static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
                                               int is_list, int wraparound, int boundscheck);

#include <string.h>

static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
    PyObject *method, *result = NULL;
    if (unlikely(!args)) return NULL;
    method = __Pyx_PyObject_GetAttrStr(obj, method_name);
    if (unlikely(!method)) goto bad;
    result = PyObject_Call(method, args, NULL);
    Py_DECREF(method);
bad:
    Py_DECREF(args);
    return result;
}
#define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \
    __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3))
#define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \
    __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2))
#define __Pyx_PyObject_CallMethod1(obj, name, arg1) \
    __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1))
#define __Pyx_PyObject_CallMethod0(obj, name) \
    __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple))

static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/

static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
                                             int is_tuple, int has_known_size, int decref_tuple);

static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
                                                   Py_ssize_t* p_orig_length, int* p_is_dict);
static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
                                              PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);

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

static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/

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

static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);

static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);

static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);

static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);

static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);

static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);

static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);

static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);

static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);

static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);

static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);

static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);

static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);

static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);

static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);

static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);

static int __Pyx_check_binary_version(void);

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

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

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

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

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

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

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

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

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


/* Module declarations from 'cython' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from 'cpython' */

/* Module declarations from 'htslibWrapper' */
static PyTypeObject *__pyx_ptype_13htslibWrapper_Samfile = 0;
static PyTypeObject *__pyx_ptype_13htslibWrapper_ReadIterator = 0;
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReverse(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsPaired(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsProperPair(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsDuplicate(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsUnmapped(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_MateIsReverse(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsQCFail(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsReadOne(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE int __pyx_f_13htslibWrapper_Read_IsSecondaryAlignment(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static void (*__pyx_f_13htslibWrapper_compressRead)(__pyx_t_13htslibWrapper_cAlignedRead *, char *, int, int, int, int); /*proto*/

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

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

/* Module declarations from 'chaplotype' */
static PyTypeObject *__pyx_ptype_10chaplotype_Haplotype = 0;

/* Module declarations from 'platypusutils' */
static double __pyx_v_13platypusutils_PI;
static double __pyx_v_13platypusutils_mLTOT;
static int __pyx_v_13platypusutils_CIGAR_M;
static int __pyx_v_13platypusutils_CIGAR_I;
static int __pyx_v_13platypusutils_CIGAR_D;
static int __pyx_v_13platypusutils_CIGAR_N;
static int __pyx_v_13platypusutils_CIGAR_S;
static double __pyx_f_13platypusutils_logFactorial(int); /*proto*/
static double __pyx_f_13platypusutils_betaBinomialCDF(int, int, int, int); /*proto*/
static PyObject *__pyx_f_13platypusutils_pruned_read_start_end(PyObject *, int, int, int __pyx_skip_dispatch); /*proto*/
static PyObject *__pyx_f_13platypusutils_pruned_ref_start_end(PyObject *, int, int, int __pyx_skip_dispatch); /*proto*/
static double __pyx_f_13platypusutils_logBetaFunction(int, int); /*proto*/
static double __pyx_f_13platypusutils_threeFTwo(int, int, int, int); /*proto*/
static PyObject *__pyx_f_13platypusutils_mergeQueries(PyObject *); /*proto*/
#define __Pyx_MODULE_NAME "platypusutils"
int __pyx_module_is_main_platypusutils = 0;

/* Implementation of 'platypusutils' */
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_StandardError;
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_round;
static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_Exception;
static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_pf_13platypusutils_expandedOpen(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_path, PyObject *__pyx_v_mode); /* proto */
static PyObject *__pyx_pf_13platypusutils_2Open(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fileName, PyObject *__pyx_v_mode, PyObject *__pyx_v_compressLevel); /* proto */
static PyObject *__pyx_pf_13platypusutils_4isIndexable(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fileName); /* proto */
static PyObject *__pyx_pf_13platypusutils_6getSampleNamesAndLoadIterators(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_bamFileNames, CYTHON_UNUSED PyObject *__pyx_v_regions, PyObject *__pyx_v_options); /* proto */
static PyObject *__pyx_pf_13platypusutils_8getBAMFileNamesFromTextFile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fileName); /* proto */
static PyObject *__pyx_pf_13platypusutils_10betaFunction(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, PyObject *__pyx_v_y); /* proto */
static PyObject *__pyx_pf_13platypusutils_12betaPDF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_alpha, PyObject *__pyx_v_beta, PyObject *__pyx_v_x); /* proto */
static PyObject *__pyx_pf_13platypusutils_14poch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, PyObject *__pyx_v_n); /* proto */
static PyObject *__pyx_pf_13platypusutils_16logPoch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, PyObject *__pyx_v_n); /* proto */
static PyObject *__pyx_pf_13platypusutils_18py_betaBinomialCDF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_k, PyObject *__pyx_v_n, PyObject *__pyx_v_alpha, PyObject *__pyx_v_beta); /* proto */
static PyObject *__pyx_pf_13platypusutils_20nPermutations(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nObjects, PyObject *__pyx_v_nChosen); /* proto */
static PyObject *__pyx_pf_13platypusutils_22nCombinations(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nObjects, PyObject *__pyx_v_nChosen); /* proto */
static PyObject *__pyx_pf_13platypusutils_24nPermutationsWithReplacement(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nObjects, PyObject *__pyx_v_nChosen); /* proto */
static PyObject *__pyx_pf_13platypusutils_26nCombinationsWithReplacement(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nObjects, PyObject *__pyx_v_nChosen); /* proto */
static PyObject *__pyx_pf_13platypusutils_28pruned_read_start_end(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read, int __pyx_v_minq, int __pyx_v_minAnchor); /* proto */
static PyObject *__pyx_pf_13platypusutils_30pruned_ref_start_end(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read, int __pyx_v_minq, int __pyx_v_minAnchor); /* proto */
static PyObject *__pyx_pf_13platypusutils_32getRegions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_options); /* proto */
static char __pyx_k_1[] = ".gz";
static char __pyx_k_3[] = ".GZ";
static char __pyx_k_5[] = ".bam";
static char __pyx_k_6[] = ".cram";
static char __pyx_k_9[] = "Input file %s is not a BAM/CRAM file";
static char __pyx_k_10[] = "Found multiple read group tags in file %s";
static char __pyx_k_11[] = "Found multiple samples in BAM file %s";
static char __pyx_k_12[] = "Samples are %s";
static char __pyx_k_13[] = "No sample information in RG tag in file %s";
static char __pyx_k_14[] = "Adding sample name %s, using BAM RG:SM tag in file %s";
static char __pyx_k_15[] = "Error in BAM header sample parsing. Error was \n%s\n";
static char __pyx_k_16[] = "/";
static char __pyx_k_19[] = "Adding sample name %s, from BAM file %s";
static char __pyx_k_20[] = "There is one sample in each BAM file. No merging is required";
static char __pyx_k_22[] = "Something is screwy here";
static char __pyx_k_23[] = "%s:%s-%s";
static char __pyx_k_24[] = "No data could be retrieved for sample %s in file %s in region %s";
static char __pyx_k_25[] = "Loaded %s reads in region %s:%s-%s";
static char __pyx_k_26[] = "Too many reads (%s) in region %s:%s-%s. Quitting now. Either reduce --bufferSize or increase --maxReads.";
static char __pyx_k_27[] = "There are %s broken pairs in BAM %s in region %s:%s-%s";
static char __pyx_k_28[] = "Querying broken mates %s:%s-%s";
static char __pyx_k_29[] = "Variants %s and %s are out of order. This should never happen.";
static char __pyx_k_30[] = "Variants out of order in haplotype!";
static char __pyx_k_31[] = "Variant %s not correctly normalised. \nRef = %s\nHap = %s";
static char __pyx_k_32[] = "";
static char __pyx_k_35[] = "Old pos = %s new pos = %s";
static char __pyx_k_36[] = "New variant in standard format %s is broken";
static char __pyx_k_37[] = "Original variant was %s";
static char __pyx_k_38[] = "Error in variant conversion to standard format";
static char __pyx_k_39[] = "Could not left-normalise variant %s. Using position as reported in BAM";
static char __pyx_k_40[] = "\n";
static char __pyx_k_44[] = ".bz2";
static char __pyx_k_46[] = ".bgz";
static char __pyx_k_48[] = "Reference file-name (%s) looks like a compressed file-name. Please un-compress the reference FASTA file before running Platypus";
static char __pyx_k_49[] = "Invalid reference FASTA file supplied";
static char __pyx_k_50[] = ".fai";
static char __pyx_k_52[] = ".txt";
static char __pyx_k_54[] = "Interpreting --regions argument (%s) as a text file with regions in the format chr:start-end";
static char __pyx_k_55[] = ":";
static char __pyx_k_57[] = "-";
static char __pyx_k_61[] = ".bed";
static char __pyx_k_63[] = "Interpreting --regions argument (%s) as a BED file with regions in the format chr\tstart\tend";
static char __pyx_k_64[] = "\t";
static char __pyx_k_66[] = "Could not parse line in regions file (%s). Skipping...";
static char __pyx_k_67[] = "Line was %s";
static char __pyx_k_69[] = "Loaded regions from BAM header, SQ tags";
static char __pyx_k_71[] = "Loading regions from FASTA index datas";
static char __pyx_k_75[] = "Input region (%s) is too long. Try again";
static char __pyx_k_76[] = "Invalid input region: %s";
static char __pyx_k_77[] = "Platypus found no regions to search. Check that you are using the correct reference FASTA file or have specified the 'regions' argument correctly";
static char __pyx_k_79[] = "The following regions will be searched: %s";
static char __pyx_k_80[] = "%s regions will be searched";
static char __pyx_k_81[] = "Reference sequence %s is not represented in reference fasta file. Skipping this sequence";
static char __pyx_k_82[] = "Skipping region %s, as start co-ord (%s) is > region length (%s)";
static char __pyx_k_83[] = "The following genomic regions will be searched: %s";
static char __pyx_k_84[] = "\nSome utility functions and constants that don't belong anywhere\nelse.\n";
static char __pyx_k_85[] = "0.8.1.1";
static char __pyx_k_89[] = "/home/chapmanb/bio/Platypus/src/cython/platypusutils.pyx";
static char __pyx_k_96[] = "getSampleNamesAndLoadIterators";
static char __pyx_k_99[] = "getBAMFileNamesFromTextFile";
static char __pyx_k__d[] = "d";
static char __pyx_k__e[] = "e";
static char __pyx_k__i[] = "i";
static char __pyx_k__k[] = "k";
static char __pyx_k__n[] = "n";
static char __pyx_k__r[] = "r";
static char __pyx_k__x[] = "x";
static char __pyx_k__y[] = "y";
static char __pyx_k_116[] = "nPermutationsWithReplacement";
static char __pyx_k_119[] = "nCombinationsWithReplacement";
static char __pyx_k__ID[] = "ID";
static char __pyx_k__LN[] = "LN";
static char __pyx_k__RG[] = "RG";
static char __pyx_k__SM[] = "SM";
static char __pyx_k__SN[] = "SN";
static char __pyx_k__SQ[] = "SQ";
static char __pyx_k__os[] = "os";
static char __pyx_k__pi[] = "pi";
static char __pyx_k__Log[] = "Log";
static char __pyx_k__end[] = "end";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__tag[] = "tag";
static char __pyx_k__zip[] = "zip";
static char __pyx_k__Open[] = "Open";
static char __pyx_k__beta[] = "beta";
static char __pyx_k__cols[] = "cols";
static char __pyx_k__file[] = "file";
static char __pyx_k__gzip[] = "gzip";
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static char __pyx_k__line[] = "line";
static char __pyx_k__math[] = "math";
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static char __pyx_k__open[] = "open";
static char __pyx_k__path[] = "path";
static char __pyx_k__poch[] = "poch";
static char __pyx_k__qual[] = "qual";
static char __pyx_k__read[] = "read";
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static char __pyx_k__alpha[] = "alpha";
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static char __pyx_k__parseNCBI[] = "parseNCBI";
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static char __pyx_k__verbosity[] = "verbosity";
static char __pyx_k____import__[] = "__import__";
static char __pyx_k__bufferSize[] = "bufferSize";
static char __pyx_k__expanduser[] = "expanduser";
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static char __pyx_k__fileCaching[] = "fileCaching";
static char __pyx_k__isIndexable[] = "isIndexable";
static char __pyx_k__qualBinSize[] = "qualBinSize";
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static char __pyx_k__samplesByID[] = "samplesByID";
static char __pyx_k__theTextFile[] = "theTextFile";
static char __pyx_k__bamFileNames[] = "bamFileNames";
static char __pyx_k__betaFunction[] = "betaFunction";
static char __pyx_k__expandedOpen[] = "expandedOpen";
static char __pyx_k__finalRegions[] = "finalRegions";
static char __pyx_k__logNumerator[] = "logNumerator";
static char __pyx_k__samplesByBAM[] = "samplesByBAM";
static char __pyx_k__samplesInBAM[] = "samplesInBAM";
static char __pyx_k__StandardError[] = "StandardError";
static char __pyx_k__compressLevel[] = "compressLevel";
static char __pyx_k__compressReads[] = "compressReads";
static char __pyx_k__nCombinations[] = "nCombinations";
static char __pyx_k__nPermutations[] = "nPermutations";
static char __pyx_k__platypusutils[] = "platypusutils";
static char __pyx_k__readGroupTags[] = "readGroupTags";
static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__";
static char __pyx_k__logDenominator[] = "logDenominator";
static char __pyx_k__PLATYPUS_VERSION[] = "PLATYPUS_VERSION";
static char __pyx_k__py_betaBinomialCDF[] = "py_betaBinomialCDF";
static char __pyx_k__assembleBrokenPairs[] = "assembleBrokenPairs";
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static PyObject *__pyx_n_s__bamFile;
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static PyObject *__pyx_n_s__bamFiles;
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static PyObject *__pyx_n_s__betaFunction;
static PyObject *__pyx_n_s__betaPDF;
static PyObject *__pyx_n_s__bufferSize;
static PyObject *__pyx_n_s__chrom;
static PyObject *__pyx_n_s__cigar;
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  int __pyx_v_windowMin;
  int __pyx_v_windowMax;
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  int __pyx_v_index;
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  int __pyx_v_newPos;
  char __pyx_v_refChar;
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  int __pyx_v_insStart;
  int __pyx_v_delStart;
  int __pyx_v_lenNewAdded;
  int __pyx_v_lenNewRemoved;
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  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
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  char *__pyx_t_13;
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 *     of sequence, then report the original position in the BAM.
 *     """
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 *     cdef int nRemoved = variant.nRemoved
 * 
 */
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  /* "platypusutils.pyx":812
 *     """
 *     cdef int nAdded   = variant.nAdded
 *     cdef int nRemoved = variant.nRemoved             # <<<<<<<<<<<<<<
 * 
 *     if nAdded == nRemoved or nAdded > 0 and nRemoved > 0:
 */
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  /* "platypusutils.pyx":814
 *     cdef int nRemoved = variant.nRemoved
 * 
 *     if nAdded == nRemoved or nAdded > 0 and nRemoved > 0:             # <<<<<<<<<<<<<<
 *         # Only left normalise indels
 *         return variant
 */
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    /* "platypusutils.pyx":816
 *     if nAdded == nRemoved or nAdded > 0 and nRemoved > 0:
 *         # Only left normalise indels
 *         return variant             # <<<<<<<<<<<<<<
 * 
 *     # Hack. Leave variants alone if they occur at the extreme left end of the contigs, otherwise
 */
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    goto __pyx_L3;
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  __pyx_L3:;

  /* "platypusutils.pyx":820
 *     # Hack. Leave variants alone if they occur at the extreme left end of the contigs, otherwise
 *     # we run out of sequence.
 *     if variant.refPos < 100:             # <<<<<<<<<<<<<<
 *         return variant
 * 
 */
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    /* "platypusutils.pyx":821
 *     # we run out of sequence.
 *     if variant.refPos < 100:
 *         return variant             # <<<<<<<<<<<<<<
 * 
 *     # We look at the reference for this many bases either side of the variant, so that we can adjust its position
 */
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    goto __pyx_L4;
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  __pyx_L4:;

  /* "platypusutils.pyx":825
 *     # We look at the reference for this many bases either side of the variant, so that we can adjust its position
 *     # accordingly, if there are homopolymers etc.
 *     cdef int window    = max(nAdded, nRemoved) + maxReadLength             # <<<<<<<<<<<<<<
 *     cdef int seqMax    = refFile.refs[variant.refName].SeqLength - 1
 *     cdef int windowMin = max(1, variant.refPos - window)
 */
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 *     # accordingly, if there are homopolymers etc.
 *     cdef int window    = max(nAdded, nRemoved) + maxReadLength
 *     cdef int seqMax    = refFile.refs[variant.refName].SeqLength - 1             # <<<<<<<<<<<<<<
 *     cdef int windowMin = max(1, variant.refPos - window)
 *     cdef int windowMax = min(variant.refPos + window, seqMax)
 */
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    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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  __pyx_v_seqMax = __pyx_t_7;

  /* "platypusutils.pyx":827
 *     cdef int window    = max(nAdded, nRemoved) + maxReadLength
 *     cdef int seqMax    = refFile.refs[variant.refName].SeqLength - 1
 *     cdef int windowMin = max(1, variant.refPos - window)             # <<<<<<<<<<<<<<
 *     cdef int windowMax = min(variant.refPos + window, seqMax)
 * 
 */
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  __pyx_v_windowMin = __pyx_t_11;

  /* "platypusutils.pyx":828
 *     cdef int seqMax    = refFile.refs[variant.refName].SeqLength - 1
 *     cdef int windowMin = max(1, variant.refPos - window)
 *     cdef int windowMax = min(variant.refPos + window, seqMax)             # <<<<<<<<<<<<<<
 * 
 *     cdef bytes bytesRefSeq = refFile.getSequence(variant.refName, windowMin, windowMax)
 */
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  __pyx_v_windowMax = __pyx_t_6;

  /* "platypusutils.pyx":830
 *     cdef int windowMax = min(variant.refPos + window, seqMax)
 * 
 *     cdef bytes bytesRefSeq = refFile.getSequence(variant.refName, windowMin, windowMax)             # <<<<<<<<<<<<<<
 *     cdef bytes bytesHapSeq = bytesRefSeq[0 : (variant.refPos - windowMin) + 1]
 * 
 */
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  __pyx_t_9 = 0;

  /* "platypusutils.pyx":831
 * 
 *     cdef bytes bytesRefSeq = refFile.getSequence(variant.refName, windowMin, windowMax)
 *     cdef bytes bytesHapSeq = bytesRefSeq[0 : (variant.refPos - windowMin) + 1]             # <<<<<<<<<<<<<<
 * 
 *     bytesHapSeq += variant.added
 */
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    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
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  __pyx_v_bytesHapSeq = ((PyObject*)__pyx_t_9);
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  /* "platypusutils.pyx":833
 *     cdef bytes bytesHapSeq = bytesRefSeq[0 : (variant.refPos - windowMin) + 1]
 * 
 *     bytesHapSeq += variant.added             # <<<<<<<<<<<<<<
 *     bytesHapSeq += bytesRefSeq[(variant.refPos - windowMin + nRemoved) + 1:]
 * 
 */
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  /* "platypusutils.pyx":834
 * 
 *     bytesHapSeq += variant.added
 *     bytesHapSeq += bytesRefSeq[(variant.refPos - windowMin + nRemoved) + 1:]             # <<<<<<<<<<<<<<
 * 
 *     # This will invariably happen at the end of chromosomes, e.g. MT
 */
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 * 
 *     # This will invariably happen at the end of chromosomes, e.g. MT
 *     if bytesHapSeq[-1] != bytesRefSeq[-1] and windowMax != seqMax:             # <<<<<<<<<<<<<<
 *         raise StandardError, "Variant %s not correctly normalised. \nRef = %s\nHap = %s" %(variant, bytesRefSeq, bytesHapSeq)
 * 
 */
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    /* "platypusutils.pyx":838
 *     # This will invariably happen at the end of chromosomes, e.g. MT
 *     if bytesHapSeq[-1] != bytesRefSeq[-1] and windowMax != seqMax:
 *         raise StandardError, "Variant %s not correctly normalised. \nRef = %s\nHap = %s" %(variant, bytesRefSeq, bytesHapSeq)             # <<<<<<<<<<<<<<
 * 
 *     cdef char* refSequence = bytesRefSeq
 */
    __pyx_t_12 = PyTuple_New(3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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    __Pyx_GIVEREF(((PyObject *)__pyx_v_variant));
    __Pyx_INCREF(((PyObject *)__pyx_v_bytesRefSeq));
    PyTuple_SET_ITEM(__pyx_t_12, 1, ((PyObject *)__pyx_v_bytesRefSeq));
    __Pyx_GIVEREF(((PyObject *)__pyx_v_bytesRefSeq));
    __Pyx_INCREF(((PyObject *)__pyx_v_bytesHapSeq));
    PyTuple_SET_ITEM(__pyx_t_12, 2, ((PyObject *)__pyx_v_bytesHapSeq));
    __Pyx_GIVEREF(((PyObject *)__pyx_v_bytesHapSeq));
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  /* "platypusutils.pyx":840
 *         raise StandardError, "Variant %s not correctly normalised. \nRef = %s\nHap = %s" %(variant, bytesRefSeq, bytesHapSeq)
 * 
 *     cdef char* refSequence = bytesRefSeq             # <<<<<<<<<<<<<<
 *     cdef char* hapSequence = bytesHapSeq
 * 
 */
  __pyx_t_13 = __Pyx_PyObject_AsString(((PyObject *)__pyx_v_bytesRefSeq)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  /* "platypusutils.pyx":841
 * 
 *     cdef char* refSequence = bytesRefSeq
 *     cdef char* hapSequence = bytesHapSeq             # <<<<<<<<<<<<<<
 * 
 *     cdef int lenRef = len(refSequence)
 */
  __pyx_t_13 = __Pyx_PyObject_AsString(((PyObject *)__pyx_v_bytesHapSeq)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  /* "platypusutils.pyx":843
 *     cdef char* hapSequence = bytesHapSeq
 * 
 *     cdef int lenRef = len(refSequence)             # <<<<<<<<<<<<<<
 *     cdef int lenHap = len(hapSequence)
 * 
 */
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  /* "platypusutils.pyx":844
 * 
 *     cdef int lenRef = len(refSequence)
 *     cdef int lenHap = len(hapSequence)             # <<<<<<<<<<<<<<
 * 
 *     cdef int index        = 0
 */
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  /* "platypusutils.pyx":846
 *     cdef int lenHap = len(hapSequence)
 * 
 *     cdef int index        = 0             # <<<<<<<<<<<<<<
 *     cdef int minLenRefHap = 0
 * 
 */
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  /* "platypusutils.pyx":847
 * 
 *     cdef int index        = 0
 *     cdef int minLenRefHap = 0             # <<<<<<<<<<<<<<
 * 
 *     minLenRefHap = lenRef if lenRef < lenHap else lenHap
 */
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  /* "platypusutils.pyx":849
 *     cdef int minLenRefHap = 0
 * 
 *     minLenRefHap = lenRef if lenRef < lenHap else lenHap             # <<<<<<<<<<<<<<
 * 
 *     # First loop forwards to find out how far to the right we can push it
 */
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  /* "platypusutils.pyx":852
 * 
 *     # First loop forwards to find out how far to the right we can push it
 *     for index from 0 <= index < minLenRefHap:             # <<<<<<<<<<<<<<
 *         if hapSequence[index] != refSequence[index]:
 *             break;
 */
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    /* "platypusutils.pyx":853
 *     # First loop forwards to find out how far to the right we can push it
 *     for index from 0 <= index < minLenRefHap:
 *         if hapSequence[index] != refSequence[index]:             # <<<<<<<<<<<<<<
 *             break;
 * 
 */
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      /* "platypusutils.pyx":854
 *     for index from 0 <= index < minLenRefHap:
 *         if hapSequence[index] != refSequence[index]:
 *             break;             # <<<<<<<<<<<<<<
 * 
 *     cdef int maxPos = windowMin + index + nRemoved
 */
      goto __pyx_L7_break;
      goto __pyx_L8;
    }
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/* "htslibWrapper.pxd":265
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 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
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 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 */
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 */

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

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 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
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 */
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/* "htslibWrapper.pxd":274
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 * 
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 */

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 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
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 * 
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 * 
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 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
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 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
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 *     file._open('r', loadIndex=True)             # <<<<<<<<<<<<<<
 *     finalRegions = []
 *     regions = []
 */
  __pyx_k_tuple_51 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__r)); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));

  /* "platypusutils.pyx":969
 * 
 *         # Text file with regions in format chr:start-end
 *         if options.regions[0].endswith(".txt"):             # <<<<<<<<<<<<<<
 * 
 *             logger.info("Interpreting --regions argument (%s) as a text file with regions in the format chr:start-end" %(options.regions[0]))
 */
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  __Pyx_GOTREF(__pyx_k_tuple_53);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));

  /* "platypusutils.pyx":975
 *             with Open(options.regions[0], 'r') as theFile:
 *                 for line in theFile:
 *                     chrom,region = line.rsplit(":", 1)             # <<<<<<<<<<<<<<
 *                     start = int(region.split("-")[0])-1
 *                     end = int(region.split("-")[1])
 */
  __pyx_k_tuple_56 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_55), __pyx_int_1); if (unlikely(!__pyx_k_tuple_56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_56));

  /* "platypusutils.pyx":976
 *                 for line in theFile:
 *                     chrom,region = line.rsplit(":", 1)
 *                     start = int(region.split("-")[0])-1             # <<<<<<<<<<<<<<
 *                     end = int(region.split("-")[1])
 * 
 */
  __pyx_k_tuple_58 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_57)); if (unlikely(!__pyx_k_tuple_58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_58));

  /* "platypusutils.pyx":977
 *                     chrom,region = line.rsplit(":", 1)
 *                     start = int(region.split("-")[0])-1
 *                     end = int(region.split("-")[1])             # <<<<<<<<<<<<<<
 * 
 *                     regions.append( (chrom,start,end) )
 */
  __pyx_k_tuple_59 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_57)); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));

  /* "platypusutils.pyx":973
 *             logger.info("Interpreting --regions argument (%s) as a text file with regions in the format chr:start-end" %(options.regions[0]))
 * 
 *             with Open(options.regions[0], 'r') as theFile:             # <<<<<<<<<<<<<<
 *                 for line in theFile:
 *                     chrom,region = line.rsplit(":", 1)
 */
  __pyx_k_tuple_60 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_60));

  /* "platypusutils.pyx":982
 * 
 *         # BED file with regions in format chr\start\tend
 *         elif options.regions[0].endswith(".bed"):             # <<<<<<<<<<<<<<
 * 
 *             logger.info("Interpreting --regions argument (%s) as a BED file with regions in the format chr\tstart\tend" %(options.regions[0]))
 */
  __pyx_k_tuple_62 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_61)); if (unlikely(!__pyx_k_tuple_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_62));

  /* "platypusutils.pyx":989
 *                 for line in theFile:
 *                     try:
 *                         cols = line.split("\t")             # <<<<<<<<<<<<<<
 *                         chrom = cols[0]
 *                         start = int(cols[1])
 */
  __pyx_k_tuple_65 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));

  /* "platypusutils.pyx":986
 *             logger.info("Interpreting --regions argument (%s) as a BED file with regions in the format chr\tstart\tend" %(options.regions[0]))
 * 
 *             with Open(options.regions[0], 'r') as theFile:             # <<<<<<<<<<<<<<
 *                 for line in theFile:
 *                     try:
 */
  __pyx_k_tuple_68 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_68);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));

  /* "platypusutils.pyx":1004
 *             header = file.header
 *             regions = [ (d['SN'], 0, d['LN']) for d in header['SQ'] ]
 *             logger.debug("Loaded regions from BAM header, SQ tags")             # <<<<<<<<<<<<<<
 *         except Exception:
 *             logger.debug("Loading regions from FASTA index datas")
 */
  __pyx_k_tuple_70 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_69)); if (unlikely(!__pyx_k_tuple_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_70);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_70));

  /* "platypusutils.pyx":1006
 *             logger.debug("Loaded regions from BAM header, SQ tags")
 *         except Exception:
 *             logger.debug("Loading regions from FASTA index datas")             # <<<<<<<<<<<<<<
 * 
 *             for region,regionTuple in refFile.refs.iteritems():
 */
  __pyx_k_tuple_72 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_71)); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_72);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));

  /* "platypusutils.pyx":1014
 *         for region in options.regions:
 * 
 *             split = region.rsplit(":", 1)             # <<<<<<<<<<<<<<
 *             chrom = bytes(split[0])
 * 
 */
  __pyx_k_tuple_73 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_55), __pyx_int_1); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73));

  /* "platypusutils.pyx":1018
 * 
 *             if len( split ) == 2 :
 *                 [ start, end ] = split[1].split("-")             # <<<<<<<<<<<<<<
 *                 regions.append((chrom,int(start)-1,int(end)))
 * 
 */
  __pyx_k_tuple_74 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_57)); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_74);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));

  /* "platypusutils.pyx":1041
 * 
 *     if len(regions) == 0:
 *         logger.error("Platypus found no regions to search. Check that you are using the correct reference FASTA file or have specified the 'regions' argument correctly")             # <<<<<<<<<<<<<<
 *     elif len(regions) < 100:
 *         logger.debug("The following regions will be searched: %s" %(regions))
 */
  __pyx_k_tuple_78 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_77)); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));

  /* "platypusutils.pyx":40
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_k_tuple_86 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__Log)); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_86);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));

  /* "platypusutils.pyx":66
 * ###################################################################################################
 * 
 * def expandedOpen(path, mode):             # <<<<<<<<<<<<<<
 *     try:
 *         return open(path, mode)
 */
  __pyx_k_tuple_87 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__path), ((PyObject *)__pyx_n_s__mode)); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_87);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
  __pyx_k_codeobj_88 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_87, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__expandedOpen, 66, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":72
 *         return open(os.path.expanduser(path), mode)
 * 
 * def Open(fileName, mode, compressLevel=9):             # <<<<<<<<<<<<<<
 *     """
 *     Function that allows transparent usage of dictzip, gzip and ordinary files
 */
  __pyx_k_tuple_90 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__fileName), ((PyObject *)__pyx_n_s__mode), ((PyObject *)__pyx_n_s__compressLevel), ((PyObject *)__pyx_n_s__fileDir)); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_90));
  __pyx_k_codeobj_91 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_90, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__Open, 72, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":87
 * ###################################################################################################
 * 
 * def isIndexable(fileName):             # <<<<<<<<<<<<<<
 *     return fileName.lower().endswith((".bam", ".cram"))
 * 
 */
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_92));
  __pyx_k_codeobj_93 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_92, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__isIndexable, 87, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":92
 * ###################################################################################################
 * 
 * def getSampleNamesAndLoadIterators(bamFileNames, regions, options):             # <<<<<<<<<<<<<<
 *     """
 *     Return a list of all the sample labels in the BAM files.
 */
  __pyx_k_tuple_94 = PyTuple_Pack(18, ((PyObject *)__pyx_n_s__bamFileNames), ((PyObject *)__pyx_n_s__regions), ((PyObject *)__pyx_n_s__options), ((PyObject *)__pyx_n_s__samples), ((PyObject *)__pyx_n_s__samplesByID), ((PyObject *)__pyx_n_s__samplesByBAM), ((PyObject *)__pyx_n_s__bamFiles), ((PyObject *)__pyx_n_s__nFiles), ((PyObject *)__pyx_n_s__bamFile), ((PyObject *)__pyx_n_s__index), ((PyObject *)__pyx_n_s__fileName), ((PyObject *)__pyx_n_s__theHeader), ((PyObject *)__pyx_n_s__readGroupTags), ((PyObject *)__pyx_n_s__samplesInBAM), ((PyObject *)__pyx_n_s__tag), ((PyObject *)__pyx_n_s__sampleName), ((PyObject *)__pyx_n_s__e), ((PyObject *)__pyx_n_s__x)); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94));
  __pyx_k_codeobj_95 = (PyObject*)__Pyx_PyCode_New(3, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_94, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s_96, 92, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_95)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":160
 * ###################################################################################################
 * 
 * def getBAMFileNamesFromTextFile(fileName):             # <<<<<<<<<<<<<<
 *     """
 *     Reads a list of BAM file names from a text file
 */
  __pyx_k_tuple_97 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__fileName), ((PyObject *)__pyx_n_s__fileNames), ((PyObject *)__pyx_n_s__theTextFile), ((PyObject *)__pyx_n_s__line)); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
  __pyx_k_codeobj_98 = (PyObject*)__Pyx_PyCode_New(1, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_97, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s_99, 160, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":197
 * ###################################################################################################
 * 
 * def betaFunction(x,y):             # <<<<<<<<<<<<<<
 *     """
 *     For the special case of positive integers, the beta function is
 */
  __pyx_k_tuple_100 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__x), ((PyObject *)__pyx_n_s__y), ((PyObject *)__pyx_n_s__logNumerator), ((PyObject *)__pyx_n_s__logDenominator)); if (unlikely(!__pyx_k_tuple_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_100));
  __pyx_k_codeobj_101 = (PyObject*)__Pyx_PyCode_New(2, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_100, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__betaFunction, 197, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":223
 * ###################################################################################################
 * 
 * def betaPDF(alpha, beta, x):             # <<<<<<<<<<<<<<
 *     """
 *     The probability density function of a beta distribution.
 */
  __pyx_k_tuple_102 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__alpha), ((PyObject *)__pyx_n_s__beta), ((PyObject *)__pyx_n_s__x)); if (unlikely(!__pyx_k_tuple_102)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_102));
  __pyx_k_codeobj_103 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_102, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__betaPDF, 223, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":231
 * ###################################################################################################
 * 
 * def poch(x, n):             # <<<<<<<<<<<<<<
 *     """
 *     The pochhammer symbol.
 */
  __pyx_k_tuple_104 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__x), ((PyObject *)__pyx_n_s__n), ((PyObject *)__pyx_n_s__answer), ((PyObject *)__pyx_n_s__i)); if (unlikely(!__pyx_k_tuple_104)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_104));
  __pyx_k_codeobj_105 = (PyObject*)__Pyx_PyCode_New(2, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_104, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__poch, 231, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_105)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":247
 * ###################################################################################################
 * 
 * def logPoch(x,n):             # <<<<<<<<<<<<<<
 *     """
 *     Natural logarithm of the pochhammer symbol
 */
  __pyx_k_tuple_106 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__x), ((PyObject *)__pyx_n_s__n), ((PyObject *)__pyx_n_s__answer), ((PyObject *)__pyx_n_s__i)); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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  __pyx_k_codeobj_107 = (PyObject*)__Pyx_PyCode_New(2, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_106, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__logPoch, 247, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_107)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":298
 * ###################################################################################################
 * 
 * def py_betaBinomialCDF(k, n, alpha, beta):             # <<<<<<<<<<<<<<
 *     """
 *     Thin Python wrapper.
 */
  __pyx_k_tuple_108 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__k), ((PyObject *)__pyx_n_s__n), ((PyObject *)__pyx_n_s__alpha), ((PyObject *)__pyx_n_s__beta)); if (unlikely(!__pyx_k_tuple_108)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_108);
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  __pyx_k_codeobj_109 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_108, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_89, __pyx_n_s__py_betaBinomialCDF, 298, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_109)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "platypusutils.pyx":341
 * ###################################################################################################
 * 
 * def nPermutations(nObjects, nChosen):             # <<<<<<<<<<<<<<
 *     """
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                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
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#if CYTHON_COMPILING_IN_PYPY
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        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
        if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
            PyObject *r = PyTuple_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    } else {
        PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
        if (likely(m && m->sq_item)) {
            if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
                Py_ssize_t l = m->sq_length(o);
                if (likely(l >= 0)) {
                    i += l;
                } else {
                    if (PyErr_ExceptionMatches(PyExc_OverflowError))
                        PyErr_Clear();
                    else
                        return NULL;
                }
            }
            return m->sq_item(o, i);
        }
    }
#else
    if (is_list || PySequence_Check(o)) {
        return PySequence_GetItem(o, i);
    }
#endif
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}

static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
        PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
        PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
        int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
    PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
    if (likely(ms && ms->sq_slice)) {
        if (!has_cstart) {
            if (_py_start && (*_py_start != Py_None)) {
                cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
                if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
            } else
                cstart = 0;
        }
        if (!has_cstop) {
            if (_py_stop && (*_py_stop != Py_None)) {
                cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
                if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
            } else
                cstop = PY_SSIZE_T_MAX;
        }
        if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
            Py_ssize_t l = ms->sq_length(obj);
            if (likely(l >= 0)) {
                if (cstop < 0) {
                    cstop += l;
                    if (cstop < 0) cstop = 0;
                }
                if (cstart < 0) {
                    cstart += l;
                    if (cstart < 0) cstart = 0;
                }
            } else {
                if (PyErr_ExceptionMatches(PyExc_OverflowError))
                    PyErr_Clear();
                else
                    goto bad;
            }
        }
        return ms->sq_slice(obj, cstart, cstop);
    }
#endif
    mp = Py_TYPE(obj)->tp_as_mapping;
    if (likely(mp && mp->mp_subscript))
#endif
    {
        PyObject* result;
        PyObject *py_slice, *py_start, *py_stop;
        if (_py_slice) {
            py_slice = *_py_slice;
        } else {
            PyObject* owned_start = NULL;
            PyObject* owned_stop = NULL;
            if (_py_start) {
                py_start = *_py_start;
            } else {
                if (has_cstart) {
                    owned_start = py_start = PyInt_FromSsize_t(cstart);
                    if (unlikely(!py_start)) goto bad;
                } else
                    py_start = Py_None;
            }
            if (_py_stop) {
                py_stop = *_py_stop;
            } else {
                if (has_cstop) {
                    owned_stop = py_stop = PyInt_FromSsize_t(cstop);
                    if (unlikely(!py_stop)) {
                        Py_XDECREF(owned_start);
                        goto bad;
                    }
                } else
                    py_stop = Py_None;
            }
            py_slice = PySlice_New(py_start, py_stop, Py_None);
            Py_XDECREF(owned_start);
            Py_XDECREF(owned_stop);
            if (unlikely(!py_slice)) goto bad;
        }
#if CYTHON_COMPILING_IN_CPYTHON
        result = mp->mp_subscript(obj, py_slice);
#else
        result = PyObject_GetItem(obj, py_slice);
#endif
        if (!_py_slice) {
            Py_DECREF(py_slice);
        }
        return result;
    }
    PyErr_Format(PyExc_TypeError,
        "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
bad:
    return NULL;
}

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 CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
    PyErr_Format(PyExc_ValueError,
                 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}

static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
    PyErr_Format(PyExc_ValueError,
                 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
                 index, (index == 1) ? "" : "s");
}

static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
    PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
}

static CYTHON_INLINE int __Pyx_IterFinish(void) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyThreadState *tstate = PyThreadState_GET();
    PyObject* exc_type = tstate->curexc_type;
    if (unlikely(exc_type)) {
        if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
            PyObject *exc_value, *exc_tb;
            exc_value = tstate->curexc_value;
            exc_tb = tstate->curexc_traceback;
            tstate->curexc_type = 0;
            tstate->curexc_value = 0;
            tstate->curexc_traceback = 0;
            Py_DECREF(exc_type);
            Py_XDECREF(exc_value);
            Py_XDECREF(exc_tb);
            return 0;
        } else {
            return -1;
        }
    }
    return 0;
#else
    if (unlikely(PyErr_Occurred())) {
        if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
            PyErr_Clear();
            return 0;
        } else {
            return -1;
        }
    }
    return 0;
#endif
}

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

static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
    if (unlikely(!type)) {
        PyErr_Format(PyExc_SystemError, "Missing type object");
        return 0;
    }
    if (likely(PyObject_TypeCheck(obj, type)))
        return 1;
    PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
                 Py_TYPE(obj)->tp_name, type->tp_name);
    return 0;
}

static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
    PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}

#if PY_MAJOR_VERSION >= 3
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d) {
    return PyObject_CallMethodObjArgs(d, __pyx_n_s__values, NULL);
}
#endif

static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
    int r;
    if (!j) return -1;
    r = PyObject_SetItem(o, j, v);
    Py_DECREF(j);
    return r;
}
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
                                               int is_list, int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (is_list || PyList_CheckExact(o)) {
        Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
        if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
            PyObject* old = PyList_GET_ITEM(o, n);
            Py_INCREF(v);
            PyList_SET_ITEM(o, n, v);
            Py_DECREF(old);
            return 1;
        }
    } else {
        PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
        if (likely(m && m->sq_ass_item)) {
            if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
                Py_ssize_t l = m->sq_length(o);
                if (likely(l >= 0)) {
                    i += l;
                } else {
                    if (PyErr_ExceptionMatches(PyExc_OverflowError))
                        PyErr_Clear();
                    else
                        return -1;
                }
            }
            return m->sq_ass_item(o, i, v);
        }
    }
#else
#if CYTHON_COMPILING_IN_PYPY
    if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) {
#else
    if (is_list || PySequence_Check(o)) {
#endif
        return PySequence_SetItem(o, i, v);
    }
#endif
    return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
}

static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
    if (t == Py_None) {
      __Pyx_RaiseNoneNotIterableError();
    } else if (PyTuple_GET_SIZE(t) < index) {
      __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
    } else {
      __Pyx_RaiseTooManyValuesError(index);
    }
}

static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
                                             int is_tuple, int has_known_size, int decref_tuple) {
    Py_ssize_t index;
    PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
    if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
        iternextfunc iternext;
        iter = PyObject_GetIter(tuple);
        if (unlikely(!iter)) goto bad;
        if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
        iternext = Py_TYPE(iter)->tp_iternext;
        value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
        value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
        if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
        Py_DECREF(iter);
    } else {
        if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
            __Pyx_UnpackTupleError(tuple, 2);
            goto bad;
        }
#if CYTHON_COMPILING_IN_PYPY
        value1 = PySequence_ITEM(tuple, 0);
        if (unlikely(!value1)) goto bad;
        value2 = PySequence_ITEM(tuple, 1);
        if (unlikely(!value2)) goto bad;
#else
        value1 = PyTuple_GET_ITEM(tuple, 0);
        value2 = PyTuple_GET_ITEM(tuple, 1);
        Py_INCREF(value1);
        Py_INCREF(value2);
#endif
        if (decref_tuple) { Py_DECREF(tuple); }
    }
    *pvalue1 = value1;
    *pvalue2 = value2;
    return 0;
unpacking_failed:
    if (!has_known_size && __Pyx_IterFinish() == 0)
        __Pyx_RaiseNeedMoreValuesError(index);
bad:
    Py_XDECREF(iter);
    Py_XDECREF(value1);
    Py_XDECREF(value2);
    if (decref_tuple) { Py_XDECREF(tuple); }
    return -1;
}

static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
                                                   Py_ssize_t* p_orig_length, int* p_source_is_dict) {
    is_dict = is_dict || likely(PyDict_CheckExact(iterable));
    *p_source_is_dict = is_dict;
#if !CYTHON_COMPILING_IN_PYPY
    if (is_dict) {
        *p_orig_length = PyDict_Size(iterable);
        Py_INCREF(iterable);
        return iterable;
    }
#endif
    *p_orig_length = 0;
    if (method_name) {
        PyObject* iter;
        iterable = __Pyx_PyObject_CallMethod0(iterable, method_name);
        if (!iterable)
            return NULL;
#if !CYTHON_COMPILING_IN_PYPY
        if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
            return iterable;
#endif
        iter = PyObject_GetIter(iterable);
        Py_DECREF(iterable);
        return iter;
    }
    return PyObject_GetIter(iterable);
}
static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
                                              PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
    PyObject* next_item;
#if !CYTHON_COMPILING_IN_PYPY
    if (source_is_dict) {
        PyObject *key, *value;
        if (unlikely(orig_length != PyDict_Size(iter_obj))) {
            PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
            return -1;
        }
        if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
            return 0;
        }
        if (pitem) {
            PyObject* tuple = PyTuple_New(2);
            if (unlikely(!tuple)) {
                return -1;
            }
            Py_INCREF(key);
            Py_INCREF(value);
            PyTuple_SET_ITEM(tuple, 0, key);
            PyTuple_SET_ITEM(tuple, 1, value);
            *pitem = tuple;
        } else {
            if (pkey) {
                Py_INCREF(key);
                *pkey = key;
            }
            if (pvalue) {
                Py_INCREF(value);
                *pvalue = value;
            }
        }
        return 1;
    } else if (PyTuple_CheckExact(iter_obj)) {
        Py_ssize_t pos = *ppos;
        if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
        *ppos = pos + 1;
        next_item = PyTuple_GET_ITEM(iter_obj, pos);
        Py_INCREF(next_item);
    } else if (PyList_CheckExact(iter_obj)) {
        Py_ssize_t pos = *ppos;
        if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
        *ppos = pos + 1;
        next_item = PyList_GET_ITEM(iter_obj, pos);
        Py_INCREF(next_item);
    } else
#endif
    {
        next_item = PyIter_Next(iter_obj);
        if (unlikely(!next_item)) {
            return __Pyx_IterFinish();
        }
    }
    if (pitem) {
        *pitem = next_item;
    } else if (pkey && pvalue) {
        if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
            return -1;
    } else if (pkey) {
        *pkey = next_item;
    } else {
        *pvalue = next_item;
    }
    return 1;
}

static void* __Pyx_GetVtable(PyObject *dict) {
    void* ptr;
    PyObject *ob = PyObject_GetItem(dict, __pyx_n_s____pyx_vtable__);
    if (!ob)
        goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(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 CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyThreadState *tstate = PyThreadState_GET();
    *type = tstate->exc_type;
    *value = tstate->exc_value;
    *tb = tstate->exc_traceback;
    Py_XINCREF(*type);
    Py_XINCREF(*value);
    Py_XINCREF(*tb);
#else
    PyErr_GetExcInfo(type, value, tb);
#endif
}
static void __Pyx_ExceptionReset(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->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = type;
    tstate->exc_value = value;
    tstate->exc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
#else
    PyErr_SetExcInfo(type, value, tb);
#endif
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

static int __Pyx_check_binary_version(void) {
    char ctversion[4], rtversion[4];
    PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
    PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
    if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
        char message[200];
        PyOS_snprintf(message, sizeof(message),
                      "compiletime version %s of module '%.100s' "
                      "does not match runtime version %s",
                      ctversion, __Pyx_MODULE_NAME, rtversion);
        #if PY_VERSION_HEX < 0x02050000
        return PyErr_Warn(NULL, message);
        #else
        return PyErr_WarnEx(NULL, message, 1);
        #endif
    }
    return 0;
}

static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    union {
        void (*fp)(void);
        void *p;
    } tmp;
    d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__");
    if (!d) {
        PyErr_Clear();
        d = PyDict_New();
        if (!d)
            goto bad;
        Py_INCREF(d);
        if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0)
            goto bad;
    }
    tmp.fp = f;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
    cobj = PyCapsule_New(tmp.p, sig, 0);
#else
    cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0);
#endif
    if (!cobj)
        goto bad;
    if (PyDict_SetItemString(d, name, cobj) < 0)
        goto bad;
    Py_DECREF(cobj);
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(cobj);
    Py_XDECREF(d);
    return -1;
}

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

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

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

#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 */
