/* Generated by Cython 0.19.1 on Wed Jun 28 05:29:59 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__htslibWrapper
#define __PYX_HAVE_API__htslibWrapper
#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[] = {
  "htslibWrapper.pyx",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_13htslibWrapper_Samfile;
struct __pyx_obj_13htslibWrapper_ReadIterator;
struct __pyx_t_13htslibWrapper_cAlignedRead;
typedef struct __pyx_t_13htslibWrapper_cAlignedRead __pyx_t_13htslibWrapper_cAlignedRead;
struct __pyx_opt_args_13htslibWrapper_7Samfile__open;

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

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

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


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



/* "htslibWrapper.pyx":41
 * ######################################################################
 * 
 * cdef class Samfile:             # <<<<<<<<<<<<<<
 *     """
 *     *(filename, mode='r', referencenames = None, referencelengths = None, text = NULL, header = None)*
 */

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.pyx":291
 *             return result
 * 
 * cdef class ReadIterator:             # <<<<<<<<<<<<<<
 *     """
 *     Iterates over mapped reads in a region.
 */

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;
#ifndef CYTHON_REFNANNY
  #define CYTHON_REFNANNY 0
#endif
#if CYTHON_REFNANNY
  typedef struct {
    void (*INCREF)(void*, PyObject*, int);
    void (*DECREF)(void*, PyObject*, int);
    void (*GOTREF)(void*, PyObject*, int);
    void (*GIVEREF)(void*, PyObject*, int);
    void* (*SetupContext)(const char*, int, const char*);
    void (*FinishContext)(void**);
  } __Pyx_RefNannyAPIStruct;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
  static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
  #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
#ifdef WITH_THREAD
  #define __Pyx_RefNannySetupContext(name, acquire_gil) \
          if (acquire_gil) { \
              PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
              PyGILState_Release(__pyx_gilstate_save); \
          } else { \
              __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
          }
#else
  #define __Pyx_RefNannySetupContext(name, acquire_gil) \
          __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
#endif
  #define __Pyx_RefNannyFinishContext() \
          __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
  #define __Pyx_INCREF(r)  __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_DECREF(r)  __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GOTREF(r)  __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
  #define __Pyx_XINCREF(r)  do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
  #define __Pyx_XDECREF(r)  do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
  #define __Pyx_XGOTREF(r)  do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
  #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
  #define __Pyx_RefNannyDeclarations
  #define __Pyx_RefNannySetupContext(name, acquire_gil)
  #define __Pyx_RefNannyFinishContext()
  #define __Pyx_INCREF(r) Py_INCREF(r)
  #define __Pyx_DECREF(r) Py_DECREF(r)
  #define __Pyx_GOTREF(r)
  #define __Pyx_GIVEREF(r)
  #define __Pyx_XINCREF(r) Py_XINCREF(r)
  #define __Pyx_XDECREF(r) Py_XDECREF(r)
  #define __Pyx_XGOTREF(r)
  #define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
#define __Pyx_CLEAR(r)    do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r)   do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
    PyTypeObject* tp = Py_TYPE(obj);
    if (likely(tp->tp_getattro))
        return tp->tp_getattro(obj, attr_name);
#if PY_MAJOR_VERSION < 3
    if (likely(tp->tp_getattr))
        return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
#endif
    return PyObject_GetAttr(obj, attr_name);
}
#else
#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
#endif

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

static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/

static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
    PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
    const char* function_name); /*proto*/

static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
    Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/

static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/

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

static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/

static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/

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

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
    PyListObject* L = (PyListObject*) list;
    Py_ssize_t len = Py_SIZE(list);
    if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
        Py_INCREF(x);
        PyList_SET_ITEM(list, len, x);
        Py_SIZE(list) = len+1;
        return 0;
    }
    return PyList_Append(list, x);
}
#else
#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif

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);

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_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
    int result = PyDict_Contains(dict, item);
    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}

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 CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x); /*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 void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);

static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);

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

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

static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
    const char *name, int exact); /*proto*/

static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/

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

static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/
#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3
static PyObject* __pyx_print = 0;
static PyObject* __pyx_print_kwargs = 0;
#endif

static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t);

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);

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*/

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 '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_IsCompressed(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetCompressed(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
static void __pyx_f_13htslibWrapper_compressSeq(__pyx_t_13htslibWrapper_cAlignedRead *, char *); /*proto*/
static void __pyx_f_13htslibWrapper_compressQual(__pyx_t_13htslibWrapper_cAlignedRead *, int); /*proto*/
static void __pyx_f_13htslibWrapper_uncompressSeq(__pyx_t_13htslibWrapper_cAlignedRead *, char *); /*proto*/
static void __pyx_f_13htslibWrapper_uncompressQual(__pyx_t_13htslibWrapper_cAlignedRead *); /*proto*/
#define __Pyx_MODULE_NAME "htslibWrapper"
int __pyx_module_is_main_htslibWrapper = 0;

/* Implementation of 'htslibWrapper' */
static PyObject *__pyx_builtin_StandardError;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_range;
static int __pyx_pf_13htslibWrapper_7Samfile___cinit__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_fileName); /* proto */
static void __pyx_pf_13htslibWrapper_7Samfile_2__dealloc__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_4_open(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_mode, PyObject *__pyx_v_loadIndex); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_6fetch(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, char const *__pyx_v_region); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_8close(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_11nreferences___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_10references___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_7lengths___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_4text___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_6header___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static int __pyx_pf_13htslibWrapper_12ReadIterator___cinit__(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_samfile, char const *__pyx_v_region); /* proto */
static void __pyx_pf_13htslibWrapper_12ReadIterator_2__dealloc__(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self); /* proto */
static PyObject *__pyx_tp_new_13htslibWrapper_Samfile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_13htslibWrapper_ReadIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_1[] = "CLEARING INDEX!!!!!!";
static char __pyx_k_3[] = "invalid file opening mode `%s`";
static char __pyx_k_4[] = "Error while opening index for file `%s`. Check that index exists ";
static char __pyx_k_5[] = "BAM file is read-only";
static char __pyx_k_6[] = "Could not open file `%s`. Check that file/path exists.";
static char __pyx_k_7[] = "tid (%s) out of range 0<=tid<%i";
static char __pyx_k_8[] = "Random access query only allowed for BAM/CRAM files.";
static char __pyx_k_9[] = "\n";
static char __pyx_k_11[] = "@";
static char __pyx_k_13[] = "Header line without '@': '%s. Total header text is %s'";
static char __pyx_k_15[] = "\t";
static char __pyx_k_17[] = "header line with invalid type '%s': '%s'";
static char __pyx_k_20[] = ":";
static char __pyx_k_22[] = "unknown field code '%s' in record '%s'";
static char __pyx_k_23[] = "multiple '%s' lines are not permitted";
static char __pyx_k_24[] = "Samfile %s is not open. Cannot read from file.";
static char __pyx_k_25[] = "Cannot retrieve random region from Samfile %s, as it does not have an index";
static char __pyx_k_26[] = "=ACMGRSVTWYHKDBN";
static char __pyx_k_27[] = "Shit 3. Qual = %s";
static char __pyx_k_28[] = "Shit 4!. Qual = %s";
static char __pyx_k_29[] = "Shit 1. Qual = %s. Count = %s!";
static char __pyx_k_30[] = "Shit 2!. Qual = %s. Count = %s";
static char __pyx_k_31[] = "number of :term:`reference` sequences in the file.";
static char __pyx_k_32[] = "tuple with the names of :term:`reference` sequences.";
static char __pyx_k_33[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as :attr:`pysam.Samfile.reference`\n        ";
static char __pyx_k_34[] = "full contents of the :term:`sam file` header as a string.";
static char __pyx_k_35[] = "header information within the :term:`sam file`. The records and fields are returned as\n        a two-level dictionary.\n        ";
static char __pyx_k__r[] = "r";
static char __pyx_k__AH[] = "AH";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__CO[] = "CO";
static char __pyx_k__DS[] = "DS";
static char __pyx_k__DT[] = "DT";
static char __pyx_k__GO[] = "GO";
static char __pyx_k__HD[] = "HD";
static char __pyx_k__ID[] = "ID";
static char __pyx_k__LB[] = "LB";
static char __pyx_k__LN[] = "LN";
static char __pyx_k__M5[] = "M5";
static char __pyx_k__PG[] = "PG";
static char __pyx_k__PI[] = "PI";
static char __pyx_k__PL[] = "PL";
static char __pyx_k__PN[] = "PN";
static char __pyx_k__PP[] = "PP";
static char __pyx_k__PU[] = "PU";
static char __pyx_k__RG[] = "RG";
static char __pyx_k__SM[] = "SM";
static char __pyx_k__SN[] = "SN";
static char __pyx_k__SO[] = "SO";
static char __pyx_k__SP[] = "SP";
static char __pyx_k__SQ[] = "SQ";
static char __pyx_k__UR[] = "UR";
static char __pyx_k__VN[] = "VN";
static char __pyx_k__os[] = "os";
static char __pyx_k__rb[] = "rb";
static char __pyx_k__Log[] = "Log";
static char __pyx_k__end[] = "end";
static char __pyx_k__rbh[] = "rbh";
static char __pyx_k__file[] = "file";
static char __pyx_k__join[] = "join";
static char __pyx_k__mode[] = "mode";
static char __pyx_k__path[] = "path";
static char __pyx_k__text[] = "text";
static char __pyx_k__zlib[] = "zlib";
static char __pyx_k___open[] = "_open";
static char __pyx_k__close[] = "close";
static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__print[] = "print";
static char __pyx_k__range[] = "range";
static char __pyx_k__split[] = "split";
static char __pyx_k__strip[] = "strip";
static char __pyx_k__types[] = "types";
static char __pyx_k__append[] = "append";
static char __pyx_k__exists[] = "exists";
static char __pyx_k__logger[] = "logger";
static char __pyx_k__region[] = "region";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__logging[] = "logging";
static char __pyx_k__samfile[] = "samfile";
static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__fileName[] = "fileName";
static char __pyx_k__getLogger[] = "getLogger";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__loadIndex[] = "loadIndex";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k____import__[] = "__import__";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__StandardError[] = "StandardError";
static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS";
static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__";
static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_11;
static PyObject *__pyx_kp_s_13;
static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_17;
static PyObject *__pyx_kp_s_20;
static PyObject *__pyx_kp_s_22;
static PyObject *__pyx_kp_s_23;
static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_kp_s_25;
static PyObject *__pyx_kp_s_27;
static PyObject *__pyx_kp_s_28;
static PyObject *__pyx_kp_s_29;
static PyObject *__pyx_kp_s_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_4;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_8;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__AH;
static PyObject *__pyx_n_s__AS;
static PyObject *__pyx_n_s__CL;
static PyObject *__pyx_n_s__CN;
static PyObject *__pyx_n_s__CO;
static PyObject *__pyx_n_s__DS;
static PyObject *__pyx_n_s__DT;
static PyObject *__pyx_n_s__GO;
static PyObject *__pyx_n_s__HD;
static PyObject *__pyx_n_s__ID;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__LB;
static PyObject *__pyx_n_s__LN;
static PyObject *__pyx_n_s__Log;
static PyObject *__pyx_n_s__M5;
static PyObject *__pyx_n_s__PG;
static PyObject *__pyx_n_s__PI;
static PyObject *__pyx_n_s__PL;
static PyObject *__pyx_n_s__PN;
static PyObject *__pyx_n_s__PP;
static PyObject *__pyx_n_s__PU;
static PyObject *__pyx_n_s__RG;
static PyObject *__pyx_n_s__SM;
static PyObject *__pyx_n_s__SN;
static PyObject *__pyx_n_s__SO;
static PyObject *__pyx_n_s__SP;
static PyObject *__pyx_n_s__SQ;
static PyObject *__pyx_n_s__StandardError;
static PyObject *__pyx_n_s__UR;
static PyObject *__pyx_n_s__VALID_HEADERS;
static PyObject *__pyx_n_s__VALID_HEADER_FIELDS;
static PyObject *__pyx_n_s__VALID_HEADER_ORDER;
static PyObject *__pyx_n_s__VALID_HEADER_TYPES;
static PyObject *__pyx_n_s__VN;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____import__;
static PyObject *__pyx_n_s____main__;
static PyObject *__pyx_n_s____pyx_vtable__;
static PyObject *__pyx_n_s____test__;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__close;
static PyObject *__pyx_n_s__end;
static PyObject *__pyx_n_s__exists;
static PyObject *__pyx_n_s__fetch;
static PyObject *__pyx_n_s__file;
static PyObject *__pyx_n_s__fileName;
static PyObject *__pyx_n_s__getLogger;
static PyObject *__pyx_n_s__itertools;
static PyObject *__pyx_n_s__join;
static PyObject *__pyx_n_s__loadIndex;
static PyObject *__pyx_n_s__logger;
static PyObject *__pyx_n_s__logging;
static PyObject *__pyx_n_s__mode;
static PyObject *__pyx_n_s__os;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__print;
static PyObject *__pyx_n_s__r;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__rb;
static PyObject *__pyx_n_s__rbh;
static PyObject *__pyx_n_s__region;
static PyObject *__pyx_n_s__samfile;
static PyObject *__pyx_n_s__split;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__strip;
static PyObject *__pyx_n_s__text;
static PyObject *__pyx_n_s__types;
static PyObject *__pyx_n_s__zlib;
static PyObject *__pyx_int_1;
static PyObject *__pyx_k_2;
static PyObject *__pyx_k_slice_14;
static PyObject *__pyx_k_slice_18;
static PyObject *__pyx_k_slice_19;
static PyObject *__pyx_k_tuple_10;
static PyObject *__pyx_k_tuple_12;
static PyObject *__pyx_k_tuple_16;
static PyObject *__pyx_k_tuple_21;
static PyObject *__pyx_k_tuple_36;
static PyObject *__pyx_k_tuple_37;
static PyObject *__pyx_k_tuple_38;
static PyObject *__pyx_k_tuple_39;
static PyObject *__pyx_k_tuple_40;
static PyObject *__pyx_k_tuple_41;

/* Python wrapper */
static int __pyx_pw_13htslibWrapper_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_13htslibWrapper_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_fileName = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fileName,0};
    PyObject* values[1] = {0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fileName)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
    }
    __pyx_v_fileName = values[0];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("htslibWrapper.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile___cinit__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self), __pyx_v_fileName);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":71
 *     access to reads via :meth:`fetch` and :meth:`pileup` is disabled.
 *     """
 *     def __cinit__(self, fileName):             # <<<<<<<<<<<<<<
 *         """
 *         Constructor.
 */

static int __pyx_pf_13htslibWrapper_7Samfile___cinit__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_fileName) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "htslibWrapper.pyx":75
 *         Constructor.
 *         """
 *         self.samfile   = NULL             # <<<<<<<<<<<<<<
 *         self.theHeader = NULL
 *         self.filename = fileName
 */
  __pyx_v_self->samfile = NULL;

  /* "htslibWrapper.pyx":76
 *         """
 *         self.samfile   = NULL
 *         self.theHeader = NULL             # <<<<<<<<<<<<<<
 *         self.filename = fileName
 *         self.index     = NULL
 */
  __pyx_v_self->theHeader = NULL;

  /* "htslibWrapper.pyx":77
 *         self.samfile   = NULL
 *         self.theHeader = NULL
 *         self.filename = fileName             # <<<<<<<<<<<<<<
 *         self.index     = NULL
 *         self.lock      = None
 */
  __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_fileName); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_v_self->filename = __pyx_t_1;

  /* "htslibWrapper.pyx":78
 *         self.theHeader = NULL
 *         self.filename = fileName
 *         self.index     = NULL             # <<<<<<<<<<<<<<
 *         self.lock      = None
 * 
 */
  __pyx_v_self->index = NULL;

  /* "htslibWrapper.pyx":79
 *         self.filename = fileName
 *         self.index     = NULL
 *         self.lock      = None             # <<<<<<<<<<<<<<
 * 
 *     def __dealloc__(self):
 */
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  __Pyx_GOTREF(__pyx_v_self->lock);
  __Pyx_DECREF(__pyx_v_self->lock);
  __pyx_v_self->lock = Py_None;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_AddTraceback("htslibWrapper.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static void __pyx_pw_13htslibWrapper_7Samfile_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_13htslibWrapper_7Samfile_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_13htslibWrapper_7Samfile_2__dealloc__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":81
 *         self.lock      = None
 * 
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         """
 *         Clean up. Here I've pasted the code from several clean-up
 */

static void __pyx_pf_13htslibWrapper_7Samfile_2__dealloc__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "htslibWrapper.pyx":89
 *         # remember: dealloc cannot call other methods
 *         # Note that __del__ is not called.
 *         if self.samfile != NULL:             # <<<<<<<<<<<<<<
 *             sam_close(self.samfile)
 *             self.samfile = NULL
 */
  __pyx_t_1 = ((__pyx_v_self->samfile != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":90
 *         # Note that __del__ is not called.
 *         if self.samfile != NULL:
 *             sam_close(self.samfile)             # <<<<<<<<<<<<<<
 *             self.samfile = NULL
 * 
 */
    sam_close(__pyx_v_self->samfile);

    /* "htslibWrapper.pyx":91
 *         if self.samfile != NULL:
 *             sam_close(self.samfile)
 *             self.samfile = NULL             # <<<<<<<<<<<<<<
 * 
 *         if self.index != NULL:
 */
    __pyx_v_self->samfile = NULL;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":93
 *             self.samfile = NULL
 * 
 *         if self.index != NULL:             # <<<<<<<<<<<<<<
 *             hts_idx_destroy(self.index);
 *             self.index = NULL
 */
  __pyx_t_1 = ((__pyx_v_self->index != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":94
 * 
 *         if self.index != NULL:
 *             hts_idx_destroy(self.index);             # <<<<<<<<<<<<<<
 *             self.index = NULL
 * 
 */
    hts_idx_destroy(__pyx_v_self->index);

    /* "htslibWrapper.pyx":95
 *         if self.index != NULL:
 *             hts_idx_destroy(self.index);
 *             self.index = NULL             # <<<<<<<<<<<<<<
 * 
 *         if self.theHeader != NULL:
 */
    __pyx_v_self->index = NULL;
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":97
 *             self.index = NULL
 * 
 *         if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL
 */
  __pyx_t_1 = ((__pyx_v_self->theHeader != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":98
 * 
 *         if self.theHeader != NULL:
 *             bam_hdr_destroy(self.theHeader)             # <<<<<<<<<<<<<<
 *             self.theHeader = NULL
 * 
 */
    bam_hdr_destroy(__pyx_v_self->theHeader);

    /* "htslibWrapper.pyx":99
 *         if self.theHeader != NULL:
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL             # <<<<<<<<<<<<<<
 * 
 *     cdef void clearHeader(self):
 */
    __pyx_v_self->theHeader = NULL;
    goto __pyx_L5;
  }
  __pyx_L5:;

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":101
 *             self.theHeader = NULL
 * 
 *     cdef void clearHeader(self):             # <<<<<<<<<<<<<<
 *         """
 *         Clear all the header data.
 */

static void __pyx_f_13htslibWrapper_7Samfile_clearHeader(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("clearHeader", 0);

  /* "htslibWrapper.pyx":105
 *         Clear all the header data.
 *         """
 *         if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL
 */
  __pyx_t_1 = ((__pyx_v_self->theHeader != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":106
 *         """
 *         if self.theHeader != NULL:
 *             bam_hdr_destroy(self.theHeader)             # <<<<<<<<<<<<<<
 *             self.theHeader = NULL
 * 
 */
    bam_hdr_destroy(__pyx_v_self->theHeader);

    /* "htslibWrapper.pyx":107
 *         if self.theHeader != NULL:
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL             # <<<<<<<<<<<<<<
 * 
 *     cdef void clearIndex(self):
 */
    __pyx_v_self->theHeader = NULL;
    goto __pyx_L3;
  }
  __pyx_L3:;

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":109
 *             self.theHeader = NULL
 * 
 *     cdef void clearIndex(self):             # <<<<<<<<<<<<<<
 *         print("CLEARING INDEX!!!!!!")
 *         """
 */

static void __pyx_f_13htslibWrapper_7Samfile_clearIndex(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("clearIndex", 0);

  /* "htslibWrapper.pyx":110
 * 
 *     cdef void clearIndex(self):
 *         print("CLEARING INDEX!!!!!!")             # <<<<<<<<<<<<<<
 *         """
 *         Clear all the index file data
 */
  if (__Pyx_PrintOne(0, ((PyObject *)__pyx_kp_s_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":114
 *         Clear all the index file data
 *         """
 *         if self.index != NULL:             # <<<<<<<<<<<<<<
 *             hts_idx_destroy(self.index);
 *             self.index = NULL
 */
  __pyx_t_1 = ((__pyx_v_self->index != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":115
 *         """
 *         if self.index != NULL:
 *             hts_idx_destroy(self.index);             # <<<<<<<<<<<<<<
 *             self.index = NULL
 * 
 */
    hts_idx_destroy(__pyx_v_self->index);

    /* "htslibWrapper.pyx":116
 *         if self.index != NULL:
 *             hts_idx_destroy(self.index);
 *             self.index = NULL             # <<<<<<<<<<<<<<
 * 
 *     cdef int _isBam(self):
 */
    __pyx_v_self->index = NULL;
    goto __pyx_L3;
  }
  __pyx_L3:;

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("htslibWrapper.Samfile.clearIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":118
 *             self.index = NULL
 * 
 *     cdef int _isBam(self):             # <<<<<<<<<<<<<<
 *         return self.samfile.is_bin
 * 
 */

static int __pyx_f_13htslibWrapper_7Samfile__isBam(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("_isBam", 0);

  /* "htslibWrapper.pyx":119
 * 
 *     cdef int _isBam(self):
 *         return self.samfile.is_bin             # <<<<<<<<<<<<<<
 * 
 *     cdef int _isCram(self):
 */
  __pyx_r = __pyx_v_self->samfile->is_bin;
  goto __pyx_L0;

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

/* "htslibWrapper.pyx":121
 *         return self.samfile.is_bin
 * 
 *     cdef int _isCram(self):             # <<<<<<<<<<<<<<
 *         return self.samfile.is_cram
 * 
 */

static int __pyx_f_13htslibWrapper_7Samfile__isCram(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("_isCram", 0);

  /* "htslibWrapper.pyx":122
 * 
 *     cdef int _isCram(self):
 *         return self.samfile.is_cram             # <<<<<<<<<<<<<<
 * 
 *     cdef int _isOpen(self):
 */
  __pyx_r = __pyx_v_self->samfile->is_cram;
  goto __pyx_L0;

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

/* "htslibWrapper.pyx":124
 *         return self.samfile.is_cram
 * 
 *     cdef int _isOpen(self):             # <<<<<<<<<<<<<<
 *         '''return true if samfile has been opened.'''
 *         return self.samfile != NULL
 */

static int __pyx_f_13htslibWrapper_7Samfile__isOpen(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("_isOpen", 0);

  /* "htslibWrapper.pyx":126
 *     cdef int _isOpen(self):
 *         '''return true if samfile has been opened.'''
 *         return self.samfile != NULL             # <<<<<<<<<<<<<<
 * 
 *     cdef _hasIndex(self):
 */
  __pyx_r = (__pyx_v_self->samfile != NULL);
  goto __pyx_L0;

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

/* "htslibWrapper.pyx":128
 *         return self.samfile != NULL
 * 
 *     cdef _hasIndex(self):             # <<<<<<<<<<<<<<
 *         '''return true if samfile has an existing (and opened) index.'''
 *         return self.index != NULL
 */

static PyObject *__pyx_f_13htslibWrapper_7Samfile__hasIndex(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("_hasIndex", 0);

  /* "htslibWrapper.pyx":130
 *     cdef _hasIndex(self):
 *         '''return true if samfile has an existing (and opened) index.'''
 *         return self.index != NULL             # <<<<<<<<<<<<<<
 * 
 *     cdef void openBAMFile(self, mode):
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":132
 *         return self.index != NULL
 * 
 *     cdef void openBAMFile(self, mode):             # <<<<<<<<<<<<<<
 *         """
 *         """
 */

static void __pyx_f_13htslibWrapper_7Samfile_openBAMFile(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_mode) {
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  char const *__pyx_t_5;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("openBAMFile", 0);

  /* "htslibWrapper.pyx":135
 *         """
 *         """
 *         if os.path.exists(self.filename):             # <<<<<<<<<<<<<<
 *             self.samfile   = sam_open(self.filename, mode)
 *             self.theHeader = bam_hdr_init()
 */
  __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_3);
  PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
  __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
  __pyx_t_2 = 0;
  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (__pyx_t_4) {

    /* "htslibWrapper.pyx":136
 *         """
 *         if os.path.exists(self.filename):
 *             self.samfile   = sam_open(self.filename, mode)             # <<<<<<<<<<<<<<
 *             self.theHeader = bam_hdr_init()
 *             self.theHeader = sam_hdr_read(self.samfile);
 */
    __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_v_self->samfile = sam_open(__pyx_v_self->filename, __pyx_t_5);

    /* "htslibWrapper.pyx":137
 *         if os.path.exists(self.filename):
 *             self.samfile   = sam_open(self.filename, mode)
 *             self.theHeader = bam_hdr_init()             # <<<<<<<<<<<<<<
 *             self.theHeader = sam_hdr_read(self.samfile);
 *         else:
 */
    __pyx_v_self->theHeader = bam_hdr_init();

    /* "htslibWrapper.pyx":138
 *             self.samfile   = sam_open(self.filename, mode)
 *             self.theHeader = bam_hdr_init()
 *             self.theHeader = sam_hdr_read(self.samfile);             # <<<<<<<<<<<<<<
 *         else:
 *             self.samfile   = NULL
 */
    __pyx_v_self->theHeader = sam_hdr_read(__pyx_v_self->samfile);
    goto __pyx_L3;
  }
  /*else*/ {

    /* "htslibWrapper.pyx":140
 *             self.theHeader = sam_hdr_read(self.samfile);
 *         else:
 *             self.samfile   = NULL             # <<<<<<<<<<<<<<
 *             self.theHeader = NULL
 * 
 */
    __pyx_v_self->samfile = NULL;

    /* "htslibWrapper.pyx":141
 *         else:
 *             self.samfile   = NULL
 *             self.theHeader = NULL             # <<<<<<<<<<<<<<
 * 
 *     cpdef _open(self, mode, loadIndex=True):
 */
    __pyx_v_self->theHeader = NULL;
  }
  __pyx_L3:;

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_WriteUnraisable("htslibWrapper.Samfile.openBAMFile", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":143
 *             self.theHeader = NULL
 * 
 *     cpdef _open(self, mode, loadIndex=True):             # <<<<<<<<<<<<<<
 *         """
 *         open a sam/bam/cram file.
 */

static PyObject *__pyx_pw_13htslibWrapper_7Samfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_f_13htslibWrapper_7Samfile__open(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_mode, int __pyx_skip_dispatch, struct __pyx_opt_args_13htslibWrapper_7Samfile__open *__pyx_optional_args) {
  PyObject *__pyx_v_loadIndex = __pyx_k_2;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("_open", 0);
  if (__pyx_optional_args) {
    if (__pyx_optional_args->__pyx_n > 0) {
      __pyx_v_loadIndex = __pyx_optional_args->loadIndex;
    }
  }
  /* Check if called by wrapper */
  if (unlikely(__pyx_skip_dispatch)) ;
  /* Check if overridden in Python */
  else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_5_open)) {
      __Pyx_XDECREF(__pyx_r);
      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_2);
      __Pyx_INCREF(__pyx_v_mode);
      PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_mode);
      __Pyx_GIVEREF(__pyx_v_mode);
      __Pyx_INCREF(__pyx_v_loadIndex);
      PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_loadIndex);
      __Pyx_GIVEREF(__pyx_v_loadIndex);
      __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
      __pyx_r = __pyx_t_3;
      __pyx_t_3 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      goto __pyx_L0;
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "htslibWrapper.pyx":150
 *         closed and a new file will be opened.
 *         """
 *         if mode not in ("r", "rb", "rbh"):             # <<<<<<<<<<<<<<
 *             raise StandardError, "invalid file opening mode `%s`" % mode
 * 
 */
  __Pyx_INCREF(__pyx_v_mode);
  __pyx_t_1 = __pyx_v_mode;
  __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (((int)__pyx_t_4)) {
    __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__rb), Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_6 = ((int)__pyx_t_5);
  } else {
    __pyx_t_6 = ((int)__pyx_t_4);
  }
  if (__pyx_t_6) {
    __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__rbh), Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_5 = ((int)__pyx_t_4);
  } else {
    __pyx_t_5 = __pyx_t_6;
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_6 = (__pyx_t_5 != 0);
  if (__pyx_t_6) {

    /* "htslibWrapper.pyx":151
 *         """
 *         if mode not in ("r", "rb", "rbh"):
 *             raise StandardError, "invalid file opening mode `%s`" % mode             # <<<<<<<<<<<<<<
 * 
 *         if self.samfile != NULL:
 */
    __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_3), __pyx_v_mode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_1));
    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_t_1), 0, 0);
    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":153
 *             raise StandardError, "invalid file opening mode `%s`" % mode
 * 
 *         if self.samfile != NULL:             # <<<<<<<<<<<<<<
 *             if loadIndex and self.index == NULL:
 *                 self.index = sam_index_load(self.samfile, self.filename)
 */
  __pyx_t_6 = ((__pyx_v_self->samfile != NULL) != 0);
  if (__pyx_t_6) {

    /* "htslibWrapper.pyx":154
 * 
 *         if self.samfile != NULL:
 *             if loadIndex and self.index == NULL:             # <<<<<<<<<<<<<<
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:
 */
    __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_loadIndex); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    if (__pyx_t_6) {
      __pyx_t_5 = (__pyx_v_self->index == NULL);
      __pyx_t_4 = __pyx_t_5;
    } else {
      __pyx_t_4 = __pyx_t_6;
    }
    if (__pyx_t_4) {

      /* "htslibWrapper.pyx":155
 *         if self.samfile != NULL:
 *             if loadIndex and self.index == NULL:
 *                 self.index = sam_index_load(self.samfile, self.filename)             # <<<<<<<<<<<<<<
 *                 if self.index == NULL:
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 */
      __pyx_v_self->index = sam_index_load(__pyx_v_self->samfile, __pyx_v_self->filename);

      /* "htslibWrapper.pyx":156
 *             if loadIndex and self.index == NULL:
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:             # <<<<<<<<<<<<<<
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 *             return
 */
      __pyx_t_4 = ((__pyx_v_self->index == NULL) != 0);
      if (__pyx_t_4) {

        /* "htslibWrapper.pyx":157
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)             # <<<<<<<<<<<<<<
 *             return
 * 
 */
        __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_1));
        __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_4), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_3));
        __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
        __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_1);
        PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_3));
        __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
        __pyx_t_3 = 0;
        __pyx_t_3 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
        __Pyx_Raise(__pyx_t_3, 0, 0, 0);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        goto __pyx_L6;
      }
      __pyx_L6:;
      goto __pyx_L5;
    }
    __pyx_L5:;

    /* "htslibWrapper.pyx":158
 *                 if self.index == NULL:
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 *             return             # <<<<<<<<<<<<<<
 * 
 *         if mode[0] == "r":
 */
    __Pyx_XDECREF(__pyx_r);
    __pyx_r = Py_None; __Pyx_INCREF(Py_None);
    goto __pyx_L0;
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":160
 *             return
 * 
 *         if mode[0] == "r":             # <<<<<<<<<<<<<<
 *             self.openBAMFile(mode)
 *         else:
 */
  __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong, 0, 0, 0); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (__pyx_t_4) {

    /* "htslibWrapper.pyx":161
 * 
 *         if mode[0] == "r":
 *             self.openBAMFile(mode)             # <<<<<<<<<<<<<<
 *         else:
 *             raise StandardError, "BAM file is read-only"
 */
    ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->openBAMFile(__pyx_v_self, __pyx_v_mode);
    goto __pyx_L7;
  }
  /*else*/ {

    /* "htslibWrapper.pyx":163
 *             self.openBAMFile(mode)
 *         else:
 *             raise StandardError, "BAM file is read-only"             # <<<<<<<<<<<<<<
 * 
 *         if self.samfile == NULL:
 */
    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_kp_s_5), 0, 0);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_L7:;

  /* "htslibWrapper.pyx":165
 *             raise StandardError, "BAM file is read-only"
 * 
 *         if self.samfile == NULL:             # <<<<<<<<<<<<<<
 *             raise IOError("Could not open file `%s`. Check that file/path exists." % self.filename)
 * 
 */
  __pyx_t_4 = ((__pyx_v_self->samfile == NULL) != 0);
  if (__pyx_t_4) {

    /* "htslibWrapper.pyx":166
 * 
 *         if self.samfile == NULL:
 *             raise IOError("Could not open file `%s`. Check that file/path exists." % self.filename)             # <<<<<<<<<<<<<<
 * 
 *         if self._isBam() or self._isCram():
 */
    __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_1));
    __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_6), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_3));
    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
    __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_3));
    __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
    __pyx_t_3 = 0;
    __pyx_t_3 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
    __Pyx_Raise(__pyx_t_3, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    goto __pyx_L8;
  }
  __pyx_L8:;

  /* "htslibWrapper.pyx":168
 *             raise IOError("Could not open file `%s`. Check that file/path exists." % self.filename)
 * 
 *         if self._isBam() or self._isCram():             # <<<<<<<<<<<<<<
 *             # returns NULL if there is no index or index could not be opened
 *             if loadIndex and self.index == NULL:
 */
  __pyx_t_4 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isBam(__pyx_v_self) != 0);
  if (!__pyx_t_4) {
    __pyx_t_6 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0);
    __pyx_t_5 = __pyx_t_6;
  } else {
    __pyx_t_5 = __pyx_t_4;
  }
  if (__pyx_t_5) {

    /* "htslibWrapper.pyx":170
 *         if self._isBam() or self._isCram():
 *             # returns NULL if there is no index or index could not be opened
 *             if loadIndex and self.index == NULL:             # <<<<<<<<<<<<<<
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:
 */
    __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_loadIndex); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    if (__pyx_t_5) {
      __pyx_t_4 = (__pyx_v_self->index == NULL);
      __pyx_t_6 = __pyx_t_4;
    } else {
      __pyx_t_6 = __pyx_t_5;
    }
    if (__pyx_t_6) {

      /* "htslibWrapper.pyx":171
 *             # returns NULL if there is no index or index could not be opened
 *             if loadIndex and self.index == NULL:
 *                 self.index = sam_index_load(self.samfile, self.filename)             # <<<<<<<<<<<<<<
 *                 if self.index == NULL:
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 */
      __pyx_v_self->index = sam_index_load(__pyx_v_self->samfile, __pyx_v_self->filename);

      /* "htslibWrapper.pyx":172
 *             if loadIndex and self.index == NULL:
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:             # <<<<<<<<<<<<<<
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 * 
 */
      __pyx_t_6 = ((__pyx_v_self->index == NULL) != 0);
      if (__pyx_t_6) {

        /* "htslibWrapper.pyx":173
 *                 self.index = sam_index_load(self.samfile, self.filename)
 *                 if self.index == NULL:
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)             # <<<<<<<<<<<<<<
 * 
 *     cdef char* getrname(self, int tid):
 */
        __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_3));
        __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_4), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_1));
        __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
        __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1));
        __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
        __pyx_t_1 = 0;
        __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
        __Pyx_Raise(__pyx_t_1, 0, 0, 0);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        goto __pyx_L11;
      }
      __pyx_L11:;
      goto __pyx_L10;
    }
    __pyx_L10:;
    goto __pyx_L9;
  }
  __pyx_L9:;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("htslibWrapper.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_13htslibWrapper_7Samfile_4_open[] = "\n        open a sam/bam/cram file.\n\n        If _open is called on an existing bamfile, the current file will be\n        closed and a new file will be opened.\n        ";
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_mode = 0;
  PyObject *__pyx_v_loadIndex = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("_open (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__mode,&__pyx_n_s__loadIndex,0};
    PyObject* values[2] = {0,0};
    values[1] = __pyx_k_2;
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__mode)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__loadIndex);
          if (value) { values[1] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_mode = values[0];
    __pyx_v_loadIndex = values[1];
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("htslibWrapper.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_4_open(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self), __pyx_v_mode, __pyx_v_loadIndex);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":143
 *             self.theHeader = NULL
 * 
 *     cpdef _open(self, mode, loadIndex=True):             # <<<<<<<<<<<<<<
 *         """
 *         open a sam/bam/cram file.
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_4_open(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_mode, PyObject *__pyx_v_loadIndex) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  struct __pyx_opt_args_13htslibWrapper_7Samfile__open __pyx_t_2;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("_open", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2.__pyx_n = 1;
  __pyx_t_2.loadIndex = __pyx_v_loadIndex;
  __pyx_t_1 = ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_open(__pyx_v_self, __pyx_v_mode, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":175
 *                     raise IOError("Error while opening index for file `%s`. Check that index exists " % self.filename)
 * 
 *     cdef char* getrname(self, int tid):             # <<<<<<<<<<<<<<
 *         '''
 *         Convert numerical :term:`tid` into :ref:`reference` name.
 */

static char *__pyx_f_13htslibWrapper_7Samfile_getrname(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, int __pyx_v_tid) {
  char *__pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("getrname", 0);

  /* "htslibWrapper.pyx":179
 *         Convert numerical :term:`tid` into :ref:`reference` name.
 *         '''
 *         if not 0 <= tid < self.theHeader.n_targets:             # <<<<<<<<<<<<<<
 *             raise ValueError( "tid (%s) out of range 0<=tid<%i" % (tid, self.theHeader.n_targets))
 * 
 */
  __pyx_t_1 = (0 <= __pyx_v_tid);
  if (__pyx_t_1) {
    __pyx_t_1 = (__pyx_v_tid < __pyx_v_self->theHeader->n_targets);
  }
  __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":180
 *         '''
 *         if not 0 <= tid < self.theHeader.n_targets:
 *             raise ValueError( "tid (%s) out of range 0<=tid<%i" % (tid, self.theHeader.n_targets))             # <<<<<<<<<<<<<<
 * 
 *         return self.theHeader.target_name[tid]
 */
    __pyx_t_3 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->theHeader->n_targets); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
    __Pyx_GIVEREF(__pyx_t_3);
    PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_4);
    __Pyx_GIVEREF(__pyx_t_4);
    __pyx_t_3 = 0;
    __pyx_t_4 = 0;
    __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_4));
    __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
    __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_5);
    PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
    __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
    __pyx_t_4 = 0;
    __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
    __Pyx_Raise(__pyx_t_4, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":182
 *             raise ValueError( "tid (%s) out of range 0<=tid<%i" % (tid, self.theHeader.n_targets))
 * 
 *         return self.theHeader.target_name[tid]             # <<<<<<<<<<<<<<
 * 
 *     cpdef ReadIterator fetch(self, const char *region):
 */
  __pyx_r = (__pyx_v_self->theHeader->target_name[__pyx_v_tid]);
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_WriteUnraisable("htslibWrapper.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":184
 *         return self.theHeader.target_name[tid]
 * 
 *     cpdef ReadIterator fetch(self, const char *region):             # <<<<<<<<<<<<<<
 *         '''
 *         Fetch reads from a specified region.
 */

static PyObject *__pyx_pw_13htslibWrapper_7Samfile_7fetch(PyObject *__pyx_v_self, PyObject *__pyx_arg_region); /*proto*/
static struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_f_13htslibWrapper_7Samfile_fetch(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, char const *__pyx_v_region, int __pyx_skip_dispatch) {
  struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  int __pyx_t_4;
  struct __pyx_opt_args_13htslibWrapper_7Samfile__open __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("fetch", 0);
  /* Check if called by wrapper */
  if (unlikely(__pyx_skip_dispatch)) ;
  /* Check if overridden in Python */
  else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__fetch); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_7fetch)) {
      __Pyx_XDECREF(((PyObject *)__pyx_r));
      __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_region); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(((PyObject *)__pyx_t_2));
      __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_3);
      PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
      __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
      __pyx_t_2 = 0;
      __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_2);
      __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
      if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_13htslibWrapper_ReadIterator))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __pyx_r = ((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_t_2);
      __pyx_t_2 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      goto __pyx_L0;
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "htslibWrapper.pyx":189
 *         '''
 *         # Need to load the index for new queries.
 *         if not self._isOpen():             # <<<<<<<<<<<<<<
 *             self._open('r', loadIndex=True)
 * 
 */
  __pyx_t_4 = ((!(((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isOpen(__pyx_v_self) != 0)) != 0);
  if (__pyx_t_4) {

    /* "htslibWrapper.pyx":190
 *         # Need to load the index for new queries.
 *         if not self._isOpen():
 *             self._open('r', loadIndex=True)             # <<<<<<<<<<<<<<
 * 
 *         if self._isBam() or self._isCram():
 */
    __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_5.__pyx_n = 1;
    __pyx_t_5.loadIndex = __pyx_t_1;
    __pyx_t_2 = ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_open(__pyx_v_self, ((PyObject *)__pyx_n_s__r), 0, &__pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":192
 *             self._open('r', loadIndex=True)
 * 
 *         if self._isBam() or self._isCram():             # <<<<<<<<<<<<<<
 *             return ReadIterator(self, region)
 *         else:
 */
  __pyx_t_4 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isBam(__pyx_v_self) != 0);
  if (!__pyx_t_4) {
    __pyx_t_6 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0);
    __pyx_t_7 = __pyx_t_6;
  } else {
    __pyx_t_7 = __pyx_t_4;
  }
  if (__pyx_t_7) {

    /* "htslibWrapper.pyx":193
 * 
 *         if self._isBam() or self._isCram():
 *             return ReadIterator(self, region)             # <<<<<<<<<<<<<<
 *         else:
 *             raise StandardError, "Random access query only allowed for BAM/CRAM files."
 */
    __Pyx_XDECREF(((PyObject *)__pyx_r));
    __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_region); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
    __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_INCREF(((PyObject *)__pyx_v_self));
    PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self));
    __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
    PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_t_2));
    __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
    __pyx_t_2 = 0;
    __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_13htslibWrapper_ReadIterator)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
    __pyx_r = ((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_t_2);
    __pyx_t_2 = 0;
    goto __pyx_L0;
    goto __pyx_L4;
  }
  /*else*/ {

    /* "htslibWrapper.pyx":195
 *             return ReadIterator(self, region)
 *         else:
 *             raise StandardError, "Random access query only allowed for BAM/CRAM files."             # <<<<<<<<<<<<<<
 * 
 *     cpdef close(self):
 */
    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_kp_s_8), 0, 0);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_L4:;

  __pyx_r = ((struct __pyx_obj_13htslibWrapper_ReadIterator *)Py_None); __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("htslibWrapper.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF((PyObject *)__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_7fetch(PyObject *__pyx_v_self, PyObject *__pyx_arg_region); /*proto*/
static char __pyx_doc_13htslibWrapper_7Samfile_6fetch[] = "\n        Fetch reads from a specified region.\n        ";
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_7fetch(PyObject *__pyx_v_self, PyObject *__pyx_arg_region) {
  char const *__pyx_v_region;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
  assert(__pyx_arg_region); {
    __pyx_v_region = __Pyx_PyObject_AsString(__pyx_arg_region); if (unlikely((!__pyx_v_region) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L3_error:;
  __Pyx_AddTraceback("htslibWrapper.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_6fetch(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self), ((char const *)__pyx_v_region));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":184
 *         return self.theHeader.target_name[tid]
 * 
 *     cpdef ReadIterator fetch(self, const char *region):             # <<<<<<<<<<<<<<
 *         '''
 *         Fetch reads from a specified region.
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_6fetch(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, char const *__pyx_v_region) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("fetch", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = ((PyObject *)((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->fetch(__pyx_v_self, __pyx_v_region, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":197
 *             raise StandardError, "Random access query only allowed for BAM/CRAM files."
 * 
 *     cpdef close(self):             # <<<<<<<<<<<<<<
 *         '''
 *         closes file.
 */

static PyObject *__pyx_pw_13htslibWrapper_7Samfile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_f_13htslibWrapper_7Samfile_close(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, int __pyx_skip_dispatch) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_t_3;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("close", 0);
  /* Check if called by wrapper */
  if (unlikely(__pyx_skip_dispatch)) ;
  /* Check if overridden in Python */
  else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_9close)) {
      __Pyx_XDECREF(__pyx_r);
      __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_r = __pyx_t_2;
      __pyx_t_2 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      goto __pyx_L0;
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "htslibWrapper.pyx":201
 *         closes file.
 *         '''
 *         if not self._isCram():             # <<<<<<<<<<<<<<
 *             if self.samfile != NULL:
 *                 sam_close(self.samfile)
 */
  __pyx_t_3 = ((!(((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0)) != 0);
  if (__pyx_t_3) {

    /* "htslibWrapper.pyx":202
 *         '''
 *         if not self._isCram():
 *             if self.samfile != NULL:             # <<<<<<<<<<<<<<
 *                 sam_close(self.samfile)
 *                 self.samfile = NULL
 */
    __pyx_t_3 = ((__pyx_v_self->samfile != NULL) != 0);
    if (__pyx_t_3) {

      /* "htslibWrapper.pyx":203
 *         if not self._isCram():
 *             if self.samfile != NULL:
 *                 sam_close(self.samfile)             # <<<<<<<<<<<<<<
 *                 self.samfile = NULL
 * 
 */
      sam_close(__pyx_v_self->samfile);

      /* "htslibWrapper.pyx":204
 *             if self.samfile != NULL:
 *                 sam_close(self.samfile)
 *                 self.samfile = NULL             # <<<<<<<<<<<<<<
 * 
 *             if self.index != NULL:
 */
      __pyx_v_self->samfile = NULL;
      goto __pyx_L4;
    }
    __pyx_L4:;

    /* "htslibWrapper.pyx":206
 *                 self.samfile = NULL
 * 
 *             if self.index != NULL:             # <<<<<<<<<<<<<<
 *                 hts_idx_destroy(self.index);
 *                 self.index = NULL
 */
    __pyx_t_3 = ((__pyx_v_self->index != NULL) != 0);
    if (__pyx_t_3) {

      /* "htslibWrapper.pyx":207
 * 
 *             if self.index != NULL:
 *                 hts_idx_destroy(self.index);             # <<<<<<<<<<<<<<
 *                 self.index = NULL
 * 
 */
      hts_idx_destroy(__pyx_v_self->index);

      /* "htslibWrapper.pyx":208
 *             if self.index != NULL:
 *                 hts_idx_destroy(self.index);
 *                 self.index = NULL             # <<<<<<<<<<<<<<
 * 
 *             if self.theHeader != NULL:
 */
      __pyx_v_self->index = NULL;
      goto __pyx_L5;
    }
    __pyx_L5:;

    /* "htslibWrapper.pyx":210
 *                 self.index = NULL
 * 
 *             if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *                 bam_hdr_destroy(self.theHeader)
 *                 self.theHeader = NULL
 */
    __pyx_t_3 = ((__pyx_v_self->theHeader != NULL) != 0);
    if (__pyx_t_3) {

      /* "htslibWrapper.pyx":211
 * 
 *             if self.theHeader != NULL:
 *                 bam_hdr_destroy(self.theHeader)             # <<<<<<<<<<<<<<
 *                 self.theHeader = NULL
 * 
 */
      bam_hdr_destroy(__pyx_v_self->theHeader);

      /* "htslibWrapper.pyx":212
 *             if self.theHeader != NULL:
 *                 bam_hdr_destroy(self.theHeader)
 *                 self.theHeader = NULL             # <<<<<<<<<<<<<<
 * 
 *     property nreferences:
 */
      __pyx_v_self->theHeader = NULL;
      goto __pyx_L6;
    }
    __pyx_L6:;
    goto __pyx_L3;
  }
  __pyx_L3:;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_AddTraceback("htslibWrapper.Samfile.close", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static char __pyx_doc_13htslibWrapper_7Samfile_8close[] = "\n        closes file.\n        ";
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("close (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_8close(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":197
 *             raise StandardError, "Random access query only allowed for BAM/CRAM files."
 * 
 *     cpdef close(self):             # <<<<<<<<<<<<<<
 *         '''
 *         closes file.
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_8close(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("close", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->close(__pyx_v_self, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.close", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_11nreferences___get__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":216
 *     property nreferences:
 *         '''number of :term:`reference` sequences in the file.'''
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             return self.theHeader.n_targets
 * 
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_11nreferences___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":217
 *         '''number of :term:`reference` sequences in the file.'''
 *         def __get__(self):
 *             return self.theHeader.n_targets             # <<<<<<<<<<<<<<
 * 
 *     property references:
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->theHeader->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_10references_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_10references___get__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":221
 *     property references:
 *         """tuple with the names of :term:`reference` sequences."""
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_10references___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_v_t = NULL;
  long __pyx_v_x;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int32_t __pyx_t_2;
  int __pyx_t_3;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":222
 *         """tuple with the names of :term:`reference` sequences."""
 *         def __get__(self):
 *             t = []             # <<<<<<<<<<<<<<
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_name[x])
 */
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_t = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":223
 *         def __get__(self):
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:             # <<<<<<<<<<<<<<
 *                 t.append(self.theHeader.target_name[x])
 *             return tuple(t)
 */
  __pyx_t_2 = __pyx_v_self->theHeader->n_targets;
  for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) {

    /* "htslibWrapper.pyx":224
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_name[x])             # <<<<<<<<<<<<<<
 *             return tuple(t)
 * 
 */
    __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_self->theHeader->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_1));
    __pyx_t_3 = __Pyx_PyList_Append(__pyx_v_t, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
  }

  /* "htslibWrapper.pyx":225
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_name[x])
 *             return tuple(t)             # <<<<<<<<<<<<<<
 * 
 *     property lengths:
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __pyx_r = ((PyObject *)__pyx_t_1);
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_t);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_7lengths___get__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":230
 *         """tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as :attr:`pysam.Samfile.reference`
 *         """
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_7lengths___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_v_t = NULL;
  long __pyx_v_x;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int32_t __pyx_t_2;
  int __pyx_t_3;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":231
 *         """
 *         def __get__(self):
 *             t = []             # <<<<<<<<<<<<<<
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_len[x])
 */
  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_t = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":232
 *         def __get__(self):
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:             # <<<<<<<<<<<<<<
 *                 t.append(self.theHeader.target_len[x])
 *             return tuple(t)
 */
  __pyx_t_2 = __pyx_v_self->theHeader->n_targets;
  for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) {

    /* "htslibWrapper.pyx":233
 *             t = []
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_len[x])             # <<<<<<<<<<<<<<
 *             return tuple(t)
 * 
 */
    __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->theHeader->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = __Pyx_PyList_Append(__pyx_v_t, __pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  }

  /* "htslibWrapper.pyx":234
 *             for x from 0 <= x < self.theHeader.n_targets:
 *                 t.append(self.theHeader.target_len[x])
 *             return tuple(t)             # <<<<<<<<<<<<<<
 * 
 *     property text:
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __pyx_r = ((PyObject *)__pyx_t_1);
  __pyx_t_1 = 0;
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_t);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_4text_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_4text___get__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":238
 *     property text:
 *         '''full contents of the :term:`sam file` header as a string.'''
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             # create a temporary 0-terminated copy
 *             cdef char * t
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_4text___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  char *__pyx_v_t;
  PyObject *__pyx_v_result = 0;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":241
 *             # create a temporary 0-terminated copy
 *             cdef char * t
 *             t = <char*>calloc(self.theHeader.l_text + 1, sizeof(char))             # <<<<<<<<<<<<<<
 *             memcpy(t, self.theHeader.text, self.theHeader.l_text)
 *             cdef bytes result = t
 */
  __pyx_v_t = ((char *)calloc((__pyx_v_self->theHeader->l_text + 1), (sizeof(char))));

  /* "htslibWrapper.pyx":242
 *             cdef char * t
 *             t = <char*>calloc(self.theHeader.l_text + 1, sizeof(char))
 *             memcpy(t, self.theHeader.text, self.theHeader.l_text)             # <<<<<<<<<<<<<<
 *             cdef bytes result = t
 *             free(t)
 */
  memcpy(__pyx_v_t, __pyx_v_self->theHeader->text, __pyx_v_self->theHeader->l_text);

  /* "htslibWrapper.pyx":243
 *             t = <char*>calloc(self.theHeader.l_text + 1, sizeof(char))
 *             memcpy(t, self.theHeader.text, self.theHeader.l_text)
 *             cdef bytes result = t             # <<<<<<<<<<<<<<
 *             free(t)
 *             return result
 */
  __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_t); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __pyx_v_result = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":244
 *             memcpy(t, self.theHeader.text, self.theHeader.l_text)
 *             cdef bytes result = t
 *             free(t)             # <<<<<<<<<<<<<<
 *             return result
 * 
 */
  free(__pyx_v_t);

  /* "htslibWrapper.pyx":245
 *             cdef bytes result = t
 *             free(t)
 *             return result             # <<<<<<<<<<<<<<
 * 
 *     property header:
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(((PyObject *)__pyx_v_result));
  __pyx_r = ((PyObject *)__pyx_v_result);
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_6header_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_6header___get__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":251
 *         a two-level dictionary.
 *         '''
 *         def __get__(self):             # <<<<<<<<<<<<<<
 *             result = {}
 * 
 */

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_6header___get__(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_v_result = NULL;
  PyObject *__pyx_v_t = NULL;
  PyObject *__pyx_v_line = NULL;
  PyObject *__pyx_v_fields = NULL;
  PyObject *__pyx_v_record = NULL;
  PyObject *__pyx_v_x = NULL;
  PyObject *__pyx_v_field = NULL;
  PyObject *__pyx_v_key = NULL;
  PyObject *__pyx_v_value = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_t_2;
  PyObject *__pyx_t_3 = NULL;
  Py_ssize_t __pyx_t_4;
  PyObject *(*__pyx_t_5)(PyObject *);
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  Py_ssize_t __pyx_t_10;
  PyObject *(*__pyx_t_11)(PyObject *);
  PyObject *__pyx_t_12 = NULL;
  PyObject *(*__pyx_t_13)(PyObject *);
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":252
 *         '''
 *         def __get__(self):
 *             result = {}             # <<<<<<<<<<<<<<
 * 
 *             if self.theHeader.text != NULL:
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __pyx_v_result = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":254
 *             result = {}
 * 
 *             if self.theHeader.text != NULL:             # <<<<<<<<<<<<<<
 *                 # convert to python string (note: call self.text to create 0-terminated string)
 *                 t = self.text
 */
  __pyx_t_2 = ((__pyx_v_self->theHeader->text != NULL) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":256
 *             if self.theHeader.text != NULL:
 *                 # convert to python string (note: call self.text to create 0-terminated string)
 *                 t = self.text             # <<<<<<<<<<<<<<
 *                 for line in t.split("\n"):
 *                     if not line.strip(): continue
 */
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_v_t = __pyx_t_1;
    __pyx_t_1 = 0;

    /* "htslibWrapper.pyx":257
 *                 # convert to python string (note: call self.text to create 0-terminated string)
 *                 t = self.text
 *                 for line in t.split("\n"):             # <<<<<<<<<<<<<<
 *                     if not line.strip(): continue
 * 
 */
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_t, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    if (PyList_CheckExact(__pyx_t_3) || PyTuple_CheckExact(__pyx_t_3)) {
      __pyx_t_1 = __pyx_t_3; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
      __pyx_t_5 = NULL;
    } else {
      __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    for (;;) {
      if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
        if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_COMPILING_IN_CPYTHON
        __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        #else
        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        #endif
      } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
        if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
        #if CYTHON_COMPILING_IN_CPYTHON
        __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        #else
        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        #endif
      } else {
        __pyx_t_3 = __pyx_t_5(__pyx_t_1);
        if (unlikely(!__pyx_t_3)) {
          if (PyErr_Occurred()) {
            if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
            else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_3);
      }
      __Pyx_XDECREF(__pyx_v_line);
      __pyx_v_line = __pyx_t_3;
      __pyx_t_3 = 0;

      /* "htslibWrapper.pyx":258
 *                 t = self.text
 *                 for line in t.split("\n"):
 *                     if not line.strip(): continue             # <<<<<<<<<<<<<<
 * 
 *                     if not line.startswith("@"):
 */
      __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_7 = ((!__pyx_t_2) != 0);
      if (__pyx_t_7) {
        goto __pyx_L4_continue;
        goto __pyx_L6;
      }
      __pyx_L6:;

      /* "htslibWrapper.pyx":260
 *                     if not line.strip(): continue
 * 
 *                     if not line.startswith("@"):             # <<<<<<<<<<<<<<
 *                         raise StandardError, "Header line without '@': '%s. Total header text is %s'" % (line,t)
 * 
 */
      __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_3 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_2 = ((!__pyx_t_7) != 0);
      if (__pyx_t_2) {

        /* "htslibWrapper.pyx":261
 * 
 *                     if not line.startswith("@"):
 *                         raise StandardError, "Header line without '@': '%s. Total header text is %s'" % (line,t)             # <<<<<<<<<<<<<<
 * 
 *                     fields = line[1:].split("\t")
 */
        __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_INCREF(__pyx_v_line);
        PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_line);
        __Pyx_GIVEREF(__pyx_v_line);
        __Pyx_INCREF(__pyx_v_t);
        PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_t);
        __Pyx_GIVEREF(__pyx_v_t);
        __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_13), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_6));
        __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
        __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_t_6), 0, 0);
        __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        goto __pyx_L7;
      }
      __pyx_L7:;

      /* "htslibWrapper.pyx":263
 *                         raise StandardError, "Header line without '@': '%s. Total header text is %s'" % (line,t)
 * 
 *                     fields = line[1:].split("\t")             # <<<<<<<<<<<<<<
 *                     record = fields[0]
 *                     assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
 */
      __pyx_t_6 = __Pyx_PyObject_GetSlice(__pyx_v_line, 1, 0, NULL, NULL, &__pyx_k_slice_14, 1, 0, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_3);
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      __pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_16), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __Pyx_XDECREF(__pyx_v_fields);
      __pyx_v_fields = __pyx_t_6;
      __pyx_t_6 = 0;

      /* "htslibWrapper.pyx":264
 * 
 *                     fields = line[1:].split("\t")
 *                     record = fields[0]             # <<<<<<<<<<<<<<
 *                     assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
 * 
 */
      __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_fields, 0, sizeof(long), PyInt_FromLong, 0, 0, 0); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __Pyx_XDECREF(__pyx_v_record);
      __pyx_v_record = __pyx_t_6;
      __pyx_t_6 = 0;

      /* "htslibWrapper.pyx":265
 *                     fields = line[1:].split("\t")
 *                     record = fields[0]
 *                     assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)             # <<<<<<<<<<<<<<
 * 
 *                     # treat comments
 */
      #ifndef CYTHON_WITHOUT_ASSERTIONS
      __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_6, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      if (unlikely(!(__pyx_t_2 != 0))) {
        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __Pyx_INCREF(__pyx_v_record);
        PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_record);
        __Pyx_GIVEREF(__pyx_v_record);
        __Pyx_INCREF(__pyx_v_line);
        PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_line);
        __Pyx_GIVEREF(__pyx_v_line);
        __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_3));
        __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
        PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_3));
        __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      }
      #endif

      /* "htslibWrapper.pyx":268
 * 
 *                     # treat comments
 *                     if record == "CO":             # <<<<<<<<<<<<<<
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))
 */
      __pyx_t_3 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      if (__pyx_t_2) {

        /* "htslibWrapper.pyx":269
 *                     # treat comments
 *                     if record == "CO":
 *                         if record not in result: result[record] = []             # <<<<<<<<<<<<<<
 *                         result[record].append("\t".join( fields[1:]))
 *                         continue
 */
        __pyx_t_2 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __pyx_t_7 = (__pyx_t_2 != 0);
        if (__pyx_t_7) {
          __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_3);
          if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
          goto __pyx_L9;
        }
        __pyx_L9:;

        /* "htslibWrapper.pyx":270
 *                     if record == "CO":
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))             # <<<<<<<<<<<<<<
 *                         continue
 * 
 */
        __pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_kp_s_15), __pyx_n_s__join); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __pyx_t_8 = __Pyx_PyObject_GetSlice(__pyx_v_fields, 1, 0, NULL, NULL, &__pyx_k_slice_18, 1, 0, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_9);
        PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
        __Pyx_GIVEREF(__pyx_t_8);
        __pyx_t_8 = 0;
        __pyx_t_8 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
        __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_3, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_9);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
        __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;

        /* "htslibWrapper.pyx":271
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))
 *                         continue             # <<<<<<<<<<<<<<
 * 
 *                     # the following is clumsy as generators do not work?
 */
        goto __pyx_L4_continue;
        goto __pyx_L8;
      }
      __pyx_L8:;

      /* "htslibWrapper.pyx":274
 * 
 *                     # the following is clumsy as generators do not work?
 *                     x = {}             # <<<<<<<<<<<<<<
 *                     for field in fields[1:]:
 *                         key, value = field.split(":",1)
 */
      __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(((PyObject *)__pyx_t_9));
      __Pyx_XDECREF(((PyObject *)__pyx_v_x));
      __pyx_v_x = ((PyObject*)__pyx_t_9);
      __pyx_t_9 = 0;

      /* "htslibWrapper.pyx":275
 *                     # the following is clumsy as generators do not work?
 *                     x = {}
 *                     for field in fields[1:]:             # <<<<<<<<<<<<<<
 *                         key, value = field.split(":",1)
 *                         if key not in VALID_HEADER_FIELDS[record]:
 */
      __pyx_t_9 = __Pyx_PyObject_GetSlice(__pyx_v_fields, 1, 0, NULL, NULL, &__pyx_k_slice_19, 1, 0, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_9);
      if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
        __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_10 = 0;
        __pyx_t_11 = NULL;
      } else {
        __pyx_t_10 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        __pyx_t_11 = Py_TYPE(__pyx_t_8)->tp_iternext;
      }
      __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
      for (;;) {
        if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) {
          if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
          #if CYTHON_COMPILING_IN_CPYTHON
          __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          #else
          __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          #endif
        } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
          if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
          #if CYTHON_COMPILING_IN_CPYTHON
          __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          #else
          __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          #endif
        } else {
          __pyx_t_9 = __pyx_t_11(__pyx_t_8);
          if (unlikely(!__pyx_t_9)) {
            if (PyErr_Occurred()) {
              if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
              else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
            }
            break;
          }
          __Pyx_GOTREF(__pyx_t_9);
        }
        __Pyx_XDECREF(__pyx_v_field);
        __pyx_v_field = __pyx_t_9;
        __pyx_t_9 = 0;

        /* "htslibWrapper.pyx":276
 *                     x = {}
 *                     for field in fields[1:]:
 *                         key, value = field.split(":",1)             # <<<<<<<<<<<<<<
 *                         if key not in VALID_HEADER_FIELDS[record]:
 *                             raise ValueError("unknown field code '%s' in record '%s'" % (key, record))
 */
        __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_field, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_9);
        __pyx_t_3 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_21), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
        if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
          PyObject* sequence = __pyx_t_3;
          #if CYTHON_COMPILING_IN_CPYTHON
          Py_ssize_t size = Py_SIZE(sequence);
          #else
          Py_ssize_t size = PySequence_Size(sequence);
          #endif
          if (unlikely(size != 2)) {
            if (size > 2) __Pyx_RaiseTooManyValuesError(2);
            else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          }
          #if CYTHON_COMPILING_IN_CPYTHON
          if (likely(PyTuple_CheckExact(sequence))) {
            __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0); 
            __pyx_t_6 = PyTuple_GET_ITEM(sequence, 1); 
          } else {
            __pyx_t_9 = PyList_GET_ITEM(sequence, 0); 
            __pyx_t_6 = PyList_GET_ITEM(sequence, 1); 
          }
          __Pyx_INCREF(__pyx_t_9);
          __Pyx_INCREF(__pyx_t_6);
          #else
          __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_9);
          __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_6);
          #endif
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        } else
        {
          Py_ssize_t index = -1;
          __pyx_t_12 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_12);
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          __pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
          index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L12_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_9);
          index = 1; __pyx_t_6 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_6)) goto __pyx_L12_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_6);
          if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __pyx_t_13 = NULL;
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          goto __pyx_L13_unpacking_done;
          __pyx_L12_unpacking_failed:;
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          __pyx_t_13 = NULL;
          if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __pyx_L13_unpacking_done:;
        }
        __Pyx_XDECREF(__pyx_v_key);
        __pyx_v_key = __pyx_t_9;
        __pyx_t_9 = 0;
        __Pyx_XDECREF(__pyx_v_value);
        __pyx_v_value = __pyx_t_6;
        __pyx_t_6 = 0;

        /* "htslibWrapper.pyx":277
 *                     for field in fields[1:]:
 *                         key, value = field.split(":",1)
 *                         if key not in VALID_HEADER_FIELDS[record]:             # <<<<<<<<<<<<<<
 *                             raise ValueError("unknown field code '%s' in record '%s'" % (key, record))
 *                         x[key] = VALID_HEADER_FIELDS[record][key](value)
 */
        __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __pyx_t_6 = PyObject_GetItem(__pyx_t_3, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __pyx_t_7 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_t_6, Py_NE)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        __pyx_t_2 = (__pyx_t_7 != 0);
        if (__pyx_t_2) {

          /* "htslibWrapper.pyx":278
 *                         key, value = field.split(":",1)
 *                         if key not in VALID_HEADER_FIELDS[record]:
 *                             raise ValueError("unknown field code '%s' in record '%s'" % (key, record))             # <<<<<<<<<<<<<<
 *                         x[key] = VALID_HEADER_FIELDS[record][key](value)
 * 
 */
          __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_6);
          __Pyx_INCREF(__pyx_v_key);
          PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_key);
          __Pyx_GIVEREF(__pyx_v_key);
          __Pyx_INCREF(__pyx_v_record);
          PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_record);
          __Pyx_GIVEREF(__pyx_v_record);
          __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_22), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(((PyObject *)__pyx_t_3));
          __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
          __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_6);
          PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_3));
          __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
          __pyx_t_3 = 0;
          __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_3);
          __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
          __Pyx_Raise(__pyx_t_3, 0, 0, 0);
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          goto __pyx_L14;
        }
        __pyx_L14:;

        /* "htslibWrapper.pyx":279
 *                         if key not in VALID_HEADER_FIELDS[record]:
 *                             raise ValueError("unknown field code '%s' in record '%s'" % (key, record))
 *                         x[key] = VALID_HEADER_FIELDS[record][key](value)             # <<<<<<<<<<<<<<
 * 
 *                     if VALID_HEADER_TYPES[record] == dict:
 */
        __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __pyx_t_6 = PyObject_GetItem(__pyx_t_3, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __pyx_t_3 = PyObject_GetItem(__pyx_t_6, __pyx_v_key); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __Pyx_INCREF(__pyx_v_value);
        PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_value);
        __Pyx_GIVEREF(__pyx_v_value);
        __pyx_t_9 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_9);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
        if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
      }
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;

      /* "htslibWrapper.pyx":281
 *                         x[key] = VALID_HEADER_FIELDS[record][key](value)
 * 
 *                     if VALID_HEADER_TYPES[record] == dict:             # <<<<<<<<<<<<<<
 *                         if record in result:
 *                             raise ValueError( "multiple '%s' lines are not permitted" % record )
 */
      __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_8);
      __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_9);
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      if (__pyx_t_2) {

        /* "htslibWrapper.pyx":282
 * 
 *                     if VALID_HEADER_TYPES[record] == dict:
 *                         if record in result:             # <<<<<<<<<<<<<<
 *                             raise ValueError( "multiple '%s' lines are not permitted" % record )
 *                         result[record] = x
 */
        __pyx_t_2 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __pyx_t_7 = (__pyx_t_2 != 0);
        if (__pyx_t_7) {

          /* "htslibWrapper.pyx":283
 *                     if VALID_HEADER_TYPES[record] == dict:
 *                         if record in result:
 *                             raise ValueError( "multiple '%s' lines are not permitted" % record )             # <<<<<<<<<<<<<<
 *                         result[record] = x
 *                     elif VALID_HEADER_TYPES[record] == list:
 */
          __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_23), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(((PyObject *)__pyx_t_8));
          __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_9);
          PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
          __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
          __pyx_t_8 = 0;
          __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_8);
          __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
          __Pyx_Raise(__pyx_t_8, 0, 0, 0);
          __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          goto __pyx_L16;
        }
        __pyx_L16:;

        /* "htslibWrapper.pyx":284
 *                         if record in result:
 *                             raise ValueError( "multiple '%s' lines are not permitted" % record )
 *                         result[record] = x             # <<<<<<<<<<<<<<
 *                     elif VALID_HEADER_TYPES[record] == list:
 *                         if record not in result: result[record] = []
 */
        if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        goto __pyx_L15;
      }

      /* "htslibWrapper.pyx":285
 *                             raise ValueError( "multiple '%s' lines are not permitted" % record )
 *                         result[record] = x
 *                     elif VALID_HEADER_TYPES[record] == list:             # <<<<<<<<<<<<<<
 *                         if record not in result: result[record] = []
 *                         result[record].append(x)
 */
      __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_8);
      __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_9);
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
      __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      if (__pyx_t_7) {

        /* "htslibWrapper.pyx":286
 *                         result[record] = x
 *                     elif VALID_HEADER_TYPES[record] == list:
 *                         if record not in result: result[record] = []             # <<<<<<<<<<<<<<
 *                         result[record].append(x)
 * 
 */
        __pyx_t_7 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __pyx_t_2 = (__pyx_t_7 != 0);
        if (__pyx_t_2) {
          __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_8);
          if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
          goto __pyx_L17;
        }
        __pyx_L17:;

        /* "htslibWrapper.pyx":287
 *                     elif VALID_HEADER_TYPES[record] == list:
 *                         if record not in result: result[record] = []
 *                         result[record].append(x)             # <<<<<<<<<<<<<<
 * 
 *             return result
 */
        __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_8, ((PyObject *)__pyx_v_x)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_9);
        __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
        __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
        goto __pyx_L15;
      }
      __pyx_L15:;
      __pyx_L4_continue:;
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":289
 *                         result[record].append(x)
 * 
 *             return result             # <<<<<<<<<<<<<<
 * 
 * cdef class ReadIterator:
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(((PyObject *)__pyx_v_result));
  __pyx_r = ((PyObject *)__pyx_v_result);
  goto __pyx_L0;

  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_12);
  __Pyx_AddTraceback("htslibWrapper.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XDECREF(__pyx_v_t);
  __Pyx_XDECREF(__pyx_v_line);
  __Pyx_XDECREF(__pyx_v_fields);
  __Pyx_XDECREF(__pyx_v_record);
  __Pyx_XDECREF(__pyx_v_x);
  __Pyx_XDECREF(__pyx_v_field);
  __Pyx_XDECREF(__pyx_v_key);
  __Pyx_XDECREF(__pyx_v_value);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_13htslibWrapper_12ReadIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_13htslibWrapper_12ReadIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_samfile = 0;
  char const *__pyx_v_region;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__region,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_samfile = ((struct __pyx_obj_13htslibWrapper_Samfile *)values[0]);
    __pyx_v_region = __Pyx_PyObject_AsString(values[1]); if (unlikely((!__pyx_v_region) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("htslibWrapper.ReadIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_13htslibWrapper_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_r = __pyx_pf_13htslibWrapper_12ReadIterator___cinit__(((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_v_self), __pyx_v_samfile, __pyx_v_region);
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":296
 *     """
 * 
 *     def __cinit__(self, Samfile samfile, const char *region):             # <<<<<<<<<<<<<<
 *         """
 *         Constructor.
 */

static int __pyx_pf_13htslibWrapper_12ReadIterator___cinit__(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_samfile, char const *__pyx_v_region) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  samFile *__pyx_t_4;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "htslibWrapper.pyx":301
 *         """
 * 
 *         self.theSamfile  = NULL             # <<<<<<<<<<<<<<
 *         self.theIterator = NULL
 *         self.b           = NULL
 */
  __pyx_v_self->theSamfile = NULL;

  /* "htslibWrapper.pyx":302
 * 
 *         self.theSamfile  = NULL
 *         self.theIterator = NULL             # <<<<<<<<<<<<<<
 *         self.b           = NULL
 * 
 */
  __pyx_v_self->theIterator = NULL;

  /* "htslibWrapper.pyx":303
 *         self.theSamfile  = NULL
 *         self.theIterator = NULL
 *         self.b           = NULL             # <<<<<<<<<<<<<<
 * 
 *         if not samfile._isOpen():
 */
  __pyx_v_self->b = NULL;

  /* "htslibWrapper.pyx":305
 *         self.b           = NULL
 * 
 *         if not samfile._isOpen():             # <<<<<<<<<<<<<<
 *             raise StandardError, "Samfile %s is not open. Cannot read from file." %(samfile.filename)
 * 
 */
  __pyx_t_1 = ((!(((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_samfile->__pyx_vtab)->_isOpen(__pyx_v_samfile) != 0)) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":306
 * 
 *         if not samfile._isOpen():
 *             raise StandardError, "Samfile %s is not open. Cannot read from file." %(samfile.filename)             # <<<<<<<<<<<<<<
 * 
 *         self.theSamfile = samfile.samfile
 */
    __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_samfile->filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
    __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_3));
    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_t_3), 0, 0);
    __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":308
 *             raise StandardError, "Samfile %s is not open. Cannot read from file." %(samfile.filename)
 * 
 *         self.theSamfile = samfile.samfile             # <<<<<<<<<<<<<<
 * 
 *         # Load from BAM by querying index for file off-set
 */
  __pyx_t_4 = __pyx_v_samfile->samfile;
  __pyx_v_self->theSamfile = __pyx_t_4;

  /* "htslibWrapper.pyx":311
 * 
 *         # Load from BAM by querying index for file off-set
 *         if samfile._hasIndex():             # <<<<<<<<<<<<<<
 *             self.theIterator = sam_itr_querys(samfile.index, samfile.theHeader, region)
 *         else:
 */
  __pyx_t_3 = ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_samfile->__pyx_vtab)->_hasIndex(__pyx_v_samfile); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":312
 *         # Load from BAM by querying index for file off-set
 *         if samfile._hasIndex():
 *             self.theIterator = sam_itr_querys(samfile.index, samfile.theHeader, region)             # <<<<<<<<<<<<<<
 *         else:
 *             raise StandardError, "Cannot retrieve random region from Samfile %s, as it does not have an index" %(samfile.filename)
 */
    __pyx_v_self->theIterator = sam_itr_querys(__pyx_v_samfile->index, __pyx_v_samfile->theHeader, __pyx_v_region);
    goto __pyx_L4;
  }
  /*else*/ {

    /* "htslibWrapper.pyx":314
 *             self.theIterator = sam_itr_querys(samfile.index, samfile.theHeader, region)
 *         else:
 *             raise StandardError, "Cannot retrieve random region from Samfile %s, as it does not have an index" %(samfile.filename)             # <<<<<<<<<<<<<<
 * 
 *         self.b = bam_init1()
 */
    __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_samfile->filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_3));
    __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_25), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(((PyObject *)__pyx_t_2));
    __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, ((PyObject *)__pyx_t_2), 0, 0);
    __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":316
 *             raise StandardError, "Cannot retrieve random region from Samfile %s, as it does not have an index" %(samfile.filename)
 * 
 *         self.b = bam_init1()             # <<<<<<<<<<<<<<
 * 
 *     def __dealloc__(self):
 */
  __pyx_v_self->b = bam_init1();

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_AddTraceback("htslibWrapper.ReadIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static void __pyx_pw_13htslibWrapper_12ReadIterator_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
static void __pyx_pw_13htslibWrapper_12ReadIterator_3__dealloc__(PyObject *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
  __pyx_pf_13htslibWrapper_12ReadIterator_2__dealloc__(((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_v_self));
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":318
 *         self.b = bam_init1()
 * 
 *     def __dealloc__(self):             # <<<<<<<<<<<<<<
 *         '''
 *         remember: dealloc cannot call other methods!
 */

static void __pyx_pf_13htslibWrapper_12ReadIterator_2__dealloc__(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("__dealloc__", 0);

  /* "htslibWrapper.pyx":322
 *         remember: dealloc cannot call other methods!
 *         '''
 *         if self.theIterator != NULL:             # <<<<<<<<<<<<<<
 *             sam_itr_destroy(self.theIterator)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->theIterator != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":323
 *         '''
 *         if self.theIterator != NULL:
 *             sam_itr_destroy(self.theIterator)             # <<<<<<<<<<<<<<
 * 
 *         if self.b != NULL:
 */
    sam_itr_destroy(__pyx_v_self->theIterator);
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":325
 *             sam_itr_destroy(self.theIterator)
 * 
 *         if self.b != NULL:             # <<<<<<<<<<<<<<
 *             bam_destroy1(self.b)
 * 
 */
  __pyx_t_1 = ((__pyx_v_self->b != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":326
 * 
 *         if self.b != NULL:
 *             bam_destroy1(self.b)             # <<<<<<<<<<<<<<
 * 
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID):
 */
    bam_destroy1(__pyx_v_self->b);
    goto __pyx_L4;
  }
  __pyx_L4:;

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":328
 *             bam_destroy1(self.b)
 * 
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID):             # <<<<<<<<<<<<<<
 *         cdef bam1_core_t *c = &self.b.core
 *         cdef uint8_t *s     = bam_get_seq(self.b)
 */

static __pyx_t_13htslibWrapper_cAlignedRead *__pyx_f_13htslibWrapper_12ReadIterator_get(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, int __pyx_v_storeRgID, char **__pyx_v_rgID) {
  bam1_core_t *__pyx_v_c;
  uint8_t *__pyx_v_s;
  uint8_t *__pyx_v_q;
  int __pyx_v_lenSeq;
  __pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead;
  char *__pyx_v_seq;
  char *__pyx_v_qual;
  uint8_t *__pyx_v_v;
  char *__pyx_v_tempRgID;
  int __pyx_v_lenRgID;
  int __pyx_v_i;
  PyObject *__pyx_v_readStart = NULL;
  short *__pyx_v_cigarOps;
  uint32_t *__pyx_v_cigar;
  int __pyx_v_cigarFlag;
  PyObject *__pyx_v_cigarFlagLen = NULL;
  __pyx_t_13htslibWrapper_cAlignedRead *__pyx_r;
  __Pyx_RefNannyDeclarations
  int32_t __pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  PyObject *__pyx_t_4 = NULL;
  uint32_t __pyx_t_5;
  short __pyx_t_6;
  int __pyx_t_7;
  int __pyx_t_8;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("get", 0);

  /* "htslibWrapper.pyx":329
 * 
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID):
 *         cdef bam1_core_t *c = &self.b.core             # <<<<<<<<<<<<<<
 *         cdef uint8_t *s     = bam_get_seq(self.b)
 *         cdef uint8_t *q     = bam_get_qual(self.b)
 */
  __pyx_v_c = (&__pyx_v_self->b->core);

  /* "htslibWrapper.pyx":330
 *     cdef cAlignedRead* get(self, int storeRgID, char** rgID):
 *         cdef bam1_core_t *c = &self.b.core
 *         cdef uint8_t *s     = bam_get_seq(self.b)             # <<<<<<<<<<<<<<
 *         cdef uint8_t *q     = bam_get_qual(self.b)
 *         cdef int lenSeq     = c.l_qseq
 */
  __pyx_v_s = bam_get_seq(__pyx_v_self->b);

  /* "htslibWrapper.pyx":331
 *         cdef bam1_core_t *c = &self.b.core
 *         cdef uint8_t *s     = bam_get_seq(self.b)
 *         cdef uint8_t *q     = bam_get_qual(self.b)             # <<<<<<<<<<<<<<
 *         cdef int lenSeq     = c.l_qseq
 * 
 */
  __pyx_v_q = bam_get_qual(__pyx_v_self->b);

  /* "htslibWrapper.pyx":332
 *         cdef uint8_t *s     = bam_get_seq(self.b)
 *         cdef uint8_t *q     = bam_get_qual(self.b)
 *         cdef int lenSeq     = c.l_qseq             # <<<<<<<<<<<<<<
 * 
 *         if lenSeq == 0:
 */
  __pyx_t_1 = __pyx_v_c->l_qseq;
  __pyx_v_lenSeq = __pyx_t_1;

  /* "htslibWrapper.pyx":334
 *         cdef int lenSeq     = c.l_qseq
 * 
 *         if lenSeq == 0:             # <<<<<<<<<<<<<<
 *             return NULL
 * 
 */
  __pyx_t_2 = ((__pyx_v_lenSeq == 0) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":335
 * 
 *         if lenSeq == 0:
 *             return NULL             # <<<<<<<<<<<<<<
 * 
 *         if q[0] == 0xff:
 */
    __pyx_r = NULL;
    goto __pyx_L0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":337
 *             return NULL
 * 
 *         if q[0] == 0xff:             # <<<<<<<<<<<<<<
 *             return NULL
 * 
 */
  __pyx_t_2 = (((__pyx_v_q[0]) == 0xff) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":338
 * 
 *         if q[0] == 0xff:
 *             return NULL             # <<<<<<<<<<<<<<
 * 
 *         cdef cAlignedRead* theRead = <cAlignedRead*>malloc(sizeof(cAlignedRead))
 */
    __pyx_r = NULL;
    goto __pyx_L0;
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":340
 *             return NULL
 * 
 *         cdef cAlignedRead* theRead = <cAlignedRead*>malloc(sizeof(cAlignedRead))             # <<<<<<<<<<<<<<
 *         cdef char* seq             = <char*>malloc((lenSeq + 1) * sizeof(char))
 *         cdef char* qual            = <char*>malloc((lenSeq + 1) * sizeof(char))
 */
  __pyx_v_theRead = ((__pyx_t_13htslibWrapper_cAlignedRead *)malloc((sizeof(__pyx_t_13htslibWrapper_cAlignedRead))));

  /* "htslibWrapper.pyx":341
 * 
 *         cdef cAlignedRead* theRead = <cAlignedRead*>malloc(sizeof(cAlignedRead))
 *         cdef char* seq             = <char*>malloc((lenSeq + 1) * sizeof(char))             # <<<<<<<<<<<<<<
 *         cdef char* qual            = <char*>malloc((lenSeq + 1) * sizeof(char))
 * 
 */
  __pyx_v_seq = ((char *)malloc(((__pyx_v_lenSeq + 1) * (sizeof(char)))));

  /* "htslibWrapper.pyx":342
 *         cdef cAlignedRead* theRead = <cAlignedRead*>malloc(sizeof(cAlignedRead))
 *         cdef char* seq             = <char*>malloc((lenSeq + 1) * sizeof(char))
 *         cdef char* qual            = <char*>malloc((lenSeq + 1) * sizeof(char))             # <<<<<<<<<<<<<<
 * 
 *         assert theRead != NULL
 */
  __pyx_v_qual = ((char *)malloc(((__pyx_v_lenSeq + 1) * (sizeof(char)))));

  /* "htslibWrapper.pyx":344
 *         cdef char* qual            = <char*>malloc((lenSeq + 1) * sizeof(char))
 * 
 *         assert theRead != NULL             # <<<<<<<<<<<<<<
 *         assert seq     != NULL
 *         assert qual    != NULL
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!((__pyx_v_theRead != NULL) != 0))) {
    PyErr_SetNone(PyExc_AssertionError);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  #endif

  /* "htslibWrapper.pyx":345
 * 
 *         assert theRead != NULL
 *         assert seq     != NULL             # <<<<<<<<<<<<<<
 *         assert qual    != NULL
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!((__pyx_v_seq != NULL) != 0))) {
    PyErr_SetNone(PyExc_AssertionError);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  #endif

  /* "htslibWrapper.pyx":346
 *         assert theRead != NULL
 *         assert seq     != NULL
 *         assert qual    != NULL             # <<<<<<<<<<<<<<
 * 
 *         # Try to grab the read-group tag value
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!((__pyx_v_qual != NULL) != 0))) {
    PyErr_SetNone(PyExc_AssertionError);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  #endif

  /* "htslibWrapper.pyx":349
 * 
 *         # Try to grab the read-group tag value
 *         cdef uint8_t* v     = NULL             # <<<<<<<<<<<<<<
 *         cdef char* tempRgID = NULL
 *         cdef int lenRgID    = 0
 */
  __pyx_v_v = NULL;

  /* "htslibWrapper.pyx":350
 *         # Try to grab the read-group tag value
 *         cdef uint8_t* v     = NULL
 *         cdef char* tempRgID = NULL             # <<<<<<<<<<<<<<
 *         cdef int lenRgID    = 0
 * 
 */
  __pyx_v_tempRgID = NULL;

  /* "htslibWrapper.pyx":351
 *         cdef uint8_t* v     = NULL
 *         cdef char* tempRgID = NULL
 *         cdef int lenRgID    = 0             # <<<<<<<<<<<<<<
 * 
 *         if storeRgID:
 */
  __pyx_v_lenRgID = 0;

  /* "htslibWrapper.pyx":353
 *         cdef int lenRgID    = 0
 * 
 *         if storeRgID:             # <<<<<<<<<<<<<<
 *             v = bam_aux_get(self.b, "RG")
 *             if (v != NULL):
 */
  __pyx_t_2 = (__pyx_v_storeRgID != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":354
 * 
 *         if storeRgID:
 *             v = bam_aux_get(self.b, "RG")             # <<<<<<<<<<<<<<
 *             if (v != NULL):
 *                 tempRgID = bam_aux2Z(v)
 */
    __pyx_v_v = bam_aux_get(__pyx_v_self->b, __pyx_k__RG);

    /* "htslibWrapper.pyx":355
 *         if storeRgID:
 *             v = bam_aux_get(self.b, "RG")
 *             if (v != NULL):             # <<<<<<<<<<<<<<
 *                 tempRgID = bam_aux2Z(v)
 *                 lenRgID  = strlen(tempRgID)
 */
    __pyx_t_2 = ((__pyx_v_v != NULL) != 0);
    if (__pyx_t_2) {

      /* "htslibWrapper.pyx":356
 *             v = bam_aux_get(self.b, "RG")
 *             if (v != NULL):
 *                 tempRgID = bam_aux2Z(v)             # <<<<<<<<<<<<<<
 *                 lenRgID  = strlen(tempRgID)
 *                 rgID[0]  = <char*>(calloc(lenRgID + 1, sizeof(char)))
 */
      __pyx_v_tempRgID = bam_aux2Z(__pyx_v_v);

      /* "htslibWrapper.pyx":357
 *             if (v != NULL):
 *                 tempRgID = bam_aux2Z(v)
 *                 lenRgID  = strlen(tempRgID)             # <<<<<<<<<<<<<<
 *                 rgID[0]  = <char*>(calloc(lenRgID + 1, sizeof(char)))
 *                 strcpy(rgID[0], tempRgID)
 */
      __pyx_v_lenRgID = strlen(__pyx_v_tempRgID);

      /* "htslibWrapper.pyx":358
 *                 tempRgID = bam_aux2Z(v)
 *                 lenRgID  = strlen(tempRgID)
 *                 rgID[0]  = <char*>(calloc(lenRgID + 1, sizeof(char)))             # <<<<<<<<<<<<<<
 *                 strcpy(rgID[0], tempRgID)
 *             else:
 */
      (__pyx_v_rgID[0]) = ((char *)calloc((__pyx_v_lenRgID + 1), (sizeof(char))));

      /* "htslibWrapper.pyx":359
 *                 lenRgID  = strlen(tempRgID)
 *                 rgID[0]  = <char*>(calloc(lenRgID + 1, sizeof(char)))
 *                 strcpy(rgID[0], tempRgID)             # <<<<<<<<<<<<<<
 *             else:
 *                 rgID[0] = NULL
 */
      strcpy((__pyx_v_rgID[0]), __pyx_v_tempRgID);
      goto __pyx_L6;
    }
    /*else*/ {

      /* "htslibWrapper.pyx":361
 *                 strcpy(rgID[0], tempRgID)
 *             else:
 *                 rgID[0] = NULL             # <<<<<<<<<<<<<<
 * 
 *         cdef int i = 0
 */
      (__pyx_v_rgID[0]) = NULL;
    }
    __pyx_L6:;
    goto __pyx_L5;
  }
  __pyx_L5:;

  /* "htslibWrapper.pyx":363
 *                 rgID[0] = NULL
 * 
 *         cdef int i = 0             # <<<<<<<<<<<<<<
 *         for i from 0 <= i < lenSeq:
 *             seq[i]  = self._getBase(s, i)
 */
  __pyx_v_i = 0;

  /* "htslibWrapper.pyx":364
 * 
 *         cdef int i = 0
 *         for i from 0 <= i < lenSeq:             # <<<<<<<<<<<<<<
 *             seq[i]  = self._getBase(s, i)
 *             qual[i] = q[i]
 */
  __pyx_t_3 = __pyx_v_lenSeq;
  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {

    /* "htslibWrapper.pyx":365
 *         cdef int i = 0
 *         for i from 0 <= i < lenSeq:
 *             seq[i]  = self._getBase(s, i)             # <<<<<<<<<<<<<<
 *             qual[i] = q[i]
 *             assert qual[i] <= 93
 */
    (__pyx_v_seq[__pyx_v_i]) = ((struct __pyx_vtabstruct_13htslibWrapper_ReadIterator *)__pyx_v_self->__pyx_vtab)->_getBase(__pyx_v_self, __pyx_v_s, __pyx_v_i);

    /* "htslibWrapper.pyx":366
 *         for i from 0 <= i < lenSeq:
 *             seq[i]  = self._getBase(s, i)
 *             qual[i] = q[i]             # <<<<<<<<<<<<<<
 *             assert qual[i] <= 93
 *             assert qual[i] >= 0
 */
    (__pyx_v_qual[__pyx_v_i]) = (__pyx_v_q[__pyx_v_i]);

    /* "htslibWrapper.pyx":367
 *             seq[i]  = self._getBase(s, i)
 *             qual[i] = q[i]
 *             assert qual[i] <= 93             # <<<<<<<<<<<<<<
 *             assert qual[i] >= 0
 *         seq[lenSeq]  = '\0'
 */
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) <= 93) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    #endif

    /* "htslibWrapper.pyx":368
 *             qual[i] = q[i]
 *             assert qual[i] <= 93
 *             assert qual[i] >= 0             # <<<<<<<<<<<<<<
 *         seq[lenSeq]  = '\0'
 *         qual[lenSeq] = '\0'
 */
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) >= 0) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    #endif
  }

  /* "htslibWrapper.pyx":369
 *             assert qual[i] <= 93
 *             assert qual[i] >= 0
 *         seq[lenSeq]  = '\0'             # <<<<<<<<<<<<<<
 *         qual[lenSeq] = '\0'
 * 
 */
  (__pyx_v_seq[__pyx_v_lenSeq]) = '\x00';

  /* "htslibWrapper.pyx":370
 *             assert qual[i] >= 0
 *         seq[lenSeq]  = '\0'
 *         qual[lenSeq] = '\0'             # <<<<<<<<<<<<<<
 * 
 *         readStart = c.pos
 */
  (__pyx_v_qual[__pyx_v_lenSeq]) = '\x00';

  /* "htslibWrapper.pyx":372
 *         qual[lenSeq] = '\0'
 * 
 *         readStart = c.pos             # <<<<<<<<<<<<<<
 *         cdef short* cigarOps = <short*>malloc(2 * c.n_cigar * sizeof(short))
 *         assert cigarOps != NULL
 */
  __pyx_t_4 = __Pyx_PyInt_to_py_int32_t(__pyx_v_c->pos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_4);
  __pyx_v_readStart = __pyx_t_4;
  __pyx_t_4 = 0;

  /* "htslibWrapper.pyx":373
 * 
 *         readStart = c.pos
 *         cdef short* cigarOps = <short*>malloc(2 * c.n_cigar * sizeof(short))             # <<<<<<<<<<<<<<
 *         assert cigarOps != NULL
 *         cdef uint32_t *cigar = bam_get_cigar(self.b)
 */
  __pyx_v_cigarOps = ((short *)malloc(((2 * __pyx_v_c->n_cigar) * (sizeof(short)))));

  /* "htslibWrapper.pyx":374
 *         readStart = c.pos
 *         cdef short* cigarOps = <short*>malloc(2 * c.n_cigar * sizeof(short))
 *         assert cigarOps != NULL             # <<<<<<<<<<<<<<
 *         cdef uint32_t *cigar = bam_get_cigar(self.b)
 *         for i from 0 <= i < c.n_cigar:
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!((__pyx_v_cigarOps != NULL) != 0))) {
    PyErr_SetNone(PyExc_AssertionError);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  #endif

  /* "htslibWrapper.pyx":375
 *         cdef short* cigarOps = <short*>malloc(2 * c.n_cigar * sizeof(short))
 *         assert cigarOps != NULL
 *         cdef uint32_t *cigar = bam_get_cigar(self.b)             # <<<<<<<<<<<<<<
 *         for i from 0 <= i < c.n_cigar:
 *             cigarFlag             = bam_cigar_op(cigar[i])
 */
  __pyx_v_cigar = bam_get_cigar(__pyx_v_self->b);

  /* "htslibWrapper.pyx":376
 *         assert cigarOps != NULL
 *         cdef uint32_t *cigar = bam_get_cigar(self.b)
 *         for i from 0 <= i < c.n_cigar:             # <<<<<<<<<<<<<<
 *             cigarFlag             = bam_cigar_op(cigar[i])
 *             cigarFlagLen          = bam_cigar_oplen(cigar[i])
 */
  __pyx_t_5 = __pyx_v_c->n_cigar;
  for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {

    /* "htslibWrapper.pyx":377
 *         cdef uint32_t *cigar = bam_get_cigar(self.b)
 *         for i from 0 <= i < c.n_cigar:
 *             cigarFlag             = bam_cigar_op(cigar[i])             # <<<<<<<<<<<<<<
 *             cigarFlagLen          = bam_cigar_oplen(cigar[i])
 *             cigarOps[2 * i]       = cigarFlag
 */
    __pyx_v_cigarFlag = bam_cigar_op((__pyx_v_cigar[__pyx_v_i]));

    /* "htslibWrapper.pyx":378
 *         for i from 0 <= i < c.n_cigar:
 *             cigarFlag             = bam_cigar_op(cigar[i])
 *             cigarFlagLen          = bam_cigar_oplen(cigar[i])             # <<<<<<<<<<<<<<
 *             cigarOps[2 * i]       = cigarFlag
 *             cigarOps[(2 * i) + 1] = cigarFlagLen
 */
    __pyx_t_4 = PyInt_FromLong(bam_cigar_oplen((__pyx_v_cigar[__pyx_v_i]))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_XDECREF(__pyx_v_cigarFlagLen);
    __pyx_v_cigarFlagLen = __pyx_t_4;
    __pyx_t_4 = 0;

    /* "htslibWrapper.pyx":379
 *             cigarFlag             = bam_cigar_op(cigar[i])
 *             cigarFlagLen          = bam_cigar_oplen(cigar[i])
 *             cigarOps[2 * i]       = cigarFlag             # <<<<<<<<<<<<<<
 *             cigarOps[(2 * i) + 1] = cigarFlagLen
 * 
 */
    (__pyx_v_cigarOps[(2 * __pyx_v_i)]) = __pyx_v_cigarFlag;

    /* "htslibWrapper.pyx":380
 *             cigarFlagLen          = bam_cigar_oplen(cigar[i])
 *             cigarOps[2 * i]       = cigarFlag
 *             cigarOps[(2 * i) + 1] = cigarFlagLen             # <<<<<<<<<<<<<<
 * 
 *             # Soft-clipping of sequence at start of read changes the mapping
 */
    __pyx_t_6 = __Pyx_PyInt_AsShort(__pyx_v_cigarFlagLen); if (unlikely((__pyx_t_6 == (short)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    (__pyx_v_cigarOps[((2 * __pyx_v_i) + 1)]) = __pyx_t_6;

    /* "htslibWrapper.pyx":386
 *             # base. I want to adjust this so that the read start refers to the first base in
 *             # the read.
 *             if i == 0 and cigarFlag == 4:             # <<<<<<<<<<<<<<
 *                 readStart -= cigarFlagLen
 * 
 */
    __pyx_t_2 = ((__pyx_v_i == 0) != 0);
    if (__pyx_t_2) {
      __pyx_t_7 = ((__pyx_v_cigarFlag == 4) != 0);
      __pyx_t_8 = __pyx_t_7;
    } else {
      __pyx_t_8 = __pyx_t_2;
    }
    if (__pyx_t_8) {

      /* "htslibWrapper.pyx":387
 *             # the read.
 *             if i == 0 and cigarFlag == 4:
 *                 readStart -= cigarFlagLen             # <<<<<<<<<<<<<<
 * 
 *         theRead.seq         = seq
 */
      __pyx_t_4 = PyNumber_InPlaceSubtract(__pyx_v_readStart, __pyx_v_cigarFlagLen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_DECREF(__pyx_v_readStart);
      __pyx_v_readStart = __pyx_t_4;
      __pyx_t_4 = 0;
      goto __pyx_L11;
    }
    __pyx_L11:;
  }

  /* "htslibWrapper.pyx":389
 *                 readStart -= cigarFlagLen
 * 
 *         theRead.seq         = seq             # <<<<<<<<<<<<<<
 *         theRead.qual        = qual
 *         theRead.cigarOps    = cigarOps
 */
  __pyx_v_theRead->seq = __pyx_v_seq;

  /* "htslibWrapper.pyx":390
 * 
 *         theRead.seq         = seq
 *         theRead.qual        = qual             # <<<<<<<<<<<<<<
 *         theRead.cigarOps    = cigarOps
 *         theRead.hash        = NULL
 */
  __pyx_v_theRead->qual = __pyx_v_qual;

  /* "htslibWrapper.pyx":391
 *         theRead.seq         = seq
 *         theRead.qual        = qual
 *         theRead.cigarOps    = cigarOps             # <<<<<<<<<<<<<<
 *         theRead.hash        = NULL
 *         theRead.mateChromID = c.mtid
 */
  __pyx_v_theRead->cigarOps = __pyx_v_cigarOps;

  /* "htslibWrapper.pyx":392
 *         theRead.qual        = qual
 *         theRead.cigarOps    = cigarOps
 *         theRead.hash        = NULL             # <<<<<<<<<<<<<<
 *         theRead.mateChromID = c.mtid
 *         theRead.cigarLen    = c.n_cigar
 */
  __pyx_v_theRead->hash = NULL;

  /* "htslibWrapper.pyx":393
 *         theRead.cigarOps    = cigarOps
 *         theRead.hash        = NULL
 *         theRead.mateChromID = c.mtid             # <<<<<<<<<<<<<<
 *         theRead.cigarLen    = c.n_cigar
 *         theRead.chromID     = c.tid
 */
  __pyx_t_1 = __pyx_v_c->mtid;
  __pyx_v_theRead->mateChromID = __pyx_t_1;

  /* "htslibWrapper.pyx":394
 *         theRead.hash        = NULL
 *         theRead.mateChromID = c.mtid
 *         theRead.cigarLen    = c.n_cigar             # <<<<<<<<<<<<<<
 *         theRead.chromID     = c.tid
 *         theRead.rlen        = lenSeq
 */
  __pyx_t_5 = __pyx_v_c->n_cigar;
  __pyx_v_theRead->cigarLen = __pyx_t_5;

  /* "htslibWrapper.pyx":395
 *         theRead.mateChromID = c.mtid
 *         theRead.cigarLen    = c.n_cigar
 *         theRead.chromID     = c.tid             # <<<<<<<<<<<<<<
 *         theRead.rlen        = lenSeq
 *         theRead.pos         = readStart
 */
  __pyx_t_1 = __pyx_v_c->tid;
  __pyx_v_theRead->chromID = __pyx_t_1;

  /* "htslibWrapper.pyx":396
 *         theRead.cigarLen    = c.n_cigar
 *         theRead.chromID     = c.tid
 *         theRead.rlen        = lenSeq             # <<<<<<<<<<<<<<
 *         theRead.pos         = readStart
 *         theRead.end         = bam_endpos(self.b)
 */
  __pyx_v_theRead->rlen = __pyx_v_lenSeq;

  /* "htslibWrapper.pyx":397
 *         theRead.chromID     = c.tid
 *         theRead.rlen        = lenSeq
 *         theRead.pos         = readStart             # <<<<<<<<<<<<<<
 *         theRead.end         = bam_endpos(self.b)
 *         theRead.insertSize  = c.isize
 */
  __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_v_readStart); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_v_theRead->pos = __pyx_t_3;

  /* "htslibWrapper.pyx":398
 *         theRead.rlen        = lenSeq
 *         theRead.pos         = readStart
 *         theRead.end         = bam_endpos(self.b)             # <<<<<<<<<<<<<<
 *         theRead.insertSize  = c.isize
 *         theRead.matePos     = c.mpos
 */
  __pyx_v_theRead->end = bam_endpos(__pyx_v_self->b);

  /* "htslibWrapper.pyx":399
 *         theRead.pos         = readStart
 *         theRead.end         = bam_endpos(self.b)
 *         theRead.insertSize  = c.isize             # <<<<<<<<<<<<<<
 *         theRead.matePos     = c.mpos
 *         theRead.bitFlag     = c.flag
 */
  __pyx_t_1 = __pyx_v_c->isize;
  __pyx_v_theRead->insertSize = __pyx_t_1;

  /* "htslibWrapper.pyx":400
 *         theRead.end         = bam_endpos(self.b)
 *         theRead.insertSize  = c.isize
 *         theRead.matePos     = c.mpos             # <<<<<<<<<<<<<<
 *         theRead.bitFlag     = c.flag
 *         theRead.mapq        = c.qual
 */
  __pyx_t_1 = __pyx_v_c->mpos;
  __pyx_v_theRead->matePos = __pyx_t_1;

  /* "htslibWrapper.pyx":401
 *         theRead.insertSize  = c.isize
 *         theRead.matePos     = c.mpos
 *         theRead.bitFlag     = c.flag             # <<<<<<<<<<<<<<
 *         theRead.mapq        = c.qual
 * 
 */
  __pyx_t_5 = __pyx_v_c->flag;
  __pyx_v_theRead->bitFlag = __pyx_t_5;

  /* "htslibWrapper.pyx":402
 *         theRead.matePos     = c.mpos
 *         theRead.bitFlag     = c.flag
 *         theRead.mapq        = c.qual             # <<<<<<<<<<<<<<
 * 
 *         Read_SetUnCompressed(theRead)
 */
  __pyx_t_5 = __pyx_v_c->qual;
  __pyx_v_theRead->mapq = __pyx_t_5;

  /* "htslibWrapper.pyx":404
 *         theRead.mapq        = c.qual
 * 
 *         Read_SetUnCompressed(theRead)             # <<<<<<<<<<<<<<
 * 
 *         return theRead
 */
  __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_v_theRead);

  /* "htslibWrapper.pyx":406
 *         Read_SetUnCompressed(theRead)
 * 
 *         return theRead             # <<<<<<<<<<<<<<
 * 
 *     cdef int cnext(self) nogil:
 */
  __pyx_r = __pyx_v_theRead;
  goto __pyx_L0;

  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_WriteUnraisable("htslibWrapper.ReadIterator.get", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_readStart);
  __Pyx_XDECREF(__pyx_v_cigarFlagLen);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "htslibWrapper.pyx":408
 *         return theRead
 * 
 *     cdef int cnext(self) nogil:             # <<<<<<<<<<<<<<
 *         '''
 *         cversion of iterator. Used by IteratorColumn
 */

static int __pyx_f_13htslibWrapper_12ReadIterator_cnext(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self) {
  int __pyx_r;

  /* "htslibWrapper.pyx":412
 *         cversion of iterator. Used by IteratorColumn
 *         '''
 *         return sam_itr_next(self.theSamfile, self.theIterator, self.b) >= 0             # <<<<<<<<<<<<<<
 * 
 *     cdef char _getBase(self, uint8_t *s, int i):
 */
  __pyx_r = (sam_itr_next(__pyx_v_self->theSamfile, __pyx_v_self->theIterator, __pyx_v_self->b) >= 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

/* "htslibWrapper.pyx":414
 *         return sam_itr_next(self.theSamfile, self.theIterator, self.b) >= 0
 * 
 *     cdef char _getBase(self, uint8_t *s, int i):             # <<<<<<<<<<<<<<
 *         cdef char* baseLookup="=ACMGRSVTWYHKDBN"
 *         return baseLookup[bam_seqi(s, i)]
 */

static char __pyx_f_13htslibWrapper_12ReadIterator__getBase(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, uint8_t *__pyx_v_s, int __pyx_v_i) {
  char *__pyx_v_baseLookup;
  char __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("_getBase", 0);

  /* "htslibWrapper.pyx":415
 * 
 *     cdef char _getBase(self, uint8_t *s, int i):
 *         cdef char* baseLookup="=ACMGRSVTWYHKDBN"             # <<<<<<<<<<<<<<
 *         return baseLookup[bam_seqi(s, i)]
 * 
 */
  __pyx_v_baseLookup = __pyx_k_26;

  /* "htslibWrapper.pyx":416
 *     cdef char _getBase(self, uint8_t *s, int i):
 *         cdef char* baseLookup="=ACMGRSVTWYHKDBN"
 *         return baseLookup[bam_seqi(s, i)]             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_r = (__pyx_v_baseLookup[bam_seqi(__pyx_v_s, __pyx_v_i)]);
  goto __pyx_L0;

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

/* "htslibWrapper.pyx":420
 * ###################################################################################################
 * 
 * cdef void destroyRead(cAlignedRead* theRead):             # <<<<<<<<<<<<<<
 *     """
 *     De-allocate memory for read.
 */

static void __pyx_f_13htslibWrapper_destroyRead(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("destroyRead", 0);

  /* "htslibWrapper.pyx":425
 *     """
 * 
 *     if theRead.seq != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.seq)
 * 
 */
  __pyx_t_1 = ((__pyx_v_theRead->seq != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":426
 * 
 *     if theRead.seq != NULL:
 *         free(theRead.seq)             # <<<<<<<<<<<<<<
 * 
 *     if theRead.qual != NULL:
 */
    free(__pyx_v_theRead->seq);
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":428
 *         free(theRead.seq)
 * 
 *     if theRead.qual != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.qual)
 * 
 */
  __pyx_t_1 = ((__pyx_v_theRead->qual != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":429
 * 
 *     if theRead.qual != NULL:
 *         free(theRead.qual)             # <<<<<<<<<<<<<<
 * 
 *     if theRead.cigarOps != NULL:
 */
    free(__pyx_v_theRead->qual);
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":431
 *         free(theRead.qual)
 * 
 *     if theRead.cigarOps != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.cigarOps)
 * 
 */
  __pyx_t_1 = ((__pyx_v_theRead->cigarOps != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":432
 * 
 *     if theRead.cigarOps != NULL:
 *         free(theRead.cigarOps)             # <<<<<<<<<<<<<<
 * 
 *     if theRead.hash != NULL:
 */
    free(__pyx_v_theRead->cigarOps);
    goto __pyx_L5;
  }
  __pyx_L5:;

  /* "htslibWrapper.pyx":434
 *         free(theRead.cigarOps)
 * 
 *     if theRead.hash != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.hash)
 * 
 */
  __pyx_t_1 = ((__pyx_v_theRead->hash != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":435
 * 
 *     if theRead.hash != NULL:
 *         free(theRead.hash)             # <<<<<<<<<<<<<<
 * 
 *     free(theRead)
 */
    free(__pyx_v_theRead->hash);
    goto __pyx_L6;
  }
  __pyx_L6:;

  /* "htslibWrapper.pyx":437
 *         free(theRead.hash)
 * 
 *     free(theRead)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  free(__pyx_v_theRead);

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":441
 * ###################################################################################################
 * 
 * cdef void compressSeq(cAlignedRead* read, char* refSeq):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin.
 */

static void __pyx_f_13htslibWrapper_compressSeq(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, char *__pyx_v_refSeq) {
  char *__pyx_v_seq;
  char *__pyx_v_newSeq;
  char *__pyx_v_finalSeq;
  int __pyx_v_i;
  int __pyx_v_nMatches;
  int __pyx_v_newSeqIndex;
  int __pyx_v_totalMatches;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  short __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  __Pyx_RefNannySetupContext("compressSeq", 0);

  /* "htslibWrapper.pyx":445
 *     Does exactly what it says on the tin.
 *     """
 *     cdef char* seq = read.seq             # <<<<<<<<<<<<<<
 *     cdef char* newSeq = <char*>(alloca(sizeof(char)*read.rlen*2))
 *     cdef char* finalSeq = NULL
 */
  __pyx_t_1 = __pyx_v_read->seq;
  __pyx_v_seq = __pyx_t_1;

  /* "htslibWrapper.pyx":446
 *     """
 *     cdef char* seq = read.seq
 *     cdef char* newSeq = <char*>(alloca(sizeof(char)*read.rlen*2))             # <<<<<<<<<<<<<<
 *     cdef char* finalSeq = NULL
 *     cdef int i = 0
 */
  __pyx_v_newSeq = ((char *)alloca((((sizeof(char)) * __pyx_v_read->rlen) * 2)));

  /* "htslibWrapper.pyx":447
 *     cdef char* seq = read.seq
 *     cdef char* newSeq = <char*>(alloca(sizeof(char)*read.rlen*2))
 *     cdef char* finalSeq = NULL             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int nMatches = 0
 */
  __pyx_v_finalSeq = NULL;

  /* "htslibWrapper.pyx":448
 *     cdef char* newSeq = <char*>(alloca(sizeof(char)*read.rlen*2))
 *     cdef char* finalSeq = NULL
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef int nMatches = 0
 *     cdef int newSeqIndex = 0
 */
  __pyx_v_i = 0;

  /* "htslibWrapper.pyx":449
 *     cdef char* finalSeq = NULL
 *     cdef int i = 0
 *     cdef int nMatches = 0             # <<<<<<<<<<<<<<
 *     cdef int newSeqIndex = 0
 *     cdef int totalMatches = 0
 */
  __pyx_v_nMatches = 0;

  /* "htslibWrapper.pyx":450
 *     cdef int i = 0
 *     cdef int nMatches = 0
 *     cdef int newSeqIndex = 0             # <<<<<<<<<<<<<<
 *     cdef int totalMatches = 0
 * 
 */
  __pyx_v_newSeqIndex = 0;

  /* "htslibWrapper.pyx":451
 *     cdef int nMatches = 0
 *     cdef int newSeqIndex = 0
 *     cdef int totalMatches = 0             # <<<<<<<<<<<<<<
 * 
 *     for i in range(read.rlen):
 */
  __pyx_v_totalMatches = 0;

  /* "htslibWrapper.pyx":453
 *     cdef int totalMatches = 0
 * 
 *     for i in range(read.rlen):             # <<<<<<<<<<<<<<
 * 
 *         # Ref match. Store count if > 40
 */
  __pyx_t_2 = __pyx_v_read->rlen;
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_i = __pyx_t_3;

    /* "htslibWrapper.pyx":456
 * 
 *         # Ref match. Store count if > 40
 *         if seq[i] == refSeq[i]:             # <<<<<<<<<<<<<<
 *             totalMatches += 1
 * 
 */
    __pyx_t_4 = (((__pyx_v_seq[__pyx_v_i]) == (__pyx_v_refSeq[__pyx_v_i])) != 0);
    if (__pyx_t_4) {

      /* "htslibWrapper.pyx":457
 *         # Ref match. Store count if > 40
 *         if seq[i] == refSeq[i]:
 *             totalMatches += 1             # <<<<<<<<<<<<<<
 * 
 *             if nMatches == 40:
 */
      __pyx_v_totalMatches = (__pyx_v_totalMatches + 1);

      /* "htslibWrapper.pyx":459
 *             totalMatches += 1
 * 
 *             if nMatches == 40:             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 */
      __pyx_t_4 = ((__pyx_v_nMatches == 40) != 0);
      if (__pyx_t_4) {

        /* "htslibWrapper.pyx":460
 * 
 *             if nMatches == 40:
 *                 newSeq[newSeqIndex] = nMatches             # <<<<<<<<<<<<<<
 *                 nMatches = 0
 *                 newSeqIndex += 1
 */
        (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = __pyx_v_nMatches;

        /* "htslibWrapper.pyx":461
 *             if nMatches == 40:
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0             # <<<<<<<<<<<<<<
 *                 newSeqIndex += 1
 * 
 */
        __pyx_v_nMatches = 0;

        /* "htslibWrapper.pyx":462
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 *                 newSeqIndex += 1             # <<<<<<<<<<<<<<
 * 
 *             nMatches += 1
 */
        __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
        goto __pyx_L6;
      }
      __pyx_L6:;

      /* "htslibWrapper.pyx":464
 *                 newSeqIndex += 1
 * 
 *             nMatches += 1             # <<<<<<<<<<<<<<
 * 
 *         # Ref mis-match. Store base.
 */
      __pyx_v_nMatches = (__pyx_v_nMatches + 1);
      goto __pyx_L5;
    }
    /*else*/ {

      /* "htslibWrapper.pyx":468
 *         # Ref mis-match. Store base.
 *         else:
 *             if nMatches > 0:             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 */
      __pyx_t_4 = ((__pyx_v_nMatches > 0) != 0);
      if (__pyx_t_4) {

        /* "htslibWrapper.pyx":469
 *         else:
 *             if nMatches > 0:
 *                 newSeq[newSeqIndex] = nMatches             # <<<<<<<<<<<<<<
 *                 nMatches = 0
 *                 newSeqIndex += 1
 */
        (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = __pyx_v_nMatches;

        /* "htslibWrapper.pyx":470
 *             if nMatches > 0:
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0             # <<<<<<<<<<<<<<
 *                 newSeqIndex += 1
 * 
 */
        __pyx_v_nMatches = 0;

        /* "htslibWrapper.pyx":471
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 *                 newSeqIndex += 1             # <<<<<<<<<<<<<<
 * 
 *             newSeq[newSeqIndex] = seq[i]
 */
        __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
        goto __pyx_L7;
      }
      __pyx_L7:;

      /* "htslibWrapper.pyx":473
 *                 newSeqIndex += 1
 * 
 *             newSeq[newSeqIndex] = seq[i]             # <<<<<<<<<<<<<<
 *             newSeqIndex += 1
 * 
 */
      (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = (__pyx_v_seq[__pyx_v_i]);

      /* "htslibWrapper.pyx":474
 * 
 *             newSeq[newSeqIndex] = seq[i]
 *             newSeqIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     # If we finish off with a load of matches, catch those
 */
      __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
    }
    __pyx_L5:;
  }

  /* "htslibWrapper.pyx":477
 * 
 *     # If we finish off with a load of matches, catch those
 *     if nMatches > 0:             # <<<<<<<<<<<<<<
 *         newSeq[newSeqIndex] = nMatches
 *         nMatches = 0
 */
  __pyx_t_4 = ((__pyx_v_nMatches > 0) != 0);
  if (__pyx_t_4) {

    /* "htslibWrapper.pyx":478
 *     # If we finish off with a load of matches, catch those
 *     if nMatches > 0:
 *         newSeq[newSeqIndex] = nMatches             # <<<<<<<<<<<<<<
 *         nMatches = 0
 *         newSeqIndex += 1
 */
    (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = __pyx_v_nMatches;

    /* "htslibWrapper.pyx":479
 *     if nMatches > 0:
 *         newSeq[newSeqIndex] = nMatches
 *         nMatches = 0             # <<<<<<<<<<<<<<
 *         newSeqIndex += 1
 * 
 */
    __pyx_v_nMatches = 0;

    /* "htslibWrapper.pyx":480
 *         newSeq[newSeqIndex] = nMatches
 *         nMatches = 0
 *         newSeqIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     newSeq[newSeqIndex] = 0
 */
    __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
    goto __pyx_L8;
  }
  __pyx_L8:;

  /* "htslibWrapper.pyx":482
 *         newSeqIndex += 1
 * 
 *     newSeq[newSeqIndex] = 0             # <<<<<<<<<<<<<<
 *     finalSeq = <char*>malloc(sizeof(char)*(newSeqIndex+1))
 *     strcpy(finalSeq, newSeq)
 */
  (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = 0;

  /* "htslibWrapper.pyx":483
 * 
 *     newSeq[newSeqIndex] = 0
 *     finalSeq = <char*>malloc(sizeof(char)*(newSeqIndex+1))             # <<<<<<<<<<<<<<
 *     strcpy(finalSeq, newSeq)
 *     finalSeq[newSeqIndex] = 0
 */
  __pyx_v_finalSeq = ((char *)malloc(((sizeof(char)) * (__pyx_v_newSeqIndex + 1))));

  /* "htslibWrapper.pyx":484
 *     newSeq[newSeqIndex] = 0
 *     finalSeq = <char*>malloc(sizeof(char)*(newSeqIndex+1))
 *     strcpy(finalSeq, newSeq)             # <<<<<<<<<<<<<<
 *     finalSeq[newSeqIndex] = 0
 *     free(read.seq)
 */
  strcpy(__pyx_v_finalSeq, __pyx_v_newSeq);

  /* "htslibWrapper.pyx":485
 *     finalSeq = <char*>malloc(sizeof(char)*(newSeqIndex+1))
 *     strcpy(finalSeq, newSeq)
 *     finalSeq[newSeqIndex] = 0             # <<<<<<<<<<<<<<
 *     free(read.seq)
 *     #free(newSeq)
 */
  (__pyx_v_finalSeq[__pyx_v_newSeqIndex]) = 0;

  /* "htslibWrapper.pyx":486
 *     strcpy(finalSeq, newSeq)
 *     finalSeq[newSeqIndex] = 0
 *     free(read.seq)             # <<<<<<<<<<<<<<
 *     #free(newSeq)
 *     read.seq = finalSeq
 */
  free(__pyx_v_read->seq);

  /* "htslibWrapper.pyx":488
 *     free(read.seq)
 *     #free(newSeq)
 *     read.seq = finalSeq             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_v_read->seq = __pyx_v_finalSeq;

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":492
 * ###################################################################################################
 * 
 * cdef void compressQual(cAlignedRead* read, int qualBinSize):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin.
 */

static void __pyx_f_13htslibWrapper_compressQual(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, int __pyx_v_qualBinSize) {
  int __pyx_v_i;
  char *__pyx_v_qual;
  char *__pyx_v_newQual;
  char *__pyx_v_finalQual;
  char __pyx_v_lastChar;
  int __pyx_v_lastCount;
  int __pyx_v_newQualIndex;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  int __pyx_t_2;
  short __pyx_t_3;
  int __pyx_t_4;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("compressQual", 0);

  /* "htslibWrapper.pyx":496
 *     Does exactly what it says on the tin.
 *     """
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef char* qual = read.qual
 *     #cdef char* newQual = <char*>(malloc(sizeof(char)*2*read.rlen))
 */
  __pyx_v_i = 0;

  /* "htslibWrapper.pyx":497
 *     """
 *     cdef int i = 0
 *     cdef char* qual = read.qual             # <<<<<<<<<<<<<<
 *     #cdef char* newQual = <char*>(malloc(sizeof(char)*2*read.rlen))
 *     cdef char* newQual = <char*>(alloca(sizeof(char)*2*read.rlen))
 */
  __pyx_t_1 = __pyx_v_read->qual;
  __pyx_v_qual = __pyx_t_1;

  /* "htslibWrapper.pyx":499
 *     cdef char* qual = read.qual
 *     #cdef char* newQual = <char*>(malloc(sizeof(char)*2*read.rlen))
 *     cdef char* newQual = <char*>(alloca(sizeof(char)*2*read.rlen))             # <<<<<<<<<<<<<<
 *     cdef char* finalQual = NULL
 *     cdef char lastChar = 0
 */
  __pyx_v_newQual = ((char *)alloca((((sizeof(char)) * 2) * __pyx_v_read->rlen)));

  /* "htslibWrapper.pyx":500
 *     #cdef char* newQual = <char*>(malloc(sizeof(char)*2*read.rlen))
 *     cdef char* newQual = <char*>(alloca(sizeof(char)*2*read.rlen))
 *     cdef char* finalQual = NULL             # <<<<<<<<<<<<<<
 *     cdef char lastChar = 0
 *     cdef int lastCount = 0
 */
  __pyx_v_finalQual = NULL;

  /* "htslibWrapper.pyx":501
 *     cdef char* newQual = <char*>(alloca(sizeof(char)*2*read.rlen))
 *     cdef char* finalQual = NULL
 *     cdef char lastChar = 0             # <<<<<<<<<<<<<<
 *     cdef int lastCount = 0
 *     cdef int newQualIndex = 0
 */
  __pyx_v_lastChar = 0;

  /* "htslibWrapper.pyx":502
 *     cdef char* finalQual = NULL
 *     cdef char lastChar = 0
 *     cdef int lastCount = 0             # <<<<<<<<<<<<<<
 *     cdef int newQualIndex = 0
 * 
 */
  __pyx_v_lastCount = 0;

  /* "htslibWrapper.pyx":503
 *     cdef char lastChar = 0
 *     cdef int lastCount = 0
 *     cdef int newQualIndex = 0             # <<<<<<<<<<<<<<
 * 
 *     if qualBinSize > 1:
 */
  __pyx_v_newQualIndex = 0;

  /* "htslibWrapper.pyx":505
 *     cdef int newQualIndex = 0
 * 
 *     if qualBinSize > 1:             # <<<<<<<<<<<<<<
 *         for i in range(read.rlen):
 *             qual[i] = (qual[i]/qualBinSize)*qualBinSize
 */
  __pyx_t_2 = ((__pyx_v_qualBinSize > 1) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":506
 * 
 *     if qualBinSize > 1:
 *         for i in range(read.rlen):             # <<<<<<<<<<<<<<
 *             qual[i] = (qual[i]/qualBinSize)*qualBinSize
 * 
 */
    __pyx_t_3 = __pyx_v_read->rlen;
    for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
      __pyx_v_i = __pyx_t_4;

      /* "htslibWrapper.pyx":507
 *     if qualBinSize > 1:
 *         for i in range(read.rlen):
 *             qual[i] = (qual[i]/qualBinSize)*qualBinSize             # <<<<<<<<<<<<<<
 * 
 *     for i in range(read.rlen):
 */
      (__pyx_v_qual[__pyx_v_i]) = (((__pyx_v_qual[__pyx_v_i]) / __pyx_v_qualBinSize) * __pyx_v_qualBinSize);
    }
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":509
 *             qual[i] = (qual[i]/qualBinSize)*qualBinSize
 * 
 *     for i in range(read.rlen):             # <<<<<<<<<<<<<<
 * 
 *         assert qual[i] >= 0, "Shit 3. Qual = %s" %(qual[i])
 */
  __pyx_t_3 = __pyx_v_read->rlen;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "htslibWrapper.pyx":511
 *     for i in range(read.rlen):
 * 
 *         assert qual[i] >= 0, "Shit 3. Qual = %s" %(qual[i])             # <<<<<<<<<<<<<<
 *         assert qual[i] <= 93, "Shit 4!. Qual = %s" %(qual[i])
 * 
 */
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) >= 0) != 0))) {
      __pyx_t_5 = PyInt_FromLong((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_27), __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(((PyObject *)__pyx_t_6));
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
      PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_6));
      __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    #endif

    /* "htslibWrapper.pyx":512
 * 
 *         assert qual[i] >= 0, "Shit 3. Qual = %s" %(qual[i])
 *         assert qual[i] <= 93, "Shit 4!. Qual = %s" %(qual[i])             # <<<<<<<<<<<<<<
 * 
 *         if i == 0:
 */
    #ifndef CYTHON_WITHOUT_ASSERTIONS
    if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) <= 93) != 0))) {
      __pyx_t_6 = PyInt_FromLong((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(__pyx_t_6);
      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_28), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __Pyx_GOTREF(((PyObject *)__pyx_t_5));
      __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
      PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_5));
      __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    #endif

    /* "htslibWrapper.pyx":514
 *         assert qual[i] <= 93, "Shit 4!. Qual = %s" %(qual[i])
 * 
 *         if i == 0:             # <<<<<<<<<<<<<<
 *             newQual[newQualIndex] = qual[i] + 33
 *             newQualIndex += 1
 */
    __pyx_t_2 = ((__pyx_v_i == 0) != 0);
    if (__pyx_t_2) {

      /* "htslibWrapper.pyx":515
 * 
 *         if i == 0:
 *             newQual[newQualIndex] = qual[i] + 33             # <<<<<<<<<<<<<<
 *             newQualIndex += 1
 *             lastChar = qual[i]
 */
      (__pyx_v_newQual[__pyx_v_newQualIndex]) = ((__pyx_v_qual[__pyx_v_i]) + 33);

      /* "htslibWrapper.pyx":516
 *         if i == 0:
 *             newQual[newQualIndex] = qual[i] + 33
 *             newQualIndex += 1             # <<<<<<<<<<<<<<
 *             lastChar = qual[i]
 *             lastCount = 1
 */
      __pyx_v_newQualIndex = (__pyx_v_newQualIndex + 1);

      /* "htslibWrapper.pyx":517
 *             newQual[newQualIndex] = qual[i] + 33
 *             newQualIndex += 1
 *             lastChar = qual[i]             # <<<<<<<<<<<<<<
 *             lastCount = 1
 *         else:
 */
      __pyx_v_lastChar = (__pyx_v_qual[__pyx_v_i]);

      /* "htslibWrapper.pyx":518
 *             newQualIndex += 1
 *             lastChar = qual[i]
 *             lastCount = 1             # <<<<<<<<<<<<<<
 *         else:
 *             if qual[i] == lastChar:
 */
      __pyx_v_lastCount = 1;
      goto __pyx_L8;
    }
    /*else*/ {

      /* "htslibWrapper.pyx":520
 *             lastCount = 1
 *         else:
 *             if qual[i] == lastChar:             # <<<<<<<<<<<<<<
 *                 lastCount += 1
 *             else:
 */
      __pyx_t_2 = (((__pyx_v_qual[__pyx_v_i]) == __pyx_v_lastChar) != 0);
      if (__pyx_t_2) {

        /* "htslibWrapper.pyx":521
 *         else:
 *             if qual[i] == lastChar:
 *                 lastCount += 1             # <<<<<<<<<<<<<<
 *             else:
 *                 newQual[newQualIndex] = lastCount
 */
        __pyx_v_lastCount = (__pyx_v_lastCount + 1);
        goto __pyx_L9;
      }
      /*else*/ {

        /* "htslibWrapper.pyx":523
 *                 lastCount += 1
 *             else:
 *                 newQual[newQualIndex] = lastCount             # <<<<<<<<<<<<<<
 *                 newQualIndex += 1
 *                 newQual[newQualIndex] = qual[i] + 33
 */
        (__pyx_v_newQual[__pyx_v_newQualIndex]) = __pyx_v_lastCount;

        /* "htslibWrapper.pyx":524
 *             else:
 *                 newQual[newQualIndex] = lastCount
 *                 newQualIndex += 1             # <<<<<<<<<<<<<<
 *                 newQual[newQualIndex] = qual[i] + 33
 *                 newQualIndex += 1
 */
        __pyx_v_newQualIndex = (__pyx_v_newQualIndex + 1);

        /* "htslibWrapper.pyx":525
 *                 newQual[newQualIndex] = lastCount
 *                 newQualIndex += 1
 *                 newQual[newQualIndex] = qual[i] + 33             # <<<<<<<<<<<<<<
 *                 newQualIndex += 1
 *                 lastChar = qual[i]
 */
        (__pyx_v_newQual[__pyx_v_newQualIndex]) = ((__pyx_v_qual[__pyx_v_i]) + 33);

        /* "htslibWrapper.pyx":526
 *                 newQualIndex += 1
 *                 newQual[newQualIndex] = qual[i] + 33
 *                 newQualIndex += 1             # <<<<<<<<<<<<<<
 *                 lastChar = qual[i]
 *                 lastCount = 1
 */
        __pyx_v_newQualIndex = (__pyx_v_newQualIndex + 1);

        /* "htslibWrapper.pyx":527
 *                 newQual[newQualIndex] = qual[i] + 33
 *                 newQualIndex += 1
 *                 lastChar = qual[i]             # <<<<<<<<<<<<<<
 *                 lastCount = 1
 * 
 */
        __pyx_v_lastChar = (__pyx_v_qual[__pyx_v_i]);

        /* "htslibWrapper.pyx":528
 *                 newQualIndex += 1
 *                 lastChar = qual[i]
 *                 lastCount = 1             # <<<<<<<<<<<<<<
 * 
 *     if lastCount > 0:
 */
        __pyx_v_lastCount = 1;
      }
      __pyx_L9:;
    }
    __pyx_L8:;
  }

  /* "htslibWrapper.pyx":530
 *                 lastCount = 1
 * 
 *     if lastCount > 0:             # <<<<<<<<<<<<<<
 *         newQual[newQualIndex] = lastCount
 *         newQualIndex += 1
 */
  __pyx_t_2 = ((__pyx_v_lastCount > 0) != 0);
  if (__pyx_t_2) {

    /* "htslibWrapper.pyx":531
 * 
 *     if lastCount > 0:
 *         newQual[newQualIndex] = lastCount             # <<<<<<<<<<<<<<
 *         newQualIndex += 1
 * 
 */
    (__pyx_v_newQual[__pyx_v_newQualIndex]) = __pyx_v_lastCount;

    /* "htslibWrapper.pyx":532
 *     if lastCount > 0:
 *         newQual[newQualIndex] = lastCount
 *         newQualIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     finalQual = <char*>malloc(sizeof(char)*(newQualIndex+1))
 */
    __pyx_v_newQualIndex = (__pyx_v_newQualIndex + 1);
    goto __pyx_L10;
  }
  __pyx_L10:;

  /* "htslibWrapper.pyx":534
 *         newQualIndex += 1
 * 
 *     finalQual = <char*>malloc(sizeof(char)*(newQualIndex+1))             # <<<<<<<<<<<<<<
 *     newQual[newQualIndex] = 0
 *     strcpy(finalQual, newQual)
 */
  __pyx_v_finalQual = ((char *)malloc(((sizeof(char)) * (__pyx_v_newQualIndex + 1))));

  /* "htslibWrapper.pyx":535
 * 
 *     finalQual = <char*>malloc(sizeof(char)*(newQualIndex+1))
 *     newQual[newQualIndex] = 0             # <<<<<<<<<<<<<<
 *     strcpy(finalQual, newQual)
 *     finalQual[newQualIndex] = 0
 */
  (__pyx_v_newQual[__pyx_v_newQualIndex]) = 0;

  /* "htslibWrapper.pyx":536
 *     finalQual = <char*>malloc(sizeof(char)*(newQualIndex+1))
 *     newQual[newQualIndex] = 0
 *     strcpy(finalQual, newQual)             # <<<<<<<<<<<<<<
 *     finalQual[newQualIndex] = 0
 *     #free(newQual)
 */
  strcpy(__pyx_v_finalQual, __pyx_v_newQual);

  /* "htslibWrapper.pyx":537
 *     newQual[newQualIndex] = 0
 *     strcpy(finalQual, newQual)
 *     finalQual[newQualIndex] = 0             # <<<<<<<<<<<<<<
 *     #free(newQual)
 *     free(read.qual)
 */
  (__pyx_v_finalQual[__pyx_v_newQualIndex]) = 0;

  /* "htslibWrapper.pyx":539
 *     finalQual[newQualIndex] = 0
 *     #free(newQual)
 *     free(read.qual)             # <<<<<<<<<<<<<<
 *     read.qual = finalQual
 * 
 */
  free(__pyx_v_read->qual);

  /* "htslibWrapper.pyx":540
 *     #free(newQual)
 *     free(read.qual)
 *     read.qual = finalQual             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_v_read->qual = __pyx_v_finalQual;

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_WriteUnraisable("htslibWrapper.compressQual", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":544
 * ###################################################################################################
 * 
 * cdef void uncompressSeq(cAlignedRead* read, char* refSeq):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin.
 */

static void __pyx_f_13htslibWrapper_uncompressSeq(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, char *__pyx_v_refSeq) {
  int __pyx_v_refIndex;
  int __pyx_v_newSeqIndex;
  int __pyx_v_i;
  int __pyx_v_j;
  int __pyx_v_seqLen;
  char *__pyx_v_seq;
  char *__pyx_v_newSeq;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  int __pyx_t_2;
  int __pyx_t_3;
  int __pyx_t_4;
  char __pyx_t_5;
  int __pyx_t_6;
  __Pyx_RefNannySetupContext("uncompressSeq", 0);

  /* "htslibWrapper.pyx":548
 *     Does exactly what it says on the tin.
 *     """
 *     cdef int refIndex = 0             # <<<<<<<<<<<<<<
 *     cdef int newSeqIndex = 0
 *     cdef int i = 0
 */
  __pyx_v_refIndex = 0;

  /* "htslibWrapper.pyx":549
 *     """
 *     cdef int refIndex = 0
 *     cdef int newSeqIndex = 0             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int j = 0
 */
  __pyx_v_newSeqIndex = 0;

  /* "htslibWrapper.pyx":550
 *     cdef int refIndex = 0
 *     cdef int newSeqIndex = 0
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef int j = 0
 *     cdef int seqLen = strlen(read.seq)
 */
  __pyx_v_i = 0;

  /* "htslibWrapper.pyx":551
 *     cdef int newSeqIndex = 0
 *     cdef int i = 0
 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef int seqLen = strlen(read.seq)
 *     cdef char* seq = read.seq
 */
  __pyx_v_j = 0;

  /* "htslibWrapper.pyx":552
 *     cdef int i = 0
 *     cdef int j = 0
 *     cdef int seqLen = strlen(read.seq)             # <<<<<<<<<<<<<<
 *     cdef char* seq = read.seq
 *     cdef char* newSeq = <char*>(malloc(sizeof(char*)*(read.rlen+1)))
 */
  __pyx_v_seqLen = strlen(__pyx_v_read->seq);

  /* "htslibWrapper.pyx":553
 *     cdef int j = 0
 *     cdef int seqLen = strlen(read.seq)
 *     cdef char* seq = read.seq             # <<<<<<<<<<<<<<
 *     cdef char* newSeq = <char*>(malloc(sizeof(char*)*(read.rlen+1)))
 * 
 */
  __pyx_t_1 = __pyx_v_read->seq;
  __pyx_v_seq = __pyx_t_1;

  /* "htslibWrapper.pyx":554
 *     cdef int seqLen = strlen(read.seq)
 *     cdef char* seq = read.seq
 *     cdef char* newSeq = <char*>(malloc(sizeof(char*)*(read.rlen+1)))             # <<<<<<<<<<<<<<
 * 
 *     for i in range(seqLen):
 */
  __pyx_v_newSeq = ((char *)malloc(((sizeof(char *)) * (__pyx_v_read->rlen + 1))));

  /* "htslibWrapper.pyx":556
 *     cdef char* newSeq = <char*>(malloc(sizeof(char*)*(read.rlen+1)))
 * 
 *     for i in range(seqLen):             # <<<<<<<<<<<<<<
 *         if seq[i] <= 40:
 *             for j in range(seq[i]):
 */
  __pyx_t_2 = __pyx_v_seqLen;
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
    __pyx_v_i = __pyx_t_3;

    /* "htslibWrapper.pyx":557
 * 
 *     for i in range(seqLen):
 *         if seq[i] <= 40:             # <<<<<<<<<<<<<<
 *             for j in range(seq[i]):
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]
 */
    __pyx_t_4 = (((__pyx_v_seq[__pyx_v_i]) <= 40) != 0);
    if (__pyx_t_4) {

      /* "htslibWrapper.pyx":558
 *     for i in range(seqLen):
 *         if seq[i] <= 40:
 *             for j in range(seq[i]):             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]
 *                 newSeqIndex += 1
 */
      __pyx_t_5 = (__pyx_v_seq[__pyx_v_i]);
      for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
        __pyx_v_j = __pyx_t_6;

        /* "htslibWrapper.pyx":559
 *         if seq[i] <= 40:
 *             for j in range(seq[i]):
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]             # <<<<<<<<<<<<<<
 *                 newSeqIndex += 1
 *             refIndex += seq[i]
 */
        (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = (__pyx_v_refSeq[(__pyx_v_j + __pyx_v_refIndex)]);

        /* "htslibWrapper.pyx":560
 *             for j in range(seq[i]):
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]
 *                 newSeqIndex += 1             # <<<<<<<<<<<<<<
 *             refIndex += seq[i]
 *         else:
 */
        __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
      }

      /* "htslibWrapper.pyx":561
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]
 *                 newSeqIndex += 1
 *             refIndex += seq[i]             # <<<<<<<<<<<<<<
 *         else:
 *             newSeq[newSeqIndex] = seq[i]
 */
      __pyx_v_refIndex = (__pyx_v_refIndex + (__pyx_v_seq[__pyx_v_i]));
      goto __pyx_L5;
    }
    /*else*/ {

      /* "htslibWrapper.pyx":563
 *             refIndex += seq[i]
 *         else:
 *             newSeq[newSeqIndex] = seq[i]             # <<<<<<<<<<<<<<
 *             refIndex += 1
 *             newSeqIndex += 1
 */
      (__pyx_v_newSeq[__pyx_v_newSeqIndex]) = (__pyx_v_seq[__pyx_v_i]);

      /* "htslibWrapper.pyx":564
 *         else:
 *             newSeq[newSeqIndex] = seq[i]
 *             refIndex += 1             # <<<<<<<<<<<<<<
 *             newSeqIndex += 1
 * 
 */
      __pyx_v_refIndex = (__pyx_v_refIndex + 1);

      /* "htslibWrapper.pyx":565
 *             newSeq[newSeqIndex] = seq[i]
 *             refIndex += 1
 *             newSeqIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     free(read.seq)
 */
      __pyx_v_newSeqIndex = (__pyx_v_newSeqIndex + 1);
    }
    __pyx_L5:;
  }

  /* "htslibWrapper.pyx":567
 *             newSeqIndex += 1
 * 
 *     free(read.seq)             # <<<<<<<<<<<<<<
 *     read.seq = newSeq
 *     read.seq[read.rlen] = 0
 */
  free(__pyx_v_read->seq);

  /* "htslibWrapper.pyx":568
 * 
 *     free(read.seq)
 *     read.seq = newSeq             # <<<<<<<<<<<<<<
 *     read.seq[read.rlen] = 0
 * 
 */
  __pyx_v_read->seq = __pyx_v_newSeq;

  /* "htslibWrapper.pyx":569
 *     free(read.seq)
 *     read.seq = newSeq
 *     read.seq[read.rlen] = 0             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  (__pyx_v_read->seq[__pyx_v_read->rlen]) = 0;

  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":573
 * ###################################################################################################
 * 
 * cdef void uncompressQual(cAlignedRead* read):             # <<<<<<<<<<<<<<
 *     """
 *     Does exactly what it says on the tin.
 */

static void __pyx_f_13htslibWrapper_uncompressQual(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read) {
  char *__pyx_v_newQual;
  char *__pyx_v_qual;
  int __pyx_v_lenQual;
  int __pyx_v_i;
  CYTHON_UNUSED int __pyx_v_j;
  int __pyx_v_newQualIndex;
  __Pyx_RefNannyDeclarations
  char *__pyx_t_1;
  long __pyx_t_2;
  int __pyx_t_3;
  char __pyx_t_4;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("uncompressQual", 0);

  /* "htslibWrapper.pyx":577
 *     Does exactly what it says on the tin.
 *     """
 *     cdef char* newQual = <char*>(malloc(sizeof(char)*(read.rlen+1)))             # <<<<<<<<<<<<<<
 *     cdef char* qual = read.qual
 * 
 */
  __pyx_v_newQual = ((char *)malloc(((sizeof(char)) * (__pyx_v_read->rlen + 1))));

  /* "htslibWrapper.pyx":578
 *     """
 *     cdef char* newQual = <char*>(malloc(sizeof(char)*(read.rlen+1)))
 *     cdef char* qual = read.qual             # <<<<<<<<<<<<<<
 * 
 *     cdef int lenQual = strlen(read.qual)
 */
  __pyx_t_1 = __pyx_v_read->qual;
  __pyx_v_qual = __pyx_t_1;

  /* "htslibWrapper.pyx":580
 *     cdef char* qual = read.qual
 * 
 *     cdef int lenQual = strlen(read.qual)             # <<<<<<<<<<<<<<
 *     cdef int i = 0
 *     cdef int j = 0
 */
  __pyx_v_lenQual = strlen(__pyx_v_read->qual);

  /* "htslibWrapper.pyx":581
 * 
 *     cdef int lenQual = strlen(read.qual)
 *     cdef int i = 0             # <<<<<<<<<<<<<<
 *     cdef int j = 0
 *     cdef int newQualIndex = 0
 */
  __pyx_v_i = 0;

  /* "htslibWrapper.pyx":582
 *     cdef int lenQual = strlen(read.qual)
 *     cdef int i = 0
 *     cdef int j = 0             # <<<<<<<<<<<<<<
 *     cdef int newQualIndex = 0
 * 
 */
  __pyx_v_j = 0;

  /* "htslibWrapper.pyx":583
 *     cdef int i = 0
 *     cdef int j = 0
 *     cdef int newQualIndex = 0             # <<<<<<<<<<<<<<
 * 
 *     #logger.info("Length = %s or %s" %(lenQual, len([x for x in qual])))
 */
  __pyx_v_newQualIndex = 0;

  /* "htslibWrapper.pyx":588
 *     #logger.info(",".join( [str(x) for x in qual] ) )
 * 
 *     for i in range(0, lenQual-1, 2):             # <<<<<<<<<<<<<<
 *         for j in range(qual[i+1]):
 *             newQual[newQualIndex] = qual[i] - 33
 */
  __pyx_t_2 = (__pyx_v_lenQual - 1);
  for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=2) {
    __pyx_v_i = __pyx_t_3;

    /* "htslibWrapper.pyx":589
 * 
 *     for i in range(0, lenQual-1, 2):
 *         for j in range(qual[i+1]):             # <<<<<<<<<<<<<<
 *             newQual[newQualIndex] = qual[i] - 33
 *             assert qual[i] - 33 >= 0, "Shit 1. Qual = %s. Count = %s!" %(qual[i], qual[i+1])
 */
    __pyx_t_4 = (__pyx_v_qual[(__pyx_v_i + 1)]);
    for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
      __pyx_v_j = __pyx_t_5;

      /* "htslibWrapper.pyx":590
 *     for i in range(0, lenQual-1, 2):
 *         for j in range(qual[i+1]):
 *             newQual[newQualIndex] = qual[i] - 33             # <<<<<<<<<<<<<<
 *             assert qual[i] - 33 >= 0, "Shit 1. Qual = %s. Count = %s!" %(qual[i], qual[i+1])
 *             assert qual[i] - 33 <= 93, "Shit 2!. Qual = %s. Count = %s" %(qual[i], qual[i+1])
 */
      (__pyx_v_newQual[__pyx_v_newQualIndex]) = ((__pyx_v_qual[__pyx_v_i]) - 33);

      /* "htslibWrapper.pyx":591
 *         for j in range(qual[i+1]):
 *             newQual[newQualIndex] = qual[i] - 33
 *             assert qual[i] - 33 >= 0, "Shit 1. Qual = %s. Count = %s!" %(qual[i], qual[i+1])             # <<<<<<<<<<<<<<
 *             assert qual[i] - 33 <= 93, "Shit 2!. Qual = %s. Count = %s" %(qual[i], qual[i+1])
 *             newQualIndex += 1
 */
      #ifndef CYTHON_WITHOUT_ASSERTIONS
      if (unlikely(!((((__pyx_v_qual[__pyx_v_i]) - 33) >= 0) != 0))) {
        __pyx_t_6 = PyInt_FromLong((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        __pyx_t_7 = PyInt_FromLong((__pyx_v_qual[(__pyx_v_i + 1)])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
        __Pyx_GIVEREF(__pyx_t_6);
        PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
        __Pyx_GIVEREF(__pyx_t_7);
        __pyx_t_6 = 0;
        __pyx_t_7 = 0;
        __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_29), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_7));
        __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
        PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_7));
        __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      }
      #endif

      /* "htslibWrapper.pyx":592
 *             newQual[newQualIndex] = qual[i] - 33
 *             assert qual[i] - 33 >= 0, "Shit 1. Qual = %s. Count = %s!" %(qual[i], qual[i+1])
 *             assert qual[i] - 33 <= 93, "Shit 2!. Qual = %s. Count = %s" %(qual[i], qual[i+1])             # <<<<<<<<<<<<<<
 *             newQualIndex += 1
 * 
 */
      #ifndef CYTHON_WITHOUT_ASSERTIONS
      if (unlikely(!((((__pyx_v_qual[__pyx_v_i]) - 33) <= 93) != 0))) {
        __pyx_t_7 = PyInt_FromLong((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_8 = PyInt_FromLong((__pyx_v_qual[(__pyx_v_i + 1)])); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_8);
        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(__pyx_t_6);
        PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
        __Pyx_GIVEREF(__pyx_t_7);
        PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_8);
        __Pyx_GIVEREF(__pyx_t_8);
        __pyx_t_7 = 0;
        __pyx_t_8 = 0;
        __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_30), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        __Pyx_GOTREF(((PyObject *)__pyx_t_8));
        __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
        PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_8));
        __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      }
      #endif

      /* "htslibWrapper.pyx":593
 *             assert qual[i] - 33 >= 0, "Shit 1. Qual = %s. Count = %s!" %(qual[i], qual[i+1])
 *             assert qual[i] - 33 <= 93, "Shit 2!. Qual = %s. Count = %s" %(qual[i], qual[i+1])
 *             newQualIndex += 1             # <<<<<<<<<<<<<<
 * 
 *     assert read.rlen == newQualIndex
 */
      __pyx_v_newQualIndex = (__pyx_v_newQualIndex + 1);
    }
  }

  /* "htslibWrapper.pyx":595
 *             newQualIndex += 1
 * 
 *     assert read.rlen == newQualIndex             # <<<<<<<<<<<<<<
 * 
 *     free(read.qual)
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!((__pyx_v_read->rlen == __pyx_v_newQualIndex) != 0))) {
    PyErr_SetNone(PyExc_AssertionError);
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  #endif

  /* "htslibWrapper.pyx":597
 *     assert read.rlen == newQualIndex
 * 
 *     free(read.qual)             # <<<<<<<<<<<<<<
 *     read.qual = newQual
 *     read.qual[read.rlen] = 0
 */
  free(__pyx_v_read->qual);

  /* "htslibWrapper.pyx":598
 * 
 *     free(read.qual)
 *     read.qual = newQual             # <<<<<<<<<<<<<<
 *     read.qual[read.rlen] = 0
 * 
 */
  __pyx_v_read->qual = __pyx_v_newQual;

  /* "htslibWrapper.pyx":599
 *     free(read.qual)
 *     read.qual = newQual
 *     read.qual[read.rlen] = 0             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  (__pyx_v_read->qual[__pyx_v_read->rlen]) = 0;

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_WriteUnraisable("htslibWrapper.uncompressQual", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":603
 * ###################################################################################################
 * 
 * cdef void compressRead(cAlignedRead* read, char* refSeq, int refStart, int refEnd, int qualBinSize, int fullComp):             # <<<<<<<<<<<<<<
 *     """
 *     To save memory use, we compress reads. The sequence is compressed using reference-based
 */

static void __pyx_f_13htslibWrapper_compressRead(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, char *__pyx_v_refSeq, int __pyx_v_refStart, CYTHON_UNUSED int __pyx_v_refEnd, int __pyx_v_qualBinSize, CYTHON_UNUSED int __pyx_v_fullComp) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("compressRead", 0);

  /* "htslibWrapper.pyx":610
 *     for candidate generation). A bit is set in the bit-field to label the read as compressed or uncompressed.
 *     """
 *     if Read_IsCompressed(read):             # <<<<<<<<<<<<<<
 *         return
 * 
 */
  __pyx_t_1 = (__pyx_f_13htslibWrapper_Read_IsCompressed(__pyx_v_read) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":611
 *     """
 *     if Read_IsCompressed(read):
 *         return             # <<<<<<<<<<<<<<
 * 
 *     if read.seq != NULL:
 */
    goto __pyx_L0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":613
 *         return
 * 
 *     if read.seq != NULL:             # <<<<<<<<<<<<<<
 *         compressSeq(read, refSeq + (read.pos - refStart))
 * 
 */
  __pyx_t_1 = ((__pyx_v_read->seq != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":614
 * 
 *     if read.seq != NULL:
 *         compressSeq(read, refSeq + (read.pos - refStart))             # <<<<<<<<<<<<<<
 * 
 *     if read.qual != NULL:
 */
    __pyx_f_13htslibWrapper_compressSeq(__pyx_v_read, (__pyx_v_refSeq + (__pyx_v_read->pos - __pyx_v_refStart)));
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":616
 *         compressSeq(read, refSeq + (read.pos - refStart))
 * 
 *     if read.qual != NULL:             # <<<<<<<<<<<<<<
 *         compressQual(read, qualBinSize)
 * 
 */
  __pyx_t_1 = ((__pyx_v_read->qual != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":617
 * 
 *     if read.qual != NULL:
 *         compressQual(read, qualBinSize)             # <<<<<<<<<<<<<<
 * 
 *     #if fullComp == 1 and read.cigarOps != NULL:
 */
    __pyx_f_13htslibWrapper_compressQual(__pyx_v_read, __pyx_v_qualBinSize);
    goto __pyx_L5;
  }
  __pyx_L5:;

  /* "htslibWrapper.pyx":623
 *     #    read.cigarOps = NULL
 * 
 *     if read.hash != NULL:             # <<<<<<<<<<<<<<
 *         free(read.hash)
 *         read.hash = NULL
 */
  __pyx_t_1 = ((__pyx_v_read->hash != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":624
 * 
 *     if read.hash != NULL:
 *         free(read.hash)             # <<<<<<<<<<<<<<
 *         read.hash = NULL
 * 
 */
    free(__pyx_v_read->hash);

    /* "htslibWrapper.pyx":625
 *     if read.hash != NULL:
 *         free(read.hash)
 *         read.hash = NULL             # <<<<<<<<<<<<<<
 * 
 *     Read_SetCompressed(read)
 */
    __pyx_v_read->hash = NULL;
    goto __pyx_L6;
  }
  __pyx_L6:;

  /* "htslibWrapper.pyx":627
 *         read.hash = NULL
 * 
 *     Read_SetCompressed(read)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_f_13htslibWrapper_Read_SetCompressed(__pyx_v_read);

  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

/* "htslibWrapper.pyx":631
 * ###################################################################################################
 * 
 * cdef void uncompressRead(cAlignedRead* read, char* refSeq, int refStart, int refEnd, int qualBinSize):             # <<<<<<<<<<<<<<
 *     """
 *     Un-compress the read.
 */

static void __pyx_f_13htslibWrapper_uncompressRead(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_read, char *__pyx_v_refSeq, int __pyx_v_refStart, CYTHON_UNUSED int __pyx_v_refEnd, CYTHON_UNUSED int __pyx_v_qualBinSize) {
  __Pyx_RefNannyDeclarations
  int __pyx_t_1;
  __Pyx_RefNannySetupContext("uncompressRead", 0);

  /* "htslibWrapper.pyx":635
 *     Un-compress the read.
 *     """
 *     if not Read_IsCompressed(read):             # <<<<<<<<<<<<<<
 *         return
 * 
 */
  __pyx_t_1 = ((!(__pyx_f_13htslibWrapper_Read_IsCompressed(__pyx_v_read) != 0)) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":636
 *     """
 *     if not Read_IsCompressed(read):
 *         return             # <<<<<<<<<<<<<<
 * 
 *     if read.seq != NULL:
 */
    goto __pyx_L0;
    goto __pyx_L3;
  }
  __pyx_L3:;

  /* "htslibWrapper.pyx":638
 *         return
 * 
 *     if read.seq != NULL:             # <<<<<<<<<<<<<<
 *         uncompressSeq(read, refSeq + (read.pos - refStart))
 * 
 */
  __pyx_t_1 = ((__pyx_v_read->seq != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":639
 * 
 *     if read.seq != NULL:
 *         uncompressSeq(read, refSeq + (read.pos - refStart))             # <<<<<<<<<<<<<<
 * 
 *     if read.qual != NULL:
 */
    __pyx_f_13htslibWrapper_uncompressSeq(__pyx_v_read, (__pyx_v_refSeq + (__pyx_v_read->pos - __pyx_v_refStart)));
    goto __pyx_L4;
  }
  __pyx_L4:;

  /* "htslibWrapper.pyx":641
 *         uncompressSeq(read, refSeq + (read.pos - refStart))
 * 
 *     if read.qual != NULL:             # <<<<<<<<<<<<<<
 *         uncompressQual(read)
 * 
 */
  __pyx_t_1 = ((__pyx_v_read->qual != NULL) != 0);
  if (__pyx_t_1) {

    /* "htslibWrapper.pyx":642
 * 
 *     if read.qual != NULL:
 *         uncompressQual(read)             # <<<<<<<<<<<<<<
 * 
 *     Read_SetUnCompressed(read)
 */
    __pyx_f_13htslibWrapper_uncompressQual(__pyx_v_read);
    goto __pyx_L5;
  }
  __pyx_L5:;

  /* "htslibWrapper.pyx":644
 *         uncompressQual(read)
 * 
 *     Read_SetUnCompressed(read)             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_v_read);

  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":260
 * 
 * cdef inline int Read_IsDuplicate(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FDUP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 1024) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":263
 * 
 * cdef inline int Read_IsUnmapped(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FUNMAP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 4) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":266
 * 
 * cdef inline int Read_MateIsUnmapped(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FMUNMAP) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 8) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":269
 * 
 * cdef inline int Read_MateIsReverse(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FMREVERSE) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 32) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":272
 * 
 * cdef inline int Read_IsQCFail(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FQCFAIL) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 512) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":275
 * 
 * cdef inline int Read_IsReadOne(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FREAD1) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_IsSecondaryAlignment(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 64) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":281
 * 
 * cdef inline int Read_IsCompressed(cAlignedRead* theRead) nogil:
 *     return ( (theRead.bitFlag & BAM_FCOMPRESSED) != 0)             # <<<<<<<<<<<<<<
 * 
 * cdef inline int Read_SetIsNotReverse(cAlignedRead* theRead) nogil:
 */
  __pyx_r = ((__pyx_v_theRead->bitFlag & 2048) != 0);
  goto __pyx_L0;

  __pyx_r = 0;
  __pyx_L0:;
  return __pyx_r;
}

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

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

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

  __pyx_r = 0;
  return __pyx_r;
}

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

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

  /* "htslibWrapper.pxd":287
 * 
 * cdef inline int Read_SetIsReverse(cAlignedRead* theRead) nogil:
 *     theRead.bitFlag |= BAM_FREVERSE             # <<<<<<<<<<<<<<
 * 
 * cdef inline void Read_SetQCFail(cAlignedRead* theRead) nogil:
 */
  __pyx_v_theRead->bitFlag = (__pyx_v_theRead->bitFlag | 16);

  __pyx_r = 0;
  return __pyx_r;
}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetQCFail(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

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

}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

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

}

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

static CYTHON_INLINE void __pyx_f_13htslibWrapper_Read_SetUnCompressed(__pyx_t_13htslibWrapper_cAlignedRead *__pyx_v_theRead) {

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

}
static struct __pyx_vtabstruct_13htslibWrapper_Samfile __pyx_vtable_13htslibWrapper_Samfile;

static PyObject *__pyx_tp_new_13htslibWrapper_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_13htslibWrapper_Samfile *p;
  PyObject *o;
  o = (*t->tp_alloc)(t, 0);
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_13htslibWrapper_Samfile *)o);
  p->__pyx_vtab = __pyx_vtabptr_13htslibWrapper_Samfile;
  p->lock = Py_None; Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_13htslibWrapper_7Samfile_1__cinit__(o, a, k) < 0)) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_13htslibWrapper_Samfile(PyObject *o) {
  struct __pyx_obj_13htslibWrapper_Samfile *p = (struct __pyx_obj_13htslibWrapper_Samfile *)o;
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_13htslibWrapper_7Samfile_3__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  Py_CLEAR(p->lock);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_13htslibWrapper_Samfile(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_13htslibWrapper_Samfile *p = (struct __pyx_obj_13htslibWrapper_Samfile *)o;
  if (p->lock) {
    e = (*v)(p->lock, a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_13htslibWrapper_Samfile(PyObject *o) {
  struct __pyx_obj_13htslibWrapper_Samfile *p = (struct __pyx_obj_13htslibWrapper_Samfile *)o;
  PyObject* tmp;
  tmp = ((PyObject*)p->lock);
  p->lock = Py_None; Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyObject *__pyx_getprop_13htslibWrapper_7Samfile_nreferences(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_13htslibWrapper_7Samfile_11nreferences_1__get__(o);
}

static PyObject *__pyx_getprop_13htslibWrapper_7Samfile_references(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_13htslibWrapper_7Samfile_10references_1__get__(o);
}

static PyObject *__pyx_getprop_13htslibWrapper_7Samfile_lengths(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_13htslibWrapper_7Samfile_7lengths_1__get__(o);
}

static PyObject *__pyx_getprop_13htslibWrapper_7Samfile_text(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_13htslibWrapper_7Samfile_4text_1__get__(o);
}

static PyObject *__pyx_getprop_13htslibWrapper_7Samfile_header(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_13htslibWrapper_7Samfile_6header_1__get__(o);
}

static PyMethodDef __pyx_methods_13htslibWrapper_Samfile[] = {
  {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_5_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_13htslibWrapper_7Samfile_4_open)},
  {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_7fetch, METH_O, __Pyx_DOCSTR(__pyx_doc_13htslibWrapper_7Samfile_6fetch)},
  {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_13htslibWrapper_7Samfile_8close)},
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_13htslibWrapper_Samfile[] = {
  {(char *)"nreferences", __pyx_getprop_13htslibWrapper_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_31), 0},
  {(char *)"references", __pyx_getprop_13htslibWrapper_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_32), 0},
  {(char *)"lengths", __pyx_getprop_13htslibWrapper_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_33), 0},
  {(char *)"text", __pyx_getprop_13htslibWrapper_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_34), 0},
  {(char *)"header", __pyx_getprop_13htslibWrapper_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_35), 0},
  {0, 0, 0, 0, 0}
};

static PyTypeObject __pyx_type_13htslibWrapper_Samfile = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("htslibWrapper.Samfile"), /*tp_name*/
  sizeof(struct __pyx_obj_13htslibWrapper_Samfile), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_13htslibWrapper_Samfile, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  __Pyx_DOCSTR("\n    *(filename, mode='r', referencenames = None, referencelengths = None, text = NULL, header = None)*\n\n    A *SAM* file. The file is automatically opened.\n\n    *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode so for binary\n    (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output.\n    Use ``h`` to output header information  in text (:term:`TAM`)  mode.\n\n    If ``b`` is present, it must immediately follow ``r`` or ``w``.\n    Currently valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``.\n\n    so to open a :term:`BAM` file for reading::\n\n        f=Samfile('ex1.bam','rb')\n\n\n    For writing, the header of a :term:`TAM` file/:term:`BAM` file can be constituted from several\n    sources:\n\n        2. If *header* is given, the header is build from a multi-level dictionary. The first level are the four types ('HD', 'SQ', ...). The second level is then a list of lines, with each line being a list of tag-value pairs.\n\n        3. If *text* is given, new header text is copied from raw text.\n\n        4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists.\n\n    If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n    access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n    "), /*tp_doc*/
  __pyx_tp_traverse_13htslibWrapper_Samfile, /*tp_traverse*/
  __pyx_tp_clear_13htslibWrapper_Samfile, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_13htslibWrapper_Samfile, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_13htslibWrapper_Samfile, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_13htslibWrapper_Samfile, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};
static struct __pyx_vtabstruct_13htslibWrapper_ReadIterator __pyx_vtable_13htslibWrapper_ReadIterator;

static PyObject *__pyx_tp_new_13htslibWrapper_ReadIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_13htslibWrapper_ReadIterator *p;
  PyObject *o;
  o = (*t->tp_alloc)(t, 0);
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_13htslibWrapper_ReadIterator *)o);
  p->__pyx_vtab = __pyx_vtabptr_13htslibWrapper_ReadIterator;
  if (unlikely(__pyx_pw_13htslibWrapper_12ReadIterator_1__cinit__(o, a, k) < 0)) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_13htslibWrapper_ReadIterator(PyObject *o) {
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_13htslibWrapper_12ReadIterator_3__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_13htslibWrapper_ReadIterator[] = {
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_13htslibWrapper_ReadIterator = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("htslibWrapper.ReadIterator"), /*tp_name*/
  sizeof(struct __pyx_obj_13htslibWrapper_ReadIterator), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_13htslibWrapper_ReadIterator, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  __Pyx_DOCSTR("\n    Iterates over mapped reads in a region.\n    "), /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_13htslibWrapper_ReadIterator, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
  0, /*tp_dict*/
  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_13htslibWrapper_ReadIterator, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};

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

#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
  #if PY_VERSION_HEX < 0x03020000
    { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
  #else
    PyModuleDef_HEAD_INIT,
  #endif
    __Pyx_NAMESTR("htslibWrapper"),
    0, /* m_doc */
    -1, /* m_size */
    __pyx_methods /* m_methods */,
    NULL, /* m_reload */
    NULL, /* m_traverse */
    NULL, /* m_clear */
    NULL /* m_free */
};
#endif

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0},
  {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
  {&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
  {&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
  {&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
  {&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
  {&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
  {&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
  {&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
  {&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 1, 0},
  {&__pyx_kp_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 0},
  {&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0},
  {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
  {&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0},
  {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
  {&__pyx_kp_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 0},
  {&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
  {&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
  {&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
  {&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0},
  {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
  {&__pyx_n_s__AH, __pyx_k__AH, sizeof(__pyx_k__AH), 0, 0, 1, 1},
  {&__pyx_n_s__AS, __pyx_k__AS, sizeof(__pyx_k__AS), 0, 0, 1, 1},
  {&__pyx_n_s__CL, __pyx_k__CL, sizeof(__pyx_k__CL), 0, 0, 1, 1},
  {&__pyx_n_s__CN, __pyx_k__CN, sizeof(__pyx_k__CN), 0, 0, 1, 1},
  {&__pyx_n_s__CO, __pyx_k__CO, sizeof(__pyx_k__CO), 0, 0, 1, 1},
  {&__pyx_n_s__DS, __pyx_k__DS, sizeof(__pyx_k__DS), 0, 0, 1, 1},
  {&__pyx_n_s__DT, __pyx_k__DT, sizeof(__pyx_k__DT), 0, 0, 1, 1},
  {&__pyx_n_s__GO, __pyx_k__GO, sizeof(__pyx_k__GO), 0, 0, 1, 1},
  {&__pyx_n_s__HD, __pyx_k__HD, sizeof(__pyx_k__HD), 0, 0, 1, 1},
  {&__pyx_n_s__ID, __pyx_k__ID, sizeof(__pyx_k__ID), 0, 0, 1, 1},
  {&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
  {&__pyx_n_s__LB, __pyx_k__LB, sizeof(__pyx_k__LB), 0, 0, 1, 1},
  {&__pyx_n_s__LN, __pyx_k__LN, sizeof(__pyx_k__LN), 0, 0, 1, 1},
  {&__pyx_n_s__Log, __pyx_k__Log, sizeof(__pyx_k__Log), 0, 0, 1, 1},
  {&__pyx_n_s__M5, __pyx_k__M5, sizeof(__pyx_k__M5), 0, 0, 1, 1},
  {&__pyx_n_s__PG, __pyx_k__PG, sizeof(__pyx_k__PG), 0, 0, 1, 1},
  {&__pyx_n_s__PI, __pyx_k__PI, sizeof(__pyx_k__PI), 0, 0, 1, 1},
  {&__pyx_n_s__PL, __pyx_k__PL, sizeof(__pyx_k__PL), 0, 0, 1, 1},
  {&__pyx_n_s__PN, __pyx_k__PN, sizeof(__pyx_k__PN), 0, 0, 1, 1},
  {&__pyx_n_s__PP, __pyx_k__PP, sizeof(__pyx_k__PP), 0, 0, 1, 1},
  {&__pyx_n_s__PU, __pyx_k__PU, sizeof(__pyx_k__PU), 0, 0, 1, 1},
  {&__pyx_n_s__RG, __pyx_k__RG, sizeof(__pyx_k__RG), 0, 0, 1, 1},
  {&__pyx_n_s__SM, __pyx_k__SM, sizeof(__pyx_k__SM), 0, 0, 1, 1},
  {&__pyx_n_s__SN, __pyx_k__SN, sizeof(__pyx_k__SN), 0, 0, 1, 1},
  {&__pyx_n_s__SO, __pyx_k__SO, sizeof(__pyx_k__SO), 0, 0, 1, 1},
  {&__pyx_n_s__SP, __pyx_k__SP, sizeof(__pyx_k__SP), 0, 0, 1, 1},
  {&__pyx_n_s__SQ, __pyx_k__SQ, sizeof(__pyx_k__SQ), 0, 0, 1, 1},
  {&__pyx_n_s__StandardError, __pyx_k__StandardError, sizeof(__pyx_k__StandardError), 0, 0, 1, 1},
  {&__pyx_n_s__UR, __pyx_k__UR, sizeof(__pyx_k__UR), 0, 0, 1, 1},
  {&__pyx_n_s__VALID_HEADERS, __pyx_k__VALID_HEADERS, sizeof(__pyx_k__VALID_HEADERS), 0, 0, 1, 1},
  {&__pyx_n_s__VALID_HEADER_FIELDS, __pyx_k__VALID_HEADER_FIELDS, sizeof(__pyx_k__VALID_HEADER_FIELDS), 0, 0, 1, 1},
  {&__pyx_n_s__VALID_HEADER_ORDER, __pyx_k__VALID_HEADER_ORDER, sizeof(__pyx_k__VALID_HEADER_ORDER), 0, 0, 1, 1},
  {&__pyx_n_s__VALID_HEADER_TYPES, __pyx_k__VALID_HEADER_TYPES, sizeof(__pyx_k__VALID_HEADER_TYPES), 0, 0, 1, 1},
  {&__pyx_n_s__VN, __pyx_k__VN, sizeof(__pyx_k__VN), 0, 0, 1, 1},
  {&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
  {&__pyx_n_s____import__, __pyx_k____import__, sizeof(__pyx_k____import__), 0, 0, 1, 1},
  {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1},
  {&__pyx_n_s____pyx_vtable__, __pyx_k____pyx_vtable__, sizeof(__pyx_k____pyx_vtable__), 0, 0, 1, 1},
  {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1},
  {&__pyx_n_s___open, __pyx_k___open, sizeof(__pyx_k___open), 0, 0, 1, 1},
  {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1},
  {&__pyx_n_s__close, __pyx_k__close, sizeof(__pyx_k__close), 0, 0, 1, 1},
  {&__pyx_n_s__end, __pyx_k__end, sizeof(__pyx_k__end), 0, 0, 1, 1},
  {&__pyx_n_s__exists, __pyx_k__exists, sizeof(__pyx_k__exists), 0, 0, 1, 1},
  {&__pyx_n_s__fetch, __pyx_k__fetch, sizeof(__pyx_k__fetch), 0, 0, 1, 1},
  {&__pyx_n_s__file, __pyx_k__file, sizeof(__pyx_k__file), 0, 0, 1, 1},
  {&__pyx_n_s__fileName, __pyx_k__fileName, sizeof(__pyx_k__fileName), 0, 0, 1, 1},
  {&__pyx_n_s__getLogger, __pyx_k__getLogger, sizeof(__pyx_k__getLogger), 0, 0, 1, 1},
  {&__pyx_n_s__itertools, __pyx_k__itertools, sizeof(__pyx_k__itertools), 0, 0, 1, 1},
  {&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1},
  {&__pyx_n_s__loadIndex, __pyx_k__loadIndex, sizeof(__pyx_k__loadIndex), 0, 0, 1, 1},
  {&__pyx_n_s__logger, __pyx_k__logger, sizeof(__pyx_k__logger), 0, 0, 1, 1},
  {&__pyx_n_s__logging, __pyx_k__logging, sizeof(__pyx_k__logging), 0, 0, 1, 1},
  {&__pyx_n_s__mode, __pyx_k__mode, sizeof(__pyx_k__mode), 0, 0, 1, 1},
  {&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1},
  {&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
  {&__pyx_n_s__print, __pyx_k__print, sizeof(__pyx_k__print), 0, 0, 1, 1},
  {&__pyx_n_s__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 1, 1},
  {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1},
  {&__pyx_n_s__rb, __pyx_k__rb, sizeof(__pyx_k__rb), 0, 0, 1, 1},
  {&__pyx_n_s__rbh, __pyx_k__rbh, sizeof(__pyx_k__rbh), 0, 0, 1, 1},
  {&__pyx_n_s__region, __pyx_k__region, sizeof(__pyx_k__region), 0, 0, 1, 1},
  {&__pyx_n_s__samfile, __pyx_k__samfile, sizeof(__pyx_k__samfile), 0, 0, 1, 1},
  {&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1},
  {&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
  {&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
  {&__pyx_n_s__text, __pyx_k__text, sizeof(__pyx_k__text), 0, 0, 1, 1},
  {&__pyx_n_s__types, __pyx_k__types, sizeof(__pyx_k__types), 0, 0, 1, 1},
  {&__pyx_n_s__zlib, __pyx_k__zlib, sizeof(__pyx_k__zlib), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_StandardError = __Pyx_GetBuiltinName(__pyx_n_s__StandardError); if (!__pyx_builtin_StandardError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  return 0;
  __pyx_L1_error:;
  return -1;
}

static int __Pyx_InitCachedConstants(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);

  /* "htslibWrapper.pyx":257
 *                 # convert to python string (note: call self.text to create 0-terminated string)
 *                 t = self.text
 *                 for line in t.split("\n"):             # <<<<<<<<<<<<<<
 *                     if not line.strip(): continue
 * 
 */
  __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_9)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_10);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));

  /* "htslibWrapper.pyx":260
 *                     if not line.strip(): continue
 * 
 *                     if not line.startswith("@"):             # <<<<<<<<<<<<<<
 *                         raise StandardError, "Header line without '@': '%s. Total header text is %s'" % (line,t)
 * 
 */
  __pyx_k_tuple_12 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_12);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));

  /* "htslibWrapper.pyx":263
 *                         raise StandardError, "Header line without '@': '%s. Total header text is %s'" % (line,t)
 * 
 *                     fields = line[1:].split("\t")             # <<<<<<<<<<<<<<
 *                     record = fields[0]
 *                     assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
 */
  __pyx_k_slice_14 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_k_slice_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_slice_14);
  __Pyx_GIVEREF(__pyx_k_slice_14);
  __pyx_k_tuple_16 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_16);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16));

  /* "htslibWrapper.pyx":270
 *                     if record == "CO":
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))             # <<<<<<<<<<<<<<
 *                         continue
 * 
 */
  __pyx_k_slice_18 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_k_slice_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_slice_18);
  __Pyx_GIVEREF(__pyx_k_slice_18);

  /* "htslibWrapper.pyx":275
 *                     # the following is clumsy as generators do not work?
 *                     x = {}
 *                     for field in fields[1:]:             # <<<<<<<<<<<<<<
 *                         key, value = field.split(":",1)
 *                         if key not in VALID_HEADER_FIELDS[record]:
 */
  __pyx_k_slice_19 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_k_slice_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_slice_19);
  __Pyx_GIVEREF(__pyx_k_slice_19);

  /* "htslibWrapper.pyx":276
 *                     x = {}
 *                     for field in fields[1:]:
 *                         key, value = field.split(":",1)             # <<<<<<<<<<<<<<
 *                         if key not in VALID_HEADER_FIELDS[record]:
 *                             raise ValueError("unknown field code '%s' in record '%s'" % (key, record))
 */
  __pyx_k_tuple_21 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_20), __pyx_int_1); if (unlikely(!__pyx_k_tuple_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_21);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_21));

  /* "htslibWrapper.pyx":11
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_k_tuple_36 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__Log)); if (unlikely(!__pyx_k_tuple_36)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_36);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_36));

  /* "htslibWrapper.pyx":23
 * 
 * # order of records within sam headers
 * VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" )             # <<<<<<<<<<<<<<
 * 
 * # type conversions within sam header records
 */
  __pyx_k_tuple_37 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_n_s__CO)); if (unlikely(!__pyx_k_tuple_37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_37);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37));

  /* "htslibWrapper.pyx":32
 * 
 * # output order of fields within records
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),             # <<<<<<<<<<<<<<
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 */
  __pyx_k_tuple_38 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__SO), ((PyObject *)__pyx_n_s__GO)); if (unlikely(!__pyx_k_tuple_38)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_38);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38));

  /* "htslibWrapper.pyx":33
 * # output order of fields within records
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),             # <<<<<<<<<<<<<<
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 *                        "PG" : ( "ID", "VN", "CL" ), }
 */
  __pyx_k_tuple_39 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__SN), ((PyObject *)__pyx_n_s__LN), ((PyObject *)__pyx_n_s__AH), ((PyObject *)__pyx_n_s__AS), ((PyObject *)__pyx_n_s__M5), ((PyObject *)__pyx_n_s__UR), ((PyObject *)__pyx_n_s__SP)); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_39);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));

  /* "htslibWrapper.pyx":34
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),             # <<<<<<<<<<<<<<
 *                        "PG" : ( "ID", "VN", "CL" ), }
 * 
 */
  __pyx_k_tuple_40 = PyTuple_Pack(10, ((PyObject *)__pyx_n_s__ID), ((PyObject *)__pyx_n_s__SM), ((PyObject *)__pyx_n_s__LB), ((PyObject *)__pyx_n_s__DS), ((PyObject *)__pyx_n_s__PU), ((PyObject *)__pyx_n_s__PI), ((PyObject *)__pyx_n_s__CN), ((PyObject *)__pyx_n_s__DT), ((PyObject *)__pyx_n_s__PL), ((PyObject *)__pyx_n_s__PG)); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_40);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));

  /* "htslibWrapper.pyx":35
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 *                        "PG" : ( "ID", "VN", "CL" ), }             # <<<<<<<<<<<<<<
 * 
 * ######################################################################
 */
  __pyx_k_tuple_41 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__ID), ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__CL)); if (unlikely(!__pyx_k_tuple_41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_k_tuple_41);
  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_41));
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_InitGlobals(void) {
  if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  return 0;
  __pyx_L1_error:;
  return -1;
}

#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC inithtslibWrapper(void); /*proto*/
PyMODINIT_FUNC inithtslibWrapper(void)
#else
PyMODINIT_FUNC PyInit_htslibWrapper(void); /*proto*/
PyMODINIT_FUNC PyInit_htslibWrapper(void)
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  #if CYTHON_REFNANNY
  __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
  if (!__Pyx_RefNanny) {
      PyErr_Clear();
      __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
      if (!__Pyx_RefNanny)
          Py_FatalError("failed to import 'refnanny' module");
  }
  #endif
  __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_htslibWrapper(void)", 0);
  if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #ifdef __Pyx_CyFunction_USED
  if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  #ifdef WITH_THREAD /* Python build with threading support? */
  PyEval_InitThreads();
  #endif
  #endif
  /*--- Module creation code ---*/
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4(__Pyx_NAMESTR("htslibWrapper"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  Py_INCREF(__pyx_d);
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    if (!PyDict_GetItemString(modules, "htslibWrapper")) {
      if (unlikely(PyDict_SetItemString(modules, "htslibWrapper", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
  }
  #endif
  __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  /*--- Initialize various global constants etc. ---*/
  if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
  if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  if (__pyx_module_is_main_htslibWrapper) {
    if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  }
  /*--- Builtin init code ---*/
  if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Constants init code ---*/
  if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Global init code ---*/
  /*--- Variable export code ---*/
  /*--- Function export code ---*/
  if (__Pyx_ExportFunction("destroyRead", (void (*)(void))__pyx_f_13htslibWrapper_destroyRead, "void (__pyx_t_13htslibWrapper_cAlignedRead *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ExportFunction("compressRead", (void (*)(void))__pyx_f_13htslibWrapper_compressRead, "void (__pyx_t_13htslibWrapper_cAlignedRead *, char *, int, int, int, int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ExportFunction("uncompressRead", (void (*)(void))__pyx_f_13htslibWrapper_uncompressRead, "void (__pyx_t_13htslibWrapper_cAlignedRead *, char *, int, int, int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Type init code ---*/
  __pyx_vtabptr_13htslibWrapper_Samfile = &__pyx_vtable_13htslibWrapper_Samfile;
  __pyx_vtable_13htslibWrapper_Samfile.clearHeader = (void (*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile_clearHeader;
  __pyx_vtable_13htslibWrapper_Samfile.clearIndex = (void (*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile_clearIndex;
  __pyx_vtable_13htslibWrapper_Samfile._isBam = (int (*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile__isBam;
  __pyx_vtable_13htslibWrapper_Samfile._isCram = (int (*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile__isCram;
  __pyx_vtable_13htslibWrapper_Samfile._isOpen = (int (*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile__isOpen;
  __pyx_vtable_13htslibWrapper_Samfile._hasIndex = (PyObject *(*)(struct __pyx_obj_13htslibWrapper_Samfile *))__pyx_f_13htslibWrapper_7Samfile__hasIndex;
  __pyx_vtable_13htslibWrapper_Samfile.openBAMFile = (void (*)(struct __pyx_obj_13htslibWrapper_Samfile *, PyObject *))__pyx_f_13htslibWrapper_7Samfile_openBAMFile;
  __pyx_vtable_13htslibWrapper_Samfile._open = (PyObject *(*)(struct __pyx_obj_13htslibWrapper_Samfile *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_13htslibWrapper_7Samfile__open *__pyx_optional_args))__pyx_f_13htslibWrapper_7Samfile__open;
  __pyx_vtable_13htslibWrapper_Samfile.getrname = (char *(*)(struct __pyx_obj_13htslibWrapper_Samfile *, int))__pyx_f_13htslibWrapper_7Samfile_getrname;
  __pyx_vtable_13htslibWrapper_Samfile.fetch = (struct __pyx_obj_13htslibWrapper_ReadIterator *(*)(struct __pyx_obj_13htslibWrapper_Samfile *, char const *, int __pyx_skip_dispatch))__pyx_f_13htslibWrapper_7Samfile_fetch;
  __pyx_vtable_13htslibWrapper_Samfile.close = (PyObject *(*)(struct __pyx_obj_13htslibWrapper_Samfile *, int __pyx_skip_dispatch))__pyx_f_13htslibWrapper_7Samfile_close;
  if (PyType_Ready(&__pyx_type_13htslibWrapper_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetVtable(__pyx_type_13htslibWrapper_Samfile.tp_dict, __pyx_vtabptr_13htslibWrapper_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_13htslibWrapper_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_13htslibWrapper_Samfile = &__pyx_type_13htslibWrapper_Samfile;
  __pyx_vtabptr_13htslibWrapper_ReadIterator = &__pyx_vtable_13htslibWrapper_ReadIterator;
  __pyx_vtable_13htslibWrapper_ReadIterator.get = (__pyx_t_13htslibWrapper_cAlignedRead *(*)(struct __pyx_obj_13htslibWrapper_ReadIterator *, int, char **))__pyx_f_13htslibWrapper_12ReadIterator_get;
  __pyx_vtable_13htslibWrapper_ReadIterator.cnext = (int (*)(struct __pyx_obj_13htslibWrapper_ReadIterator *))__pyx_f_13htslibWrapper_12ReadIterator_cnext;
  __pyx_vtable_13htslibWrapper_ReadIterator._getBase = (char (*)(struct __pyx_obj_13htslibWrapper_ReadIterator *, uint8_t *, int))__pyx_f_13htslibWrapper_12ReadIterator__getBase;
  if (PyType_Ready(&__pyx_type_13htslibWrapper_ReadIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetVtable(__pyx_type_13htslibWrapper_ReadIterator.tp_dict, __pyx_vtabptr_13htslibWrapper_ReadIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_SetAttrString(__pyx_m, "ReadIterator", (PyObject *)&__pyx_type_13htslibWrapper_ReadIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_13htslibWrapper_ReadIterator = &__pyx_type_13htslibWrapper_ReadIterator;
  /*--- Type import code ---*/
  __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", 
  #if CYTHON_COMPILING_IN_PYPY
  sizeof(PyTypeObject),
  #else
  sizeof(PyHeapTypeObject),
  #endif
  0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Variable import code ---*/
  /*--- Function import code ---*/
  /*--- Execution code ---*/

  /* "htslibWrapper.pyx":1
 * import os             # <<<<<<<<<<<<<<
 * import types
 * import itertools
 */
  __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__os), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__os, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":2
 * import os
 * import types             # <<<<<<<<<<<<<<
 * import itertools
 * import logging
 */
  __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__types), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":3
 * import os
 * import types
 * import itertools             # <<<<<<<<<<<<<<
 * import logging
 * cimport cython
 */
  __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__itertools), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__itertools, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":4
 * import types
 * import itertools
 * import logging             # <<<<<<<<<<<<<<
 * cimport cython
 * import zlib
 */
  __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__logging), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__logging, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":6
 * import logging
 * cimport cython
 * import zlib             # <<<<<<<<<<<<<<
 * #import zlib
 * 
 */
  __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__zlib), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__zlib, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":11
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s__logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s__getLogger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_36), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__logger, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":16
 * 
 * # valid types for sam headers
 * VALID_HEADER_TYPES = { "HD" : dict,             # <<<<<<<<<<<<<<
 *                        "SQ" : list,
 *                        "RG" : list,
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":17
 * # valid types for sam headers
 * VALID_HEADER_TYPES = { "HD" : dict,
 *                        "SQ" : list,             # <<<<<<<<<<<<<<
 *                        "RG" : list,
 *                        "PG" : list,
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":18
 * VALID_HEADER_TYPES = { "HD" : dict,
 *                        "SQ" : list,
 *                        "RG" : list,             # <<<<<<<<<<<<<<
 *                        "PG" : list,
 *                        "CO" : list }
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":19
 *                        "SQ" : list,
 *                        "RG" : list,
 *                        "PG" : list,             # <<<<<<<<<<<<<<
 *                        "CO" : list }
 * 
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":20
 *                        "RG" : list,
 *                        "PG" : list,
 *                        "CO" : list }             # <<<<<<<<<<<<<<
 * 
 * # order of records within sam headers
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":23
 * 
 * # order of records within sam headers
 * VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" )             # <<<<<<<<<<<<<<
 * 
 * # type conversions within sam header records
 */
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_37)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":26
 * 
 * # type conversions within sam header records
 * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },             # <<<<<<<<<<<<<<
 *                         "SQ" : { "SN" : str, "LN" : int, "AH": str, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
 *                         "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, "PG" : str},
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;

  /* "htslibWrapper.pyx":27
 * # type conversions within sam header records
 * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
 *                         "SQ" : { "SN" : str, "LN" : int, "AH": str, "AS" : str, "M5" : str, "UR" : str, "SP" : str },             # <<<<<<<<<<<<<<
 *                         "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, "PG" : str},
 *                         "PG" : { "ID" : str, "VN" : str, "CL" : str , "PN" : str, "PP" : str, "DS": str},  }
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__AH), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;

  /* "htslibWrapper.pyx":28
 * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
 *                         "SQ" : { "SN" : str, "LN" : int, "AH": str, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
 *                         "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, "PG" : str},             # <<<<<<<<<<<<<<
 *                         "PG" : { "ID" : str, "VN" : str, "CL" : str , "PN" : str, "PP" : str, "DS": str},  }
 * 
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;

  /* "htslibWrapper.pyx":29
 *                         "SQ" : { "SN" : str, "LN" : int, "AH": str, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
 *                         "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, "PG" : str},
 *                         "PG" : { "ID" : str, "VN" : str, "CL" : str , "PN" : str, "PP" : str, "DS": str},  }             # <<<<<<<<<<<<<<
 * 
 * # output order of fields within records
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":32
 * 
 * # output order of fields within records
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),             # <<<<<<<<<<<<<<
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_38)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":33
 * # output order of fields within records
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),             # <<<<<<<<<<<<<<
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 *                        "PG" : ( "ID", "VN", "CL" ), }
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_39)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":34
 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),             # <<<<<<<<<<<<<<
 *                        "PG" : ( "ID", "VN", "CL" ), }
 * 
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_40)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}

  /* "htslibWrapper.pyx":35
 *                        "SQ" : ( "SN", "LN", "AH", "AS", "M5" , "UR" , "SP" ),
 *                        "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" , "PG"),
 *                        "PG" : ( "ID", "VN", "CL" ), }             # <<<<<<<<<<<<<<
 * 
 * ######################################################################
 */
  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_41)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (PyDict_SetItem(__pyx_d, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":143
 *             self.theHeader = NULL
 * 
 *     cpdef _open(self, mode, loadIndex=True):             # <<<<<<<<<<<<<<
 *         """
 *         open a sam/bam/cram file.
 */
  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_k_2 = __pyx_t_1;
  __Pyx_GIVEREF(__pyx_t_1);
  __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":1
 * import os             # <<<<<<<<<<<<<<
 * import types
 * import itertools
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
  if (PyDict_SetItem(__pyx_d, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;

  /* "htslibWrapper.pxd":295
 *     theRead.bitFlag |= BAM_FCOMPRESSED
 * 
 * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead) nogil:             # <<<<<<<<<<<<<<
 *     theRead.bitFlag &= (~BAM_FCOMPRESSED)
 * 
 */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  if (__pyx_m) {
    __Pyx_AddTraceback("init htslibWrapper", __pyx_clineno, __pyx_lineno, __pyx_filename);
    Py_DECREF(__pyx_m); __pyx_m = 0;
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init htslibWrapper");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if PY_MAJOR_VERSION < 3
  return;
  #else
  return __pyx_m;
  #endif
}

/* Runtime support code */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
    PyObject *m = NULL, *p = NULL;
    void *r = NULL;
    m = PyImport_ImportModule((char *)modname);
    if (!m) goto end;
    p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
    if (!p) goto end;
    r = PyLong_AsVoidPtr(p);
end:
    Py_XDECREF(p);
    Py_XDECREF(m);
    return (__Pyx_RefNannyAPIStruct *)r;
}
#endif /* CYTHON_REFNANNY */

static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
    PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
    if (unlikely(!result)) {
        PyErr_Format(PyExc_NameError,
#if PY_MAJOR_VERSION >= 3
            "name '%U' is not defined", name);
#else
            "name '%s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

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

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

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

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

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

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

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

static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
    PyObject *r;
    if (!j) return NULL;
    r = PyObject_GetItem(o, j);
    Py_DECREF(j);
    return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
    if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
        PyObject *r = PyList_GET_ITEM(o, i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
    if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
        PyObject *r = PyTuple_GET_ITEM(o, i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                     int is_list, int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (is_list || PyList_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
        if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
            PyObject *r = PyList_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    }
    else if (PyTuple_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
        if ((!boundscheck) || likely((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 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 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 CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
    if (likely(PyList_CheckExact(L))) {
        if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return NULL;
        Py_INCREF(Py_None);
        return Py_None; /* this is just to have an accurate signature */
    } else {
        return __Pyx_PyObject_CallMethod1(L, __pyx_n_s__append, x);
    }
}

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 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 int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
    const char *name, int exact)
{
    if (!type) {
        PyErr_Format(PyExc_SystemError, "Missing type object");
        return 0;
    }
    if (none_allowed && obj == Py_None) return 1;
    else if (exact) {
        if (Py_TYPE(obj) == type) return 1;
    }
    else {
        if (PyObject_TypeCheck(obj, type)) return 1;
    }
    PyErr_Format(PyExc_TypeError,
        "Argument '%s' has incorrect type (expected %s, got %s)",
        name, type->tp_name, Py_TYPE(obj)->tp_name);
    return 0;
}

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

static 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;
}

#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3
static PyObject *__Pyx_GetStdout(void) {
    PyObject *f = PySys_GetObject((char *)"stdout");
    if (!f) {
        PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
    }
    return f;
}
static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
    int i;
    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    Py_INCREF(f);
    for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
        PyObject* v;
        if (PyFile_SoftSpace(f, 1)) {
            if (PyFile_WriteString(" ", f) < 0)
                goto error;
        }
        v = PyTuple_GET_ITEM(arg_tuple, i);
        if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
            goto error;
        if (PyString_Check(v)) {
            char *s = PyString_AsString(v);
            Py_ssize_t len = PyString_Size(v);
            if (len > 0 &&
                isspace(Py_CHARMASK(s[len-1])) &&
                s[len-1] != ' ')
                    PyFile_SoftSpace(f, 0);
        }
    }
    if (newline) {
        if (PyFile_WriteString("\n", f) < 0)
            goto error;
        PyFile_SoftSpace(f, 0);
    }
    Py_DECREF(f);
    return 0;
error:
    Py_DECREF(f);
    return -1;
}
#else /* Python 3 has a print function */
static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
    PyObject* kwargs = 0;
    PyObject* result = 0;
    PyObject* end_string;
    if (unlikely(!__pyx_print)) {
        __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s__print);
        if (!__pyx_print)
            return -1;
    }
    if (stream) {
        kwargs = PyDict_New();
        if (unlikely(!kwargs))
            return -1;
        if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s__file, stream) < 0))
            goto bad;
        if (!newline) {
            end_string = PyUnicode_FromStringAndSize(" ", 1);
            if (unlikely(!end_string))
                goto bad;
            if (PyDict_SetItem(kwargs, __pyx_n_s__end, end_string) < 0) {
                Py_DECREF(end_string);
                goto bad;
            }
            Py_DECREF(end_string);
        }
    } else if (!newline) {
        if (unlikely(!__pyx_print_kwargs)) {
            __pyx_print_kwargs = PyDict_New();
            if (unlikely(!__pyx_print_kwargs))
                return -1;
            end_string = PyUnicode_FromStringAndSize(" ", 1);
            if (unlikely(!end_string))
                return -1;
            if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s__end, end_string) < 0) {
                Py_DECREF(end_string);
                return -1;
            }
            Py_DECREF(end_string);
        }
        kwargs = __pyx_print_kwargs;
    }
    result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
    if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
        Py_DECREF(kwargs);
    if (!result)
        return -1;
    Py_DECREF(result);
    return 0;
bad:
    if (kwargs != __pyx_print_kwargs)
        Py_XDECREF(kwargs);
    return -1;
}
#endif

#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3
static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    Py_INCREF(f);
    if (PyFile_SoftSpace(f, 0)) {
        if (PyFile_WriteString(" ", f) < 0)
            goto error;
    }
    if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
        goto error;
    if (PyFile_WriteString("\n", f) < 0)
        goto error;
    Py_DECREF(f);
    return 0;
error:
    Py_DECREF(f);
    return -1;
    /* the line below is just to avoid C compiler
     * warnings about unused functions */
    return __Pyx_Print(f, NULL, 0);
}
#else /* Python 3 has a print function */
static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
    int res;
    PyObject* arg_tuple = PyTuple_Pack(1, o);
    if (unlikely(!arg_tuple))
        return -1;
    res = __Pyx_Print(stream, arg_tuple, 1);
    Py_DECREF(arg_tuple);
    return res;
}
#endif

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) {
    const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
    const int is_unsigned = const_zero < neg_one;
    if ((sizeof(int32_t) == sizeof(char))  ||
        (sizeof(int32_t) == sizeof(short))) {
        return PyInt_FromLong((long)val);
    } else if ((sizeof(int32_t) == sizeof(int)) ||
               (sizeof(int32_t) == sizeof(long))) {
        if (is_unsigned)
            return PyLong_FromUnsignedLong((unsigned long)val);
        else
            return PyInt_FromLong((long)val);
    } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
        else
            return PyLong_FromLongLong((PY_LONG_LONG)val);
    } else {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&val;
        return _PyLong_FromByteArray(bytes, sizeof(int32_t),
                                     little, !is_unsigned);
    }
}

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
    const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
    const int is_unsigned = const_zero < neg_one;
    if ((sizeof(uint32_t) == sizeof(char))  ||
        (sizeof(uint32_t) == sizeof(short))) {
        return PyInt_FromLong((long)val);
    } else if ((sizeof(uint32_t) == sizeof(int)) ||
               (sizeof(uint32_t) == sizeof(long))) {
        if (is_unsigned)
            return PyLong_FromUnsignedLong((unsigned long)val);
        else
            return PyInt_FromLong((long)val);
    } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
        else
            return PyLong_FromLongLong((PY_LONG_LONG)val);
    } else {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&val;
        return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
                                     little, !is_unsigned);
    }
}

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

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 */
