/* Generated by Cython 0.29.4 */

#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
    #error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
    #error Cython requires Python 2.6+ or Python 3.3+.
#else
#define CYTHON_ABI "0_29_4"
#define CYTHON_HEX_VERSION 0x001D04F0
#define CYTHON_FUTURE_DIVISION 0
#include <stddef.h>
#ifndef offsetof
  #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
#if !defined(WIN32) && !defined(MS_WINDOWS)
  #ifndef __stdcall
    #define __stdcall
  #endif
  #ifndef __cdecl
    #define __cdecl
  #endif
  #ifndef __fastcall
    #define __fastcall
  #endif
#endif
#ifndef DL_IMPORT
  #define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
  #define DL_EXPORT(t) t
#endif
#define __PYX_COMMA ,
#ifndef HAVE_LONG_LONG
  #if PY_VERSION_HEX >= 0x02070000
    #define HAVE_LONG_LONG
  #endif
#endif
#ifndef PY_LONG_LONG
  #define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
  #define Py_HUGE_VAL HUGE_VAL
#endif
#ifdef PYPY_VERSION
  #define CYTHON_COMPILING_IN_PYPY 1
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #undef CYTHON_USE_TYPE_SLOTS
  #define CYTHON_USE_TYPE_SLOTS 0
  #undef CYTHON_USE_PYTYPE_LOOKUP
  #define CYTHON_USE_PYTYPE_LOOKUP 0
  #if PY_VERSION_HEX < 0x03050000
    #undef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 0
  #elif !defined(CYTHON_USE_ASYNC_SLOTS)
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #undef CYTHON_USE_UNICODE_INTERNALS
  #define CYTHON_USE_UNICODE_INTERNALS 0
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #undef CYTHON_AVOID_BORROWED_REFS
  #define CYTHON_AVOID_BORROWED_REFS 1
  #undef CYTHON_ASSUME_SAFE_MACROS
  #define CYTHON_ASSUME_SAFE_MACROS 0
  #undef CYTHON_UNPACK_METHODS
  #define CYTHON_UNPACK_METHODS 0
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
  #undef CYTHON_PEP489_MULTI_PHASE_INIT
  #define CYTHON_PEP489_MULTI_PHASE_INIT 0
  #undef CYTHON_USE_TP_FINALIZE
  #define CYTHON_USE_TP_FINALIZE 0
  #undef CYTHON_USE_DICT_VERSIONS
  #define CYTHON_USE_DICT_VERSIONS 0
  #undef CYTHON_USE_EXC_INFO_STACK
  #define CYTHON_USE_EXC_INFO_STACK 0
#elif defined(PYSTON_VERSION)
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 1
  #define CYTHON_COMPILING_IN_CPYTHON 0
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #undef CYTHON_USE_PYTYPE_LOOKUP
  #define CYTHON_USE_PYTYPE_LOOKUP 0
  #undef CYTHON_USE_ASYNC_SLOTS
  #define CYTHON_USE_ASYNC_SLOTS 0
  #undef CYTHON_USE_PYLIST_INTERNALS
  #define CYTHON_USE_PYLIST_INTERNALS 0
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #undef CYTHON_USE_UNICODE_WRITER
  #define CYTHON_USE_UNICODE_WRITER 0
  #undef CYTHON_USE_PYLONG_INTERNALS
  #define CYTHON_USE_PYLONG_INTERNALS 0
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #undef CYTHON_FAST_THREAD_STATE
  #define CYTHON_FAST_THREAD_STATE 0
  #undef CYTHON_FAST_PYCALL
  #define CYTHON_FAST_PYCALL 0
  #undef CYTHON_PEP489_MULTI_PHASE_INIT
  #define CYTHON_PEP489_MULTI_PHASE_INIT 0
  #undef CYTHON_USE_TP_FINALIZE
  #define CYTHON_USE_TP_FINALIZE 0
  #undef CYTHON_USE_DICT_VERSIONS
  #define CYTHON_USE_DICT_VERSIONS 0
  #undef CYTHON_USE_EXC_INFO_STACK
  #define CYTHON_USE_EXC_INFO_STACK 0
#else
  #define CYTHON_COMPILING_IN_PYPY 0
  #define CYTHON_COMPILING_IN_PYSTON 0
  #define CYTHON_COMPILING_IN_CPYTHON 1
  #ifndef CYTHON_USE_TYPE_SLOTS
    #define CYTHON_USE_TYPE_SLOTS 1
  #endif
  #if PY_VERSION_HEX < 0x02070000
    #undef CYTHON_USE_PYTYPE_LOOKUP
    #define CYTHON_USE_PYTYPE_LOOKUP 0
  #elif !defined(CYTHON_USE_PYTYPE_LOOKUP)
    #define CYTHON_USE_PYTYPE_LOOKUP 1
  #endif
  #if PY_MAJOR_VERSION < 3
    #undef CYTHON_USE_ASYNC_SLOTS
    #define CYTHON_USE_ASYNC_SLOTS 0
  #elif !defined(CYTHON_USE_ASYNC_SLOTS)
    #define CYTHON_USE_ASYNC_SLOTS 1
  #endif
  #if PY_VERSION_HEX < 0x02070000
    #undef CYTHON_USE_PYLONG_INTERNALS
    #define CYTHON_USE_PYLONG_INTERNALS 0
  #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
    #define CYTHON_USE_PYLONG_INTERNALS 1
  #endif
  #ifndef CYTHON_USE_PYLIST_INTERNALS
    #define CYTHON_USE_PYLIST_INTERNALS 1
  #endif
  #ifndef CYTHON_USE_UNICODE_INTERNALS
    #define CYTHON_USE_UNICODE_INTERNALS 1
  #endif
  #if PY_VERSION_HEX < 0x030300F0
    #undef CYTHON_USE_UNICODE_WRITER
    #define CYTHON_USE_UNICODE_WRITER 0
  #elif !defined(CYTHON_USE_UNICODE_WRITER)
    #define CYTHON_USE_UNICODE_WRITER 1
  #endif
  #ifndef CYTHON_AVOID_BORROWED_REFS
    #define CYTHON_AVOID_BORROWED_REFS 0
  #endif
  #ifndef CYTHON_ASSUME_SAFE_MACROS
    #define CYTHON_ASSUME_SAFE_MACROS 1
  #endif
  #ifndef CYTHON_UNPACK_METHODS
    #define CYTHON_UNPACK_METHODS 1
  #endif
  #ifndef CYTHON_FAST_THREAD_STATE
    #define CYTHON_FAST_THREAD_STATE 1
  #endif
  #ifndef CYTHON_FAST_PYCALL
    #define CYTHON_FAST_PYCALL 1
  #endif
  #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
    #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000)
  #endif
  #ifndef CYTHON_USE_TP_FINALIZE
    #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1)
  #endif
  #ifndef CYTHON_USE_DICT_VERSIONS
    #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1)
  #endif
  #ifndef CYTHON_USE_EXC_INFO_STACK
    #define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
  #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
  #include "longintrepr.h"
  #undef SHIFT
  #undef BASE
  #undef MASK
  #ifdef SIZEOF_VOID_P
    enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) };
  #endif
#endif
#ifndef __has_attribute
  #define __has_attribute(x) 0
#endif
#ifndef __has_cpp_attribute
  #define __has_cpp_attribute(x) 0
#endif
#ifndef CYTHON_RESTRICT
  #if defined(__GNUC__)
    #define CYTHON_RESTRICT __restrict__
  #elif defined(_MSC_VER) && _MSC_VER >= 1400
    #define CYTHON_RESTRICT __restrict
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_RESTRICT restrict
  #else
    #define CYTHON_RESTRICT
  #endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
#   if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
#     define CYTHON_UNUSED __attribute__ ((__unused__))
#   else
#     define CYTHON_UNUSED
#   endif
# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
#   define CYTHON_UNUSED __attribute__ ((__unused__))
# else
#   define CYTHON_UNUSED
# endif
#endif
#ifndef CYTHON_MAYBE_UNUSED_VAR
#  if defined(__cplusplus)
     template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
#  else
#    define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
#  endif
#endif
#ifndef CYTHON_NCP_UNUSED
# if CYTHON_COMPILING_IN_CPYTHON
#  define CYTHON_NCP_UNUSED
# else
#  define CYTHON_NCP_UNUSED CYTHON_UNUSED
# endif
#endif
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
#ifdef _MSC_VER
    #ifndef _MSC_STDINT_H_
        #if _MSC_VER < 1300
           typedef unsigned char     uint8_t;
           typedef unsigned int      uint32_t;
        #else
           typedef unsigned __int8   uint8_t;
           typedef unsigned __int32  uint32_t;
        #endif
    #endif
#else
   #include <stdint.h>
#endif
#ifndef CYTHON_FALLTHROUGH
  #if defined(__cplusplus) && __cplusplus >= 201103L
    #if __has_cpp_attribute(fallthrough)
      #define CYTHON_FALLTHROUGH [[fallthrough]]
    #elif __has_cpp_attribute(clang::fallthrough)
      #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
    #elif __has_cpp_attribute(gnu::fallthrough)
      #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
    #endif
  #endif
  #ifndef CYTHON_FALLTHROUGH
    #if __has_attribute(fallthrough)
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
    #else
      #define CYTHON_FALLTHROUGH
    #endif
  #endif
  #if defined(__clang__ ) && defined(__apple_build_version__)
    #if __apple_build_version__ < 7000000
      #undef  CYTHON_FALLTHROUGH
      #define CYTHON_FALLTHROUGH
    #endif
  #endif
#endif

#ifndef CYTHON_INLINE
  #if defined(__clang__)
    #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
  #elif defined(__GNUC__)
    #define CYTHON_INLINE __inline__
  #elif defined(_MSC_VER)
    #define CYTHON_INLINE __inline
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_INLINE inline
  #else
    #define CYTHON_INLINE
  #endif
#endif

#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
  #define Py_OptimizeFlag 0
#endif
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyClass_Type
#else
  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyType_Type
#endif
#ifndef Py_TPFLAGS_CHECKTYPES
  #define Py_TPFLAGS_CHECKTYPES 0
#endif
#ifndef Py_TPFLAGS_HAVE_INDEX
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#ifndef Py_TPFLAGS_HAVE_NEWBUFFER
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#ifndef Py_TPFLAGS_HAVE_FINALIZE
  #define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
#ifndef METH_STACKLESS
  #define METH_STACKLESS 0
#endif
#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL)
  #ifndef METH_FASTCALL
     #define METH_FASTCALL 0x80
  #endif
  typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs);
  typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
                                                          Py_ssize_t nargs, PyObject *kwnames);
#else
  #define __Pyx_PyCFunctionFast _PyCFunctionFast
  #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
#endif
#if CYTHON_FAST_PYCCALL
#define __Pyx_PyFastCFunction_Check(func)\
    ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS)))))
#else
#define __Pyx_PyFastCFunction_Check(func) 0
#endif
#if CYTHON_USE_DICT_VERSIONS
#define __PYX_GET_DICT_VERSION(dict)  (((PyDictObject*)(dict))->ma_version_tag)
#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\
    (version_var) = __PYX_GET_DICT_VERSION(dict);\
    (cache_var) = (value);
#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\
        static PY_UINT64_T __pyx_dict_version = 0;\
        static PyObject *__pyx_dict_cached_value = NULL;\
        if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\
            (VAR) = __pyx_dict_cached_value;\
        } else {\
            (VAR) = __pyx_dict_cached_value = (LOOKUP);\
            __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\
        }\
    }
#else
#define __PYX_GET_DICT_VERSION(dict)  (0)
#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)
#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP)  (VAR) = (LOOKUP);
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
  #define PyObject_Malloc(s)   PyMem_Malloc(s)
  #define PyObject_Free(p)     PyMem_Free(p)
  #define PyObject_Realloc(p)  PyMem_Realloc(p)
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030400A1
  #define PyMem_RawMalloc(n)           PyMem_Malloc(n)
  #define PyMem_RawRealloc(p, n)       PyMem_Realloc(p, n)
  #define PyMem_RawFree(p)             PyMem_Free(p)
#endif
#if CYTHON_COMPILING_IN_PYSTON
  #define __Pyx_PyCode_HasFreeVars(co)  PyCode_HasFreeVars(co)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
#else
  #define __Pyx_PyCode_HasFreeVars(co)  (PyCode_GetNumFree(co) > 0)
  #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
#endif
#if !CYTHON_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000
  #define __Pyx_PyThreadState_Current PyThreadState_GET()
#elif PY_VERSION_HEX >= 0x03060000
  #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet()
#elif PY_VERSION_HEX >= 0x03000000
  #define __Pyx_PyThreadState_Current PyThreadState_GET()
#else
  #define __Pyx_PyThreadState_Current _PyThreadState_Current
#endif
#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT)
#include "pythread.h"
#define Py_tss_NEEDS_INIT 0
typedef int Py_tss_t;
static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) {
  *key = PyThread_create_key();
  return 0;
}
static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) {
  Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t));
  *key = Py_tss_NEEDS_INIT;
  return key;
}
static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) {
  PyObject_Free(key);
}
static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) {
  return *key != Py_tss_NEEDS_INIT;
}
static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) {
  PyThread_delete_key(*key);
  *key = Py_tss_NEEDS_INIT;
}
static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) {
  return PyThread_set_key_value(*key, value);
}
static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
  return PyThread_get_key_value(*key);
}
#endif
#if CYTHON_COMPILING_IN_CPYTHON || defined(_PyDict_NewPresized)
#define __Pyx_PyDict_NewPresized(n)  ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n))
#else
#define __Pyx_PyDict_NewPresized(n)  PyDict_New()
#endif
#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
#else
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_Divide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(x,y)
#endif
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS
#define __Pyx_PyDict_GetItemStr(dict, name)  _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash)
#else
#define __Pyx_PyDict_GetItemStr(dict, name)  PyDict_GetItem(dict, name)
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
  #define CYTHON_PEP393_ENABLED 1
  #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ?\
                                              0 : _PyUnicode_Ready((PyObject *)(op)))
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   PyUnicode_MAX_CHAR_VALUE(u)
  #define __Pyx_PyUnicode_KIND(u)         PyUnicode_KIND(u)
  #define __Pyx_PyUnicode_DATA(u)         PyUnicode_DATA(u)
  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  PyUnicode_WRITE(k, d, i, ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#else
  #define CYTHON_PEP393_ENABLED 0
  #define PyUnicode_1BYTE_KIND  1
  #define PyUnicode_2BYTE_KIND  2
  #define PyUnicode_4BYTE_KIND  4
  #define __Pyx_PyUnicode_READY(op)       (0)
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
  #define __Pyx_PyUnicode_KIND(u)         (sizeof(Py_UNICODE))
  #define __Pyx_PyUnicode_DATA(u)         ((void*)PyUnicode_AS_UNICODE(u))
  #define __Pyx_PyUnicode_READ(k, d, i)   ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
  #define __Pyx_PyUnicode_Concat(a, b)      PyNumber_Add(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  PyNumber_Add(a, b)
#else
  #define __Pyx_PyUnicode_Concat(a, b)      PyUnicode_Concat(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
      PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
  #define PyUnicode_Contains(u, s)  PySequence_Contains(u, s)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
  #define PyByteArray_Check(obj)  PyObject_TypeCheck(obj, &PyByteArray_Type)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
  #define PyObject_Format(obj, fmt)  PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
#define __Pyx_PyString_FormatSafe(a, b)   ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b)  ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyString_Format(a, b)  PyUnicode_Format(a, b)
#else
  #define __Pyx_PyString_Format(a, b)  PyString_Format(a, b)
#endif
#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
  #define PyObject_ASCII(o)            PyObject_Repr(o)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBaseString_Type            PyUnicode_Type
  #define PyStringObject               PyUnicodeObject
  #define PyString_Type                PyUnicode_Type
  #define PyString_Check               PyUnicode_Check
  #define PyString_CheckExact          PyUnicode_CheckExact
  #define PyObject_Unicode             PyObject_Str
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
  #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
#else
  #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
  #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
#endif
#ifndef PySet_CheckExact
  #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
#endif
#if CYTHON_ASSUME_SAFE_MACROS
  #define __Pyx_PySequence_SIZE(seq)  Py_SIZE(seq)
#else
  #define __Pyx_PySequence_SIZE(seq)  PySequence_Size(seq)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyIntObject                  PyLongObject
  #define PyInt_Type                   PyLong_Type
  #define PyInt_Check(op)              PyLong_Check(op)
  #define PyInt_CheckExact(op)         PyLong_CheckExact(op)
  #define PyInt_FromString             PyLong_FromString
  #define PyInt_FromUnicode            PyLong_FromUnicode
  #define PyInt_FromLong               PyLong_FromLong
  #define PyInt_FromSize_t             PyLong_FromSize_t
  #define PyInt_FromSsize_t            PyLong_FromSsize_t
  #define PyInt_AsLong                 PyLong_AsLong
  #define PyInt_AS_LONG                PyLong_AS_LONG
  #define PyInt_AsSsize_t              PyLong_AsSsize_t
  #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
  #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
  #define PyNumber_Int                 PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBoolObject                 PyLongObject
#endif
#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
  #ifndef PyUnicode_InternFromString
    #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
  #endif
#endif
#if PY_VERSION_HEX < 0x030200A4
  typedef long Py_hash_t;
  #define __Pyx_PyInt_FromHash_t PyInt_FromLong
  #define __Pyx_PyInt_AsHash_t   PyInt_AsLong
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), func))
#else
  #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
#if CYTHON_USE_ASYNC_SLOTS
  #if PY_VERSION_HEX >= 0x030500B1
    #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
    #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
  #else
    #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
  #endif
#else
  #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef __Pyx_PyAsyncMethodsStruct
    typedef struct {
        unaryfunc am_await;
        unaryfunc am_aiter;
        unaryfunc am_anext;
    } __Pyx_PyAsyncMethodsStruct;
#endif

#if defined(WIN32) || defined(MS_WINDOWS)
  #define _USE_MATH_DEFINES
#endif
#include <math.h>
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
  float value;
  memset(&value, 0xFF, sizeof(value));
  return value;
}
#endif
#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
#define __Pyx_truncl trunc
#else
#define __Pyx_truncl truncl
#endif


#define __PYX_ERR(f_index, lineno, Ln_error) \
{ \
  __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \
}

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

#define __PYX_HAVE__htslibWrapper
#define __PYX_HAVE_API__htslibWrapper
/* Early includes */
#include <string.h>
#include <stdio.h>
#include "pythread.h"
#include "stdlib.h"
#include "math.h"
#include "stdio.h"
#include "ctype.h"
#include "string.h"
#include "stdint.h"
#include "htslib/bgzf.h"
#include "htslib/hts.h"
#include "htslib/sam.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */

#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
#define CYTHON_WITHOUT_ASSERTIONS
#endif

typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;

#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#define __Pyx_uchar_cast(c) ((unsigned char)c)
#define __Pyx_long_cast(x) ((long)x)
#define __Pyx_fits_Py_ssize_t(v, type, is_signed)  (\
    (sizeof(type) < sizeof(Py_ssize_t))  ||\
    (sizeof(type) > sizeof(Py_ssize_t) &&\
          likely(v < (type)PY_SSIZE_T_MAX ||\
                 v == (type)PY_SSIZE_T_MAX)  &&\
          (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
                                v == (type)PY_SSIZE_T_MIN)))  ||\
    (sizeof(type) == sizeof(Py_ssize_t) &&\
          (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
                               v == (type)PY_SSIZE_T_MAX)))  )
static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
    return (size_t) i < (size_t) limit;
}
#if defined (__cplusplus) && __cplusplus >= 201103L
    #include <cstdlib>
    #define __Pyx_sst_abs(value) std::abs(value)
#elif SIZEOF_INT >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) abs(value)
#elif SIZEOF_LONG >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) labs(value)
#elif defined (_MSC_VER)
    #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define __Pyx_sst_abs(value) llabs(value)
#elif defined (__GNUC__)
    #define __Pyx_sst_abs(value) __builtin_llabs(value)
#else
    #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
#endif
static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
#define __Pyx_PyBytes_FromString        PyBytes_FromString
#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
#if PY_MAJOR_VERSION < 3
    #define __Pyx_PyStr_FromString        __Pyx_PyBytes_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#else
    #define __Pyx_PyStr_FromString        __Pyx_PyUnicode_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
#endif
#define __Pyx_PyBytes_AsWritableString(s)     ((char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsWritableSString(s)    ((signed char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsWritableUString(s)    ((unsigned char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsString(s)     ((const char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsSString(s)    ((const signed char*) PyBytes_AS_STRING(s))
#define __Pyx_PyBytes_AsUString(s)    ((const unsigned char*) PyBytes_AS_STRING(s))
#define __Pyx_PyObject_AsWritableString(s)    ((char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsWritableSString(s)    ((signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsWritableUString(s)    ((unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsSString(s)    ((const signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsUString(s)    ((const unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_FromCString(s)  __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromCString(s)   __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
    const Py_UNICODE *u_end = u;
    while (*u_end++) ;
    return (size_t)(u_end - u - 1);
}
#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
#define __Pyx_PySequence_Tuple(obj)\
    (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
#else
#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
#endif
#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    const char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    if (strcmp(default_encoding_c, "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        char ascii_chars[128];
        int c;
        for (c = 0; c < 128; c++) {
            ascii_chars[c] = c;
        }
        __Pyx_sys_getdefaultencoding_not_ascii = 1;
        ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
        if (!ascii_chars_u) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
            PyErr_Format(
                PyExc_ValueError,
                "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
        Py_DECREF(ascii_chars_u);
        Py_DECREF(ascii_chars_b);
    }
    Py_DECREF(default_encoding);
    return 0;
bad:
    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(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
    if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
    strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    return -1;
}
#endif
#endif


/* Test for GCC > 2.95 */
#if defined(__GNUC__)     && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
  #define likely(x)   __builtin_expect(!!(x), 1)
  #define unlikely(x) __builtin_expect(!!(x), 0)
#else /* !__GNUC__ or GCC < 2.95 */
  #define likely(x)   (x)
  #define unlikely(x) (x)
#endif /* __GNUC__ */
static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }

static PyObject *__pyx_m = NULL;
static PyObject *__pyx_d;
static PyObject *__pyx_b;
static PyObject *__pyx_cython_runtime = NULL;
static PyObject *__pyx_empty_tuple;
static PyObject *__pyx_empty_bytes;
static PyObject *__pyx_empty_unicode;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;


static const char *__pyx_f[] = {
  "cython/htslibWrapper.pyx",
  "stringsource",
  "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;

/* --- Runtime support code (head) --- */
/* Refnanny.proto */
#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);
  #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
#define __Pyx_XDECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_XDECREF(tmp);\
    } while (0)
#define __Pyx_DECREF_SET(r, v) do {\
        PyObject *tmp = (PyObject *) r;\
        r = v; __Pyx_DECREF(tmp);\
    } while (0)
#define __Pyx_CLEAR(r)    do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
#define __Pyx_XCLEAR(r)   do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)

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

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

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

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

/* RaiseArgTupleInvalid.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);

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

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

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

/* GetModuleGlobalName.proto */
#if CYTHON_USE_DICT_VERSIONS
#define __Pyx_GetModuleGlobalName(var, name)  {\
    static PY_UINT64_T __pyx_dict_version = 0;\
    static PyObject *__pyx_dict_cached_value = NULL;\
    (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\
        (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\
        __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
}
#define __Pyx_GetModuleGlobalNameUncached(var, name)  {\
    PY_UINT64_T __pyx_dict_version;\
    PyObject *__pyx_dict_cached_value;\
    (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
}
static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value);
#else
#define __Pyx_GetModuleGlobalName(var, name)  (var) = __Pyx__GetModuleGlobalName(name)
#define __Pyx_GetModuleGlobalNameUncached(var, name)  (var) = __Pyx__GetModuleGlobalName(name)
static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name);
#endif

/* PyCFunctionFastCall.proto */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
#else
#define __Pyx_PyCFunction_FastCall(func, args, nargs)  (assert(0), NULL)
#endif

/* PyFunctionFastCall.proto */
#if CYTHON_FAST_PYCALL
#define __Pyx_PyFunction_FastCall(func, args, nargs)\
    __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs);
#else
#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
#endif
#define __Pyx_BUILD_ASSERT_EXPR(cond)\
    (sizeof(char [1 - 2*!(cond)]) - 1)
#ifndef Py_MEMBER_SIZE
#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
#endif
  static size_t __pyx_pyframe_localsplus_offset = 0;
  #include "frameobject.h"
  #define __Pxy_PyFrame_Initialize_Offsets()\
    ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
     (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
  #define __Pyx_PyFrame_GetLocalsplus(frame)\
    (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
#endif

/* PyObjectCall.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
#else
#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
#endif

/* PyObjectCall2Args.proto */
static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2);

/* PyObjectCallMethO.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
#endif

/* PyObjectCallOneArg.proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);

/* IncludeStringH.proto */
#include <string.h>

/* BytesEquals.proto */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);

/* UnicodeEquals.proto */
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);

/* StrEquals.proto */
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
#else
#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
#endif

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

/* GetItemInt.proto */
#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
    (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
               __Pyx_GetItemInt_Generic(o, to_py_func(i))))
#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
    (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
    (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
    __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
    (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck);
static 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);

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

/* PyObjectCallNoArg.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#else
#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
#endif

/* ListAppend.proto */
#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
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

/* SliceObject.proto */
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);

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

/* PyDictContains.proto */
static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) {
    int result = PyDict_Contains(dict, item);
    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}

/* PyObjectGetMethod.proto */
static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method);

/* PyObjectCallMethod1.proto */
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);

/* append.proto */
static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x);

/* DictGetItem.proto */
#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key);
#define __Pyx_PyObject_Dict_GetItem(obj, name)\
    (likely(PyDict_CheckExact(obj)) ?\
     __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name))
#else
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#define __Pyx_PyObject_Dict_GetItem(obj, name)  PyObject_GetItem(obj, name)
#endif

/* StringJoin.proto */
#if PY_MAJOR_VERSION < 3
#define __Pyx_PyString_Join __Pyx_PyBytes_Join
#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v))
#else
#define __Pyx_PyString_Join PyUnicode_Join
#define __Pyx_PyBaseString_Join PyUnicode_Join
#endif
#if CYTHON_COMPILING_IN_CPYTHON
    #if PY_MAJOR_VERSION < 3
    #define __Pyx_PyBytes_Join _PyString_Join
    #else
    #define __Pyx_PyBytes_Join _PyBytes_Join
    #endif
#else
static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values);
#endif

/* RaiseTooManyValuesToUnpack.proto */
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);

/* RaiseNeedMoreValuesToUnpack.proto */
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);

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

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

/* ObjectGetItem.proto */
#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key);
#else
#define __Pyx_PyObject_GetItem(obj, key)  PyObject_GetItem(obj, key)
#endif

/* ArgTypeTest.proto */
#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\
    ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\
        __Pyx__ArgTypeTest(obj, type, name, exact))
static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact);

/* PyObject_GenericGetAttrNoDict.proto */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name);
#else
#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr
#endif

/* PyObject_GenericGetAttr.proto */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name);
#else
#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr
#endif

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

/* SetupReduce.proto */
static int __Pyx_setup_reduce(PyObject* type_obj);

/* TypeImport.proto */
#ifndef __PYX_HAVE_RT_ImportType_proto
#define __PYX_HAVE_RT_ImportType_proto
enum __Pyx_ImportType_CheckSize {
   __Pyx_ImportType_CheckSize_Error = 0,
   __Pyx_ImportType_CheckSize_Warn = 1,
   __Pyx_ImportType_CheckSize_Ignore = 2
};
static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size);
#endif

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

/* CLineInTraceback.proto */
#ifdef CYTHON_CLINE_IN_TRACEBACK
#define __Pyx_CLineForTraceback(tstate, c_line)  (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
#else
static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
#endif

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

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

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

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

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

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value);

/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value);

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

/* CIntFromPy.proto */
static CYTHON_INLINE short __Pyx_PyInt_As_short(PyObject *);

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

/* CIntFromPy.proto */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);

/* FastTypeChecks.proto */
#if CYTHON_COMPILING_IN_CPYTHON
#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
#else
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
#endif
#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)

/* CheckBinaryVersion.proto */
static int __Pyx_check_binary_version(void);

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

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

static void __pyx_f_13htslibWrapper_7Samfile_clearHeader(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static void __pyx_f_13htslibWrapper_7Samfile_clearIndex(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static int __pyx_f_13htslibWrapper_7Samfile__isBam(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static int __pyx_f_13htslibWrapper_7Samfile__isCram(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static int __pyx_f_13htslibWrapper_7Samfile__isOpen(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_13htslibWrapper_7Samfile__hasIndex(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto*/
static void __pyx_f_13htslibWrapper_7Samfile_openBAMFile(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, PyObject *__pyx_v_mode); /* 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); /* proto*/
static char *__pyx_f_13htslibWrapper_7Samfile_getrname(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, int __pyx_v_tid); /* 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); /* proto*/
static PyObject *__pyx_f_13htslibWrapper_7Samfile_close(struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
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); /* proto*/
static int __pyx_f_13htslibWrapper_12ReadIterator_cnext(struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self); /* proto*/
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); /* proto*/

/* Module declarations from 'cython' */

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

/* Module declarations from '__builtin__' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from 'cpython' */

/* Module declarations from 'htslibWrapper' */
static PyTypeObject *__pyx_ptype_13htslibWrapper_Samfile = 0;
static PyTypeObject *__pyx_ptype_13htslibWrapper_ReadIterator = 0;
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"
extern int __pyx_module_is_main_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_TypeError;
static PyObject *__pyx_builtin_range;
static const char __pyx_k_[] = "\n";
static const char __pyx_k_r[] = "r";
static const char __pyx_k_AH[] = "AH";
static const char __pyx_k_AS[] = "AS";
static const char __pyx_k_CL[] = "CL";
static const char __pyx_k_CN[] = "CN";
static const char __pyx_k_CO[] = "CO";
static const char __pyx_k_DS[] = "DS";
static const char __pyx_k_DT[] = "DT";
static const char __pyx_k_GO[] = "GO";
static const char __pyx_k_HD[] = "HD";
static const char __pyx_k_ID[] = "ID";
static const char __pyx_k_LB[] = "LB";
static const char __pyx_k_LN[] = "LN";
static const char __pyx_k_M5[] = "M5";
static const char __pyx_k_PG[] = "PG";
static const char __pyx_k_PI[] = "PI";
static const char __pyx_k_PL[] = "PL";
static const char __pyx_k_PN[] = "PN";
static const char __pyx_k_PP[] = "PP";
static const char __pyx_k_PU[] = "PU";
static const char __pyx_k_RG[] = "RG";
static const char __pyx_k_SM[] = "SM";
static const char __pyx_k_SN[] = "SN";
static const char __pyx_k_SO[] = "SO";
static const char __pyx_k_SP[] = "SP";
static const char __pyx_k_SQ[] = "SQ";
static const char __pyx_k_UR[] = "UR";
static const char __pyx_k_VN[] = "VN";
static const char __pyx_k__2[] = "@";
static const char __pyx_k__4[] = "\t";
static const char __pyx_k__5[] = ":";
static const char __pyx_k_os[] = "os";
static const char __pyx_k_rb[] = "rb";
static const char __pyx_k_Log[] = "Log";
static const char __pyx_k_end[] = "end";
static const char __pyx_k_rbh[] = "rbh";
static const char __pyx_k_file[] = "file";
static const char __pyx_k_join[] = "join";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_mode[] = "mode";
static const char __pyx_k_name[] = "__name__";
static const char __pyx_k_open[] = "_open";
static const char __pyx_k_path[] = "path";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_text[] = "text";
static const char __pyx_k_zlib[] = "zlib";
static const char __pyx_k_close[] = "close";
static const char __pyx_k_fetch[] = "fetch";
static const char __pyx_k_print[] = "print";
static const char __pyx_k_range[] = "range";
static const char __pyx_k_split[] = "split";
static const char __pyx_k_strip[] = "strip";
static const char __pyx_k_types[] = "types";
static const char __pyx_k_append[] = "append";
static const char __pyx_k_exists[] = "exists";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_logger[] = "logger";
static const char __pyx_k_reduce[] = "__reduce__";
static const char __pyx_k_region[] = "region";
static const char __pyx_k_IOError[] = "IOError";
static const char __pyx_k_Samfile[] = "Samfile";
static const char __pyx_k_logging[] = "logging";
static const char __pyx_k_samfile[] = "samfile";
static const char __pyx_k_fileName[] = "fileName";
static const char __pyx_k_getstate[] = "__getstate__";
static const char __pyx_k_setstate[] = "__setstate__";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_getLogger[] = "getLogger";
static const char __pyx_k_itertools[] = "itertools";
static const char __pyx_k_loadIndex[] = "loadIndex";
static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
static const char __pyx_k_startswith[] = "startswith";
static const char __pyx_k_ReadIterator[] = "ReadIterator";
static const char __pyx_k_Shit_3_Qual_s[] = "Shit 3. Qual = %s";
static const char __pyx_k_Shit_4_Qual_s[] = "Shit 4!. Qual = %s";
static const char __pyx_k_StandardError[] = "StandardError";
static const char __pyx_k_VALID_HEADERS[] = "VALID_HEADERS";
static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
static const char __pyx_k_CLEARING_INDEX[] = "CLEARING INDEX!!!!!!";
static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
static const char __pyx_k_VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static const char __pyx_k_VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
static const char __pyx_k_BAM_file_is_read_only[] = "BAM file is read-only";
static const char __pyx_k_Shit_1_Qual_s_Count_s[] = "Shit 1. Qual = %s. Count = %s!";
static const char __pyx_k_Shit_2_Qual_s_Count_s[] = "Shit 2!. Qual = %s. Count = %s";
static const char __pyx_k_tid_s_out_of_range_0_tid_i[] = "tid (%s) out of range 0<=tid<%i";
static const char __pyx_k_invalid_file_opening_mode_s[] = "invalid file opening mode `%s`";
static const char __pyx_k_header_line_with_invalid_type_s[] = "header line with invalid type '%s': '%s'";
static const char __pyx_k_Cannot_retrieve_random_region_fr[] = "Cannot retrieve random region from Samfile %s, as it does not have an index";
static const char __pyx_k_Could_not_open_file_s_Check_that[] = "Could not open file `%s`. Check that file/path exists.";
static const char __pyx_k_Error_while_opening_index_for_fi[] = "Error while opening index for file `%s`. Check that index exists ";
static const char __pyx_k_Header_line_without_s_Total_head[] = "Header line without '@': '%s. Total header text is %s'";
static const char __pyx_k_Random_access_query_only_allowed[] = "Random access query only allowed for BAM/CRAM files.";
static const char __pyx_k_Samfile_s_is_not_open_Cannot_rea[] = "Samfile %s is not open. Cannot read from file.";
static const char __pyx_k_multiple_s_lines_are_not_permitt[] = "multiple '%s' lines are not permitted";
static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__";
static const char __pyx_k_unknown_field_code_s_in_record_s[] = "unknown field code '%s' in record '%s'";
static PyObject *__pyx_kp_s_;
static PyObject *__pyx_n_s_AH;
static PyObject *__pyx_n_s_AS;
static PyObject *__pyx_kp_s_BAM_file_is_read_only;
static PyObject *__pyx_n_s_CL;
static PyObject *__pyx_kp_s_CLEARING_INDEX;
static PyObject *__pyx_n_s_CN;
static PyObject *__pyx_n_s_CO;
static PyObject *__pyx_kp_s_Cannot_retrieve_random_region_fr;
static PyObject *__pyx_kp_s_Could_not_open_file_s_Check_that;
static PyObject *__pyx_n_s_DS;
static PyObject *__pyx_n_s_DT;
static PyObject *__pyx_kp_s_Error_while_opening_index_for_fi;
static PyObject *__pyx_n_s_GO;
static PyObject *__pyx_n_s_HD;
static PyObject *__pyx_kp_s_Header_line_without_s_Total_head;
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_kp_s_Random_access_query_only_allowed;
static PyObject *__pyx_n_s_ReadIterator;
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_Samfile;
static PyObject *__pyx_kp_s_Samfile_s_is_not_open_Cannot_rea;
static PyObject *__pyx_kp_s_Shit_1_Qual_s_Count_s;
static PyObject *__pyx_kp_s_Shit_2_Qual_s_Count_s;
static PyObject *__pyx_kp_s_Shit_3_Qual_s;
static PyObject *__pyx_kp_s_Shit_4_Qual_s;
static PyObject *__pyx_n_s_StandardError;
static PyObject *__pyx_n_s_TypeError;
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_kp_s__2;
static PyObject *__pyx_kp_s__4;
static PyObject *__pyx_kp_s__5;
static PyObject *__pyx_n_s_append;
static PyObject *__pyx_n_s_cline_in_traceback;
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_getstate;
static PyObject *__pyx_kp_s_header_line_with_invalid_type_s;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_kp_s_invalid_file_opening_mode_s;
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_main;
static PyObject *__pyx_n_s_mode;
static PyObject *__pyx_kp_s_multiple_s_lines_are_not_permitt;
static PyObject *__pyx_n_s_name;
static PyObject *__pyx_kp_s_no_default___reduce___due_to_non;
static PyObject *__pyx_n_s_open;
static PyObject *__pyx_n_s_os;
static PyObject *__pyx_n_s_path;
static PyObject *__pyx_n_s_print;
static PyObject *__pyx_n_s_pyx_vtable;
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_reduce;
static PyObject *__pyx_n_s_reduce_cython;
static PyObject *__pyx_n_s_reduce_ex;
static PyObject *__pyx_n_s_region;
static PyObject *__pyx_n_s_samfile;
static PyObject *__pyx_n_s_setstate;
static PyObject *__pyx_n_s_setstate_cython;
static PyObject *__pyx_n_s_split;
static PyObject *__pyx_n_s_startswith;
static PyObject *__pyx_n_s_strip;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_text;
static PyObject *__pyx_kp_s_tid_s_out_of_range_0_tid_i;
static PyObject *__pyx_n_s_types;
static PyObject *__pyx_kp_s_unknown_field_code_s_in_record_s;
static PyObject *__pyx_n_s_zlib;
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 PyObject *__pyx_pf_13htslibWrapper_7Samfile_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_7Samfile_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* 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_pf_13htslibWrapper_12ReadIterator_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_13htslibWrapper_12ReadIterator_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* 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 PyObject *__pyx_int_1;
static PyObject *__pyx_slice__3;
static PyObject *__pyx_tuple__6;
static PyObject *__pyx_tuple__7;
static PyObject *__pyx_tuple__8;
static PyObject *__pyx_tuple__9;
static PyObject *__pyx_tuple__10;
static PyObject *__pyx_tuple__11;
static PyObject *__pyx_tuple__12;
static PyObject *__pyx_tuple__13;
static PyObject *__pyx_tuple__14;
static PyObject *__pyx_tuple__15;
static PyObject *__pyx_tuple__16;
/* Late includes */

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

/* 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_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);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__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_ERR(0, 71, __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_ERR(0, 71, __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);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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_AsWritableString(__pyx_v_fileName); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 77, __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;

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

  /* function exit code */
  __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;
}

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

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

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
 * 
 */
    (void)(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;

    /* "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
 */
  }

  /* "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;

    /* "htslibWrapper.pyx":93
 *             self.samfile = NULL
 * 
 *         if self.index != NULL:             # <<<<<<<<<<<<<<
 *             hts_idx_destroy(self.index);
 *             self.index = NULL
 */
  }

  /* "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;

    /* "htslibWrapper.pyx":97
 *             self.index = NULL
 * 
 *         if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL
 */
  }

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

  /* function exit code */
  __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;

    /* "htslibWrapper.pyx":105
 *         Clear all the header data.
 *         """
 *         if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *             bam_hdr_destroy(self.theHeader)
 *             self.theHeader = NULL
 */
  }

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

  /* function exit code */
  __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;
  __Pyx_RefNannySetupContext("clearIndex", 0);

  /* "htslibWrapper.pyx":110
 * 
 *     cdef void clearIndex(self):
 *         print("CLEARING INDEX!!!!!!")             # <<<<<<<<<<<<<<
 *         """
 *         Clear all the index file data
 */
  if (__Pyx_PrintOne(0, __pyx_kp_s_CLEARING_INDEX) < 0) __PYX_ERR(0, 110, __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;

    /* "htslibWrapper.pyx":114
 *         Clear all the index file data
 *         """
 *         if self.index != NULL:             # <<<<<<<<<<<<<<
 *             hts_idx_destroy(self.index);
 *             self.index = NULL
 */
  }

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

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_WriteUnraisable("htslibWrapper.Samfile.clearIndex", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __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;

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

  /* function exit code */
  __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;

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

  /* function exit code */
  __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;

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

  /* function exit code */
  __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;
  __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_ERR(0, 130, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

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

  /* function exit code */
  __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;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  char const *__pyx_t_6;
  __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_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_os); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_path); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_4 = NULL;
  if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_4)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_4);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  __pyx_t_1 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_4, __pyx_t_3) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 135, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (__pyx_t_5) {

    /* "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_6 = __Pyx_PyObject_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 136, __pyx_L1_error)
    __pyx_v_self->samfile = sam_open(__pyx_v_self->filename, __pyx_t_6);

    /* "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);

    /* "htslibWrapper.pyx":135
 *         """
 *         """
 *         if os.path.exists(self.filename):             # <<<<<<<<<<<<<<
 *             self.samfile   = sam_open(self.filename, mode)
 *             self.theHeader = bam_hdr_init()
 */
    goto __pyx_L3;
  }

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

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

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_WriteUnraisable("htslibWrapper.Samfile.openBAMFile", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __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 = ((PyObject *)Py_True);
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  int __pyx_t_7;
  int __pyx_t_8;
  __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) || (Py_TYPE(((PyObject *)__pyx_v_self))->tp_flags & (Py_TPFLAGS_IS_ABSTRACT | Py_TPFLAGS_HEAPTYPE)))) {
    #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    static PY_UINT64_T tp_dict_version = 0, obj_dict_version = 0;
    if (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict && tp_dict_version == __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) && (!Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset || obj_dict_version == __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))))));
    else {
      PY_UINT64_T type_dict_guard = (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict)) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      #endif
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 143, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)(void*)__pyx_pw_13htslibWrapper_7Samfile_5_open)) {
        __Pyx_XDECREF(__pyx_r);
        __Pyx_INCREF(__pyx_t_1);
        __pyx_t_3 = __pyx_t_1; __pyx_t_4 = NULL;
        __pyx_t_5 = 0;
        if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) {
          __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
          if (likely(__pyx_t_4)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
            __Pyx_INCREF(__pyx_t_4);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_3, function);
            __pyx_t_5 = 1;
          }
        }
        #if CYTHON_FAST_PYCALL
        if (PyFunction_Check(__pyx_t_3)) {
          PyObject *__pyx_temp[3] = {__pyx_t_4, __pyx_v_mode, __pyx_v_loadIndex};
          __pyx_t_2 = __Pyx_PyFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_5, 2+__pyx_t_5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 143, __pyx_L1_error)
          __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
          __Pyx_GOTREF(__pyx_t_2);
        } else
        #endif
        #if CYTHON_FAST_PYCCALL
        if (__Pyx_PyFastCFunction_Check(__pyx_t_3)) {
          PyObject *__pyx_temp[3] = {__pyx_t_4, __pyx_v_mode, __pyx_v_loadIndex};
          __pyx_t_2 = __Pyx_PyCFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_5, 2+__pyx_t_5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 143, __pyx_L1_error)
          __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
          __Pyx_GOTREF(__pyx_t_2);
        } else
        #endif
        {
          __pyx_t_6 = PyTuple_New(2+__pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 143, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_6);
          if (__pyx_t_4) {
            __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4); __pyx_t_4 = NULL;
          }
          __Pyx_INCREF(__pyx_v_mode);
          __Pyx_GIVEREF(__pyx_v_mode);
          PyTuple_SET_ITEM(__pyx_t_6, 0+__pyx_t_5, __pyx_v_mode);
          __Pyx_INCREF(__pyx_v_loadIndex);
          __Pyx_GIVEREF(__pyx_v_loadIndex);
          PyTuple_SET_ITEM(__pyx_t_6, 1+__pyx_t_5, __pyx_v_loadIndex);
          __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 143, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        }
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __pyx_r = __pyx_t_2;
        __pyx_t_2 = 0;
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        goto __pyx_L0;
      }
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
      tp_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      obj_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset) ? __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))) : 0;
      if (unlikely(type_dict_guard != tp_dict_version)) {
        tp_dict_version = obj_dict_version = 0;
      }
      #endif
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    }
    #endif
  }

  /* "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_8 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_r, Py_NE)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 150, __pyx_L1_error)
  if (__pyx_t_8) {
  } else {
    __pyx_t_7 = __pyx_t_8;
    goto __pyx_L4_bool_binop_done;
  }
  __pyx_t_8 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_rb, Py_NE)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 150, __pyx_L1_error)
  if (__pyx_t_8) {
  } else {
    __pyx_t_7 = __pyx_t_8;
    goto __pyx_L4_bool_binop_done;
  }
  __pyx_t_8 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_rbh, Py_NE)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 150, __pyx_L1_error)
  __pyx_t_7 = __pyx_t_8;
  __pyx_L4_bool_binop_done:;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_8 = (__pyx_t_7 != 0);
  if (unlikely(__pyx_t_8)) {

    /* "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 = __Pyx_PyString_FormatSafe(__pyx_kp_s_invalid_file_opening_mode_s, __pyx_v_mode); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 151, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_1, 0, 0);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __PYX_ERR(0, 151, __pyx_L1_error)

    /* "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
 * 
 */
  }

  /* "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_8 = ((__pyx_v_self->samfile != NULL) != 0);
  if (__pyx_t_8) {

    /* "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_7 = __Pyx_PyObject_IsTrue(__pyx_v_loadIndex); if (unlikely(__pyx_t_7 < 0)) __PYX_ERR(0, 154, __pyx_L1_error)
    if (__pyx_t_7) {
    } else {
      __pyx_t_8 = __pyx_t_7;
      goto __pyx_L9_bool_binop_done;
    }
    __pyx_t_7 = ((__pyx_v_self->index == NULL) != 0);
    __pyx_t_8 = __pyx_t_7;
    __pyx_L9_bool_binop_done:;
    if (__pyx_t_8) {

      /* "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_8 = ((__pyx_v_self->index == NULL) != 0);
      if (unlikely(__pyx_t_8)) {

        /* "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_ERR(0, 157, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_Error_while_opening_index_for_fi, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 157, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 157, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __Pyx_Raise(__pyx_t_1, 0, 0, 0);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __PYX_ERR(0, 157, __pyx_L1_error)

        /* "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
 */
      }

      /* "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:
 */
    }

    /* "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;

    /* "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)
 */
  }

  /* "htslibWrapper.pyx":160
 *             return
 * 
 *         if mode[0] == "r":             # <<<<<<<<<<<<<<
 *             self.openBAMFile(mode)
 *         else:
 */
  __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_mode, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 160, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_8 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_r, Py_EQ)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 160, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  if (likely(__pyx_t_8)) {

    /* "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);

    /* "htslibWrapper.pyx":160
 *             return
 * 
 *         if mode[0] == "r":             # <<<<<<<<<<<<<<
 *             self.openBAMFile(mode)
 *         else:
 */
    goto __pyx_L12;
  }

  /* "htslibWrapper.pyx":163
 *             self.openBAMFile(mode)
 *         else:
 *             raise StandardError, "BAM file is read-only"             # <<<<<<<<<<<<<<
 * 
 *         if self.samfile == NULL:
 */
  /*else*/ {
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_kp_s_BAM_file_is_read_only, 0, 0);
    __PYX_ERR(0, 163, __pyx_L1_error)
  }
  __pyx_L12:;

  /* "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_8 = ((__pyx_v_self->samfile == NULL) != 0);
  if (unlikely(__pyx_t_8)) {

    /* "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_ERR(0, 166, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_Could_not_open_file_s_Check_that, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 166, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 166, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __Pyx_Raise(__pyx_t_1, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __PYX_ERR(0, 166, __pyx_L1_error)

    /* "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)
 * 
 */
  }

  /* "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_7 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isBam(__pyx_v_self) != 0);
  if (!__pyx_t_7) {
  } else {
    __pyx_t_8 = __pyx_t_7;
    goto __pyx_L15_bool_binop_done;
  }
  __pyx_t_7 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0);
  __pyx_t_8 = __pyx_t_7;
  __pyx_L15_bool_binop_done:;
  if (__pyx_t_8) {

    /* "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_7 = __Pyx_PyObject_IsTrue(__pyx_v_loadIndex); if (unlikely(__pyx_t_7 < 0)) __PYX_ERR(0, 170, __pyx_L1_error)
    if (__pyx_t_7) {
    } else {
      __pyx_t_8 = __pyx_t_7;
      goto __pyx_L18_bool_binop_done;
    }
    __pyx_t_7 = ((__pyx_v_self->index == NULL) != 0);
    __pyx_t_8 = __pyx_t_7;
    __pyx_L18_bool_binop_done:;
    if (__pyx_t_8) {

      /* "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_8 = ((__pyx_v_self->index == NULL) != 0);
      if (unlikely(__pyx_t_8)) {

        /* "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_1 = __Pyx_PyBytes_FromString(__pyx_v_self->filename); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 173, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_Error_while_opening_index_for_fi, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 173, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 173, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __Pyx_Raise(__pyx_t_1, 0, 0, 0);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __PYX_ERR(0, 173, __pyx_L1_error)

        /* "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)
 * 
 */
      }

      /* "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:
 */
    }

    /* "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:
 */
  }

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

  /* function exit code */
  __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_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_6);
  __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;
  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] = ((PyObject *)Py_True);
    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);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_mode)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (kw_args > 0) {
          PyObject* value = __Pyx_PyDict_GetItemStr(__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_ERR(0, 143, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        CYTHON_FALLTHROUGH;
        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_ERR(0, 143, __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);

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __Pyx_RefNannySetupContext("_open", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2.__pyx_n = 1;
  __pyx_t_2.loadIndex = __pyx_v_loadIndex;
  __pyx_t_1 = __pyx_vtabptr_13htslibWrapper_Samfile->_open(__pyx_v_self, __pyx_v_mode, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 143, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* function exit code */
  __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;
  __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 (unlikely(__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 = __Pyx_PyInt_From_int(__pyx_v_tid); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 180, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_self->theHeader->n_targets); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 180, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 180, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_GIVEREF(__pyx_t_3);
    PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
    __Pyx_GIVEREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_4);
    __pyx_t_3 = 0;
    __pyx_t_4 = 0;
    __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_tid_s_out_of_range_0_tid_i, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 180, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 180, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __Pyx_Raise(__pyx_t_5, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    __PYX_ERR(0, 180, __pyx_L1_error)

    /* "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))
 * 
 */
  }

  /* "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;

  /* "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.
 */

  /* function exit code */
  __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, 1, 0);
  __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;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  int __pyx_t_6;
  struct __pyx_opt_args_13htslibWrapper_7Samfile__open __pyx_t_7;
  int __pyx_t_8;
  __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) || (Py_TYPE(((PyObject *)__pyx_v_self))->tp_flags & (Py_TPFLAGS_IS_ABSTRACT | Py_TPFLAGS_HEAPTYPE)))) {
    #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    static PY_UINT64_T tp_dict_version = 0, obj_dict_version = 0;
    if (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict && tp_dict_version == __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) && (!Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset || obj_dict_version == __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))))));
    else {
      PY_UINT64_T type_dict_guard = (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict)) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      #endif
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fetch); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 184, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)(void*)__pyx_pw_13htslibWrapper_7Samfile_7fetch)) {
        __Pyx_XDECREF(((PyObject *)__pyx_r));
        __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_region); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 184, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_INCREF(__pyx_t_1);
        __pyx_t_4 = __pyx_t_1; __pyx_t_5 = NULL;
        if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) {
          __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4);
          if (likely(__pyx_t_5)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
            __Pyx_INCREF(__pyx_t_5);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_4, function);
          }
        }
        __pyx_t_2 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_5, __pyx_t_3) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3);
        __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 184, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_13htslibWrapper_ReadIterator))))) __PYX_ERR(0, 184, __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;
      }
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
      tp_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      obj_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset) ? __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))) : 0;
      if (unlikely(type_dict_guard != tp_dict_version)) {
        tp_dict_version = obj_dict_version = 0;
      }
      #endif
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    }
    #endif
  }

  /* "htslibWrapper.pyx":189
 *         '''
 *         # Need to load the index for new queries.
 *         if not self._isOpen():             # <<<<<<<<<<<<<<
 *             self._open('r', loadIndex=True)
 * 
 */
  __pyx_t_6 = ((!(((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isOpen(__pyx_v_self) != 0)) != 0);
  if (__pyx_t_6) {

    /* "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_7.__pyx_n = 1;
    __pyx_t_7.loadIndex = Py_True;
    __pyx_t_1 = ((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_open(__pyx_v_self, __pyx_n_s_r, 0, &__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 190, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __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)
 * 
 */
  }

  /* "htslibWrapper.pyx":192
 *             self._open('r', loadIndex=True)
 * 
 *         if self._isBam() or self._isCram():             # <<<<<<<<<<<<<<
 *             return ReadIterator(self, region)
 *         else:
 */
  __pyx_t_8 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isBam(__pyx_v_self) != 0);
  if (!__pyx_t_8) {
  } else {
    __pyx_t_6 = __pyx_t_8;
    goto __pyx_L5_bool_binop_done;
  }
  __pyx_t_8 = (((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0);
  __pyx_t_6 = __pyx_t_8;
  __pyx_L5_bool_binop_done:;
  if (likely(__pyx_t_6)) {

    /* "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_1 = __Pyx_PyBytes_FromString(__pyx_v_region); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 193, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 193, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_INCREF(((PyObject *)__pyx_v_self));
    __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
    PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
    __Pyx_GIVEREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
    __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_13htslibWrapper_ReadIterator), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 193, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_r = ((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_t_1);
    __pyx_t_1 = 0;
    goto __pyx_L0;

    /* "htslibWrapper.pyx":192
 *             self._open('r', loadIndex=True)
 * 
 *         if self._isBam() or self._isCram():             # <<<<<<<<<<<<<<
 *             return ReadIterator(self, region)
 *         else:
 */
  }

  /* "htslibWrapper.pyx":195
 *             return ReadIterator(self, region)
 *         else:
 *             raise StandardError, "Random access query only allowed for BAM/CRAM files."             # <<<<<<<<<<<<<<
 * 
 *     cpdef close(self):
 */
  /*else*/ {
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_kp_s_Random_access_query_only_allowed, 0, 0);
    __PYX_ERR(0, 195, __pyx_L1_error)
  }

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

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __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;
  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_ERR(0, 184, __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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __Pyx_RefNannySetupContext("fetch", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = ((PyObject *)__pyx_f_13htslibWrapper_7Samfile_fetch(__pyx_v_self, __pyx_v_region, 1)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 184, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* function exit code */
  __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;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  int __pyx_t_5;
  __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) || (Py_TYPE(((PyObject *)__pyx_v_self))->tp_flags & (Py_TPFLAGS_IS_ABSTRACT | Py_TPFLAGS_HEAPTYPE)))) {
    #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    static PY_UINT64_T tp_dict_version = 0, obj_dict_version = 0;
    if (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict && tp_dict_version == __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) && (!Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset || obj_dict_version == __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))))));
    else {
      PY_UINT64_T type_dict_guard = (likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict)) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      #endif
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 197, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)(void*)__pyx_pw_13htslibWrapper_7Samfile_9close)) {
        __Pyx_XDECREF(__pyx_r);
        __Pyx_INCREF(__pyx_t_1);
        __pyx_t_3 = __pyx_t_1; __pyx_t_4 = NULL;
        if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) {
          __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
          if (likely(__pyx_t_4)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
            __Pyx_INCREF(__pyx_t_4);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_3, function);
          }
        }
        __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4) : __Pyx_PyObject_CallNoArg(__pyx_t_3);
        __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
        if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 197, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_2);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
        __pyx_r = __pyx_t_2;
        __pyx_t_2 = 0;
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        goto __pyx_L0;
      }
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
      tp_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) ? __PYX_GET_DICT_VERSION(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dict) : 0;
      obj_dict_version = likely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset) ? __PYX_GET_DICT_VERSION(_PyObject_GetDictPtr(((PyObject *)__pyx_v_self))) : 0;
      if (unlikely(type_dict_guard != tp_dict_version)) {
        tp_dict_version = obj_dict_version = 0;
      }
      #endif
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP
    }
    #endif
  }

  /* "htslibWrapper.pyx":201
 *         closes file.
 *         '''
 *         if not self._isCram():             # <<<<<<<<<<<<<<
 *             if self.samfile != NULL:
 *                 sam_close(self.samfile)
 */
  __pyx_t_5 = ((!(((struct __pyx_vtabstruct_13htslibWrapper_Samfile *)__pyx_v_self->__pyx_vtab)->_isCram(__pyx_v_self) != 0)) != 0);
  if (__pyx_t_5) {

    /* "htslibWrapper.pyx":202
 *         '''
 *         if not self._isCram():
 *             if self.samfile != NULL:             # <<<<<<<<<<<<<<
 *                 sam_close(self.samfile)
 *                 self.samfile = NULL
 */
    __pyx_t_5 = ((__pyx_v_self->samfile != NULL) != 0);
    if (__pyx_t_5) {

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

      /* "htslibWrapper.pyx":202
 *         '''
 *         if not self._isCram():
 *             if self.samfile != NULL:             # <<<<<<<<<<<<<<
 *                 sam_close(self.samfile)
 *                 self.samfile = NULL
 */
    }

    /* "htslibWrapper.pyx":206
 *                 self.samfile = NULL
 * 
 *             if self.index != NULL:             # <<<<<<<<<<<<<<
 *                 hts_idx_destroy(self.index);
 *                 self.index = NULL
 */
    __pyx_t_5 = ((__pyx_v_self->index != NULL) != 0);
    if (__pyx_t_5) {

      /* "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;

      /* "htslibWrapper.pyx":206
 *                 self.samfile = NULL
 * 
 *             if self.index != NULL:             # <<<<<<<<<<<<<<
 *                 hts_idx_destroy(self.index);
 *                 self.index = NULL
 */
    }

    /* "htslibWrapper.pyx":210
 *                 self.index = NULL
 * 
 *             if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *                 bam_hdr_destroy(self.theHeader)
 *                 self.theHeader = NULL
 */
    __pyx_t_5 = ((__pyx_v_self->theHeader != NULL) != 0);
    if (__pyx_t_5) {

      /* "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;

      /* "htslibWrapper.pyx":210
 *                 self.index = NULL
 * 
 *             if self.theHeader != NULL:             # <<<<<<<<<<<<<<
 *                 bam_hdr_destroy(self.theHeader)
 *                 self.theHeader = NULL
 */
    }

    /* "htslibWrapper.pyx":201
 *         closes file.
 *         '''
 *         if not self._isCram():             # <<<<<<<<<<<<<<
 *             if self.samfile != NULL:
 *                 sam_close(self.samfile)
 */
  }

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

  /* function exit code */
  __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_XDECREF(__pyx_t_4);
  __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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __Pyx_RefNannySetupContext("close", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __pyx_f_13htslibWrapper_7Samfile_close(__pyx_v_self, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 197, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* function exit code */
  __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;
}

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

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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_From_int32_t(__pyx_v_self->theHeader->n_targets); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 217, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

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

  /* function exit code */
  __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;
}

/* "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:
 */

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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_ERR(0, 222, __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_ERR(0, 224, __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 == ((int)-1))) __PYX_ERR(0, 224, __pyx_L1_error)
    __Pyx_DECREF(__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 = PyList_AsTuple(__pyx_v_t); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 225, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "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:
 */

  /* function exit code */
  __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;
}

/* "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:
 */

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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_ERR(0, 231, __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_From_uint32_t((__pyx_v_self->theHeader->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 233, __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 == ((int)-1))) __PYX_ERR(0, 233, __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 = PyList_AsTuple(__pyx_v_t); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 234, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* "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:
 */

  /* function exit code */
  __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;
}

/* "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
 */

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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)
 */
  (void)(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_ERR(0, 243, __pyx_L1_error)
  __Pyx_GOTREF(__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(__pyx_v_result);
  __pyx_r = __pyx_v_result;
  goto __pyx_L0;

  /* "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
 */

  /* function exit code */
  __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;
}

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

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  PyObject *__pyx_t_4 = NULL;
  Py_ssize_t __pyx_t_5;
  PyObject *(*__pyx_t_6)(PyObject *);
  PyObject *__pyx_t_7 = NULL;
  int __pyx_t_8;
  int __pyx_t_9;
  Py_ssize_t __pyx_t_10;
  PyObject *(*__pyx_t_11)(PyObject *);
  PyObject *__pyx_t_12 = NULL;
  PyObject *__pyx_t_13 = NULL;
  PyObject *(*__pyx_t_14)(PyObject *);
  __Pyx_RefNannySetupContext("__get__", 0);

  /* "htslibWrapper.pyx":252
 *         '''
 *         def __get__(self):
 *             result = {}             # <<<<<<<<<<<<<<
 * 
 *             if self.theHeader.text != NULL:
 */
  __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 252, __pyx_L1_error)
  __Pyx_GOTREF(__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_ERR(0, 256, __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_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_t, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 257, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = NULL;
    if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) {
      __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
      if (likely(__pyx_t_4)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
        __Pyx_INCREF(__pyx_t_4);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_3, function);
      }
    }
    __pyx_t_1 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_4, __pyx_kp_s_) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_kp_s_);
    __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
    if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 257, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
      __pyx_t_3 = __pyx_t_1; __Pyx_INCREF(__pyx_t_3); __pyx_t_5 = 0;
      __pyx_t_6 = NULL;
    } else {
      __pyx_t_5 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 257, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_6 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 257, __pyx_L1_error)
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    for (;;) {
      if (likely(!__pyx_t_6)) {
        if (likely(PyList_CheckExact(__pyx_t_3))) {
          if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 257, __pyx_L1_error)
          #else
          __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 257, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_1);
          #endif
        } else {
          if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 257, __pyx_L1_error)
          #else
          __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 257, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_1);
          #endif
        }
      } else {
        __pyx_t_1 = __pyx_t_6(__pyx_t_3);
        if (unlikely(!__pyx_t_1)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(0, 257, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_1);
      }
      __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_1);
      __pyx_t_1 = 0;

      /* "htslibWrapper.pyx":258
 *                 t = self.text
 *                 for line in t.split("\n"):
 *                     if not line.strip(): continue             # <<<<<<<<<<<<<<
 * 
 *                     if not line.startswith("@"):
 */
      __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 258, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_7 = NULL;
      if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_4))) {
        __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
        if (likely(__pyx_t_7)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
          __Pyx_INCREF(__pyx_t_7);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_4, function);
        }
      }
      __pyx_t_1 = (__pyx_t_7) ? __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_7) : __Pyx_PyObject_CallNoArg(__pyx_t_4);
      __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
      if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 258, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 258, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_8 = ((!__pyx_t_2) != 0);
      if (__pyx_t_8) {
        goto __pyx_L4_continue;
      }

      /* "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_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 260, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __pyx_t_7 = NULL;
      if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_4))) {
        __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_4);
        if (likely(__pyx_t_7)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
          __Pyx_INCREF(__pyx_t_7);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_4, function);
        }
      }
      __pyx_t_1 = (__pyx_t_7) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_7, __pyx_kp_s__2) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_kp_s__2);
      __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
      if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 260, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
      __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 260, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_2 = ((!__pyx_t_8) != 0);
      if (unlikely(__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_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 261, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_INCREF(__pyx_v_line);
        __Pyx_GIVEREF(__pyx_v_line);
        PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
        __Pyx_INCREF(__pyx_v_t);
        __Pyx_GIVEREF(__pyx_v_t);
        PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_t);
        __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Header_line_without_s_Total_head, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 261, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_4, 0, 0);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        __PYX_ERR(0, 261, __pyx_L1_error)

        /* "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)
 * 
 */
      }

      /* "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_1 = __Pyx_PyObject_GetSlice(__pyx_v_line, 1, 0, NULL, NULL, &__pyx_slice__3, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 263, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_split); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 263, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_1 = NULL;
      if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_7))) {
        __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_7);
        if (likely(__pyx_t_1)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
          __Pyx_INCREF(__pyx_t_1);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_7, function);
        }
      }
      __pyx_t_4 = (__pyx_t_1) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_1, __pyx_kp_s__4) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_kp_s__4);
      __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
      if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 263, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __Pyx_XDECREF_SET(__pyx_v_fields, __pyx_t_4);
      __pyx_t_4 = 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_4 = __Pyx_GetItemInt(__pyx_v_fields, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 264, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_XDECREF_SET(__pyx_v_record, __pyx_t_4);
      __pyx_t_4 = 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
      if (unlikely(!Py_OptimizeFlag)) {
        __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_VALID_HEADER_TYPES); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 265, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_record, __pyx_t_4, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 265, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        if (unlikely(!(__pyx_t_2 != 0))) {
          __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 265, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          __Pyx_INCREF(__pyx_v_record);
          __Pyx_GIVEREF(__pyx_v_record);
          PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_record);
          __Pyx_INCREF(__pyx_v_line);
          __Pyx_GIVEREF(__pyx_v_line);
          PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_line);
          __pyx_t_7 = __Pyx_PyString_Format(__pyx_kp_s_header_line_with_invalid_type_s, __pyx_t_4); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 265, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
          PyErr_SetObject(PyExc_AssertionError, __pyx_t_7);
          __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
          __PYX_ERR(0, 265, __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_2 = (__Pyx_PyString_Equals(__pyx_v_record, __pyx_n_s_CO, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 268, __pyx_L1_error)
      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_ContainsTF(__pyx_v_record, __pyx_v_result, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 269, __pyx_L1_error)
        __pyx_t_8 = (__pyx_t_2 != 0);
        if (__pyx_t_8) {
          __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 269, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          if (unlikely(PyDict_SetItem(__pyx_v_result, __pyx_v_record, __pyx_t_7) < 0)) __PYX_ERR(0, 269, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        }

        /* "htslibWrapper.pyx":270
 *                     if record == "CO":
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))             # <<<<<<<<<<<<<<
 *                         continue
 * 
 */
        __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_v_record); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 270, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_4 = __Pyx_PyObject_GetSlice(__pyx_v_fields, 1, 0, NULL, NULL, &__pyx_slice__3, 1, 0, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 270, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __pyx_t_1 = __Pyx_PyString_Join(__pyx_kp_s__4, __pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 270, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_7, __pyx_t_1); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 270, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 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;

        /* "htslibWrapper.pyx":268
 * 
 *                     # treat comments
 *                     if record == "CO":             # <<<<<<<<<<<<<<
 *                         if record not in result: result[record] = []
 *                         result[record].append("\t".join( fields[1:]))
 */
      }

      /* "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_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 274, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_XDECREF_SET(__pyx_v_x, ((PyObject*)__pyx_t_1));
      __pyx_t_1 = 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_1 = __Pyx_PyObject_GetSlice(__pyx_v_fields, 1, 0, NULL, NULL, &__pyx_slice__3, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 275, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
        __pyx_t_7 = __pyx_t_1; __Pyx_INCREF(__pyx_t_7); __pyx_t_10 = 0;
        __pyx_t_11 = NULL;
      } else {
        __pyx_t_10 = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 275, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_11 = Py_TYPE(__pyx_t_7)->tp_iternext; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 275, __pyx_L1_error)
      }
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      for (;;) {
        if (likely(!__pyx_t_11)) {
          if (likely(PyList_CheckExact(__pyx_t_7))) {
            if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_7)) break;
            #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
            __pyx_t_1 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_1); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 275, __pyx_L1_error)
            #else
            __pyx_t_1 = PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 275, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_1);
            #endif
          } else {
            if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_7)) break;
            #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
            __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_1); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 275, __pyx_L1_error)
            #else
            __pyx_t_1 = PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 275, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_1);
            #endif
          }
        } else {
          __pyx_t_1 = __pyx_t_11(__pyx_t_7);
          if (unlikely(!__pyx_t_1)) {
            PyObject* exc_type = PyErr_Occurred();
            if (exc_type) {
              if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
              else __PYX_ERR(0, 275, __pyx_L1_error)
            }
            break;
          }
          __Pyx_GOTREF(__pyx_t_1);
        }
        __Pyx_XDECREF_SET(__pyx_v_field, __pyx_t_1);
        __pyx_t_1 = 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_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_field, __pyx_n_s_split); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 276, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 276, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
          PyObject* sequence = __pyx_t_4;
          Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
          if (unlikely(size != 2)) {
            if (size > 2) __Pyx_RaiseTooManyValuesError(2);
            else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
            __PYX_ERR(0, 276, __pyx_L1_error)
          }
          #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
          if (likely(PyTuple_CheckExact(sequence))) {
            __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); 
            __pyx_t_12 = PyTuple_GET_ITEM(sequence, 1); 
          } else {
            __pyx_t_1 = PyList_GET_ITEM(sequence, 0); 
            __pyx_t_12 = PyList_GET_ITEM(sequence, 1); 
          }
          __Pyx_INCREF(__pyx_t_1);
          __Pyx_INCREF(__pyx_t_12);
          #else
          __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 276, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_1);
          __pyx_t_12 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 276, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          #endif
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        } else {
          Py_ssize_t index = -1;
          __pyx_t_13 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 276, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_13);
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
          __pyx_t_14 = Py_TYPE(__pyx_t_13)->tp_iternext;
          index = 0; __pyx_t_1 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_1);
          index = 1; __pyx_t_12 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_12)) goto __pyx_L12_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_12);
          if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_13), 2) < 0) __PYX_ERR(0, 276, __pyx_L1_error)
          __pyx_t_14 = NULL;
          __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
          goto __pyx_L13_unpacking_done;
          __pyx_L12_unpacking_failed:;
          __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
          __pyx_t_14 = NULL;
          if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
          __PYX_ERR(0, 276, __pyx_L1_error)
          __pyx_L13_unpacking_done:;
        }
        __Pyx_XDECREF_SET(__pyx_v_key, __pyx_t_1);
        __pyx_t_1 = 0;
        __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_12);
        __pyx_t_12 = 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_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 277, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __pyx_t_12 = __Pyx_PyObject_GetItem(__pyx_t_4, __pyx_v_record); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 277, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_12);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        __pyx_t_8 = (__Pyx_PySequence_ContainsTF(__pyx_v_key, __pyx_t_12, Py_NE)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 277, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
        __pyx_t_2 = (__pyx_t_8 != 0);
        if (unlikely(__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_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 278, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          __Pyx_INCREF(__pyx_v_key);
          __Pyx_GIVEREF(__pyx_v_key);
          PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_v_key);
          __Pyx_INCREF(__pyx_v_record);
          __Pyx_GIVEREF(__pyx_v_record);
          PyTuple_SET_ITEM(__pyx_t_12, 1, __pyx_v_record);
          __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_unknown_field_code_s_in_record_s, __pyx_t_12); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 278, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_4);
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          __pyx_t_12 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_4); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 278, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
          __Pyx_Raise(__pyx_t_12, 0, 0, 0);
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          __PYX_ERR(0, 278, __pyx_L1_error)

          /* "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)
 */
        }

        /* "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_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 279, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __pyx_t_1 = __Pyx_PyObject_GetItem(__pyx_t_4, __pyx_v_record); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 279, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        __pyx_t_4 = __Pyx_PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 279, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_4);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __pyx_t_1 = NULL;
        if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) {
          __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
          if (likely(__pyx_t_1)) {
            PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
            __Pyx_INCREF(__pyx_t_1);
            __Pyx_INCREF(function);
            __Pyx_DECREF_SET(__pyx_t_4, function);
          }
        }
        __pyx_t_12 = (__pyx_t_1) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_1, __pyx_v_value) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_v_value);
        __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
        if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 279, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_12);
        __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        if (unlikely(PyDict_SetItem(__pyx_v_x, __pyx_v_key, __pyx_t_12) < 0)) __PYX_ERR(0, 279, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 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_DECREF(__pyx_t_7); __pyx_t_7 = 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_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_VALID_HEADER_TYPES); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 281, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __pyx_t_12 = __Pyx_PyObject_GetItem(__pyx_t_7, __pyx_v_record); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 281, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_12);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_7 = PyObject_RichCompare(__pyx_t_12, ((PyObject *)(&PyDict_Type)), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 281, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
      __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 281, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 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_ContainsTF(__pyx_v_record, __pyx_v_result, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 282, __pyx_L1_error)
        __pyx_t_8 = (__pyx_t_2 != 0);
        if (unlikely(__pyx_t_8)) {

          /* "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_7 = __Pyx_PyString_FormatSafe(__pyx_kp_s_multiple_s_lines_are_not_permitt, __pyx_v_record); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 283, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_7);
          __pyx_t_12 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_7); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 283, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
          __Pyx_Raise(__pyx_t_12, 0, 0, 0);
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          __PYX_ERR(0, 283, __pyx_L1_error)

          /* "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
 */
        }

        /* "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 (unlikely(PyDict_SetItem(__pyx_v_result, __pyx_v_record, __pyx_v_x) < 0)) __PYX_ERR(0, 284, __pyx_L1_error)

        /* "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 )
 */
        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_GetModuleGlobalName(__pyx_t_12, __pyx_n_s_VALID_HEADER_TYPES); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 285, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_12);
      __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_12, __pyx_v_record); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 285, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
      __pyx_t_12 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)(&PyList_Type)), Py_EQ); __Pyx_XGOTREF(__pyx_t_12); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 285, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_12); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 285, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
      if (__pyx_t_8) {

        /* "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_8 = (__Pyx_PyDict_ContainsTF(__pyx_v_record, __pyx_v_result, Py_NE)); if (unlikely(__pyx_t_8 < 0)) __PYX_ERR(0, 286, __pyx_L1_error)
        __pyx_t_2 = (__pyx_t_8 != 0);
        if (__pyx_t_2) {
          __pyx_t_12 = PyList_New(0); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 286, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          if (unlikely(PyDict_SetItem(__pyx_v_result, __pyx_v_record, __pyx_t_12) < 0)) __PYX_ERR(0, 286, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
        }

        /* "htslibWrapper.pyx":287
 *                     elif VALID_HEADER_TYPES[record] == list:
 *                         if record not in result: result[record] = []
 *                         result[record].append(x)             # <<<<<<<<<<<<<<
 * 
 *             return result
 */
        __pyx_t_12 = __Pyx_PyDict_GetItem(__pyx_v_result, __pyx_v_record); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 287, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_12);
        __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_12, __pyx_v_x); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 287, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;

        /* "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_L15:;

      /* "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_L4_continue:;
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 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
 */
  }

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

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

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_12);
  __Pyx_XDECREF(__pyx_t_13);
  __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;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_11__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_11__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_10__reduce_cython__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_10__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(1, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_13__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_7Samfile_13__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_7Samfile_12__setstate_cython__(((struct __pyx_obj_13htslibWrapper_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_13htslibWrapper_7Samfile_12__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(1, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.Samfile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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

/* 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_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);
        CYTHON_FALLTHROUGH;
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        CYTHON_FALLTHROUGH;
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_samfile)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        CYTHON_FALLTHROUGH;
        case  1:
        if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_region)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); __PYX_ERR(0, 296, __pyx_L3_error)
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) __PYX_ERR(0, 296, __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_ERR(0, 296, __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_ERR(0, 296, __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_ERR(0, 296, __pyx_L1_error)
  __pyx_r = __pyx_pf_13htslibWrapper_12ReadIterator___cinit__(((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_v_self), __pyx_v_samfile, __pyx_v_region);

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

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;
  __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 (unlikely(__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_ERR(0, 306, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_Samfile_s_is_not_open_Cannot_rea, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 306, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_3, 0, 0);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __PYX_ERR(0, 306, __pyx_L1_error)

    /* "htslibWrapper.pyx":305
 *         self.b           = NULL
 * 
 *         if not samfile._isOpen():             # <<<<<<<<<<<<<<
 *             raise StandardError, "Samfile %s is not open. Cannot read from file." %(samfile.filename)
 * 
 */
  }

  /* "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_ERR(0, 311, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 311, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  if (likely(__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);

    /* "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:
 */
    goto __pyx_L4;
  }

  /* "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()
 */
  /*else*/ {
    __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_samfile->filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 314, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_Cannot_retrieve_random_region_fr, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 314, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_Raise(__pyx_builtin_StandardError, __pyx_t_2, 0, 0);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __PYX_ERR(0, 314, __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();

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

  /* function exit code */
  __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;
}

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

/* 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));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
}

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);

    /* "htslibWrapper.pyx":322
 *         remember: dealloc cannot call other methods!
 *         '''
 *         if self.theIterator != NULL:             # <<<<<<<<<<<<<<
 *             sam_itr_destroy(self.theIterator)
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":325
 *             sam_itr_destroy(self.theIterator)
 * 
 *         if self.b != NULL:             # <<<<<<<<<<<<<<
 *             bam_destroy1(self.b)
 * 
 */
  }

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

  /* function exit code */
  __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;
  __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;

    /* "htslibWrapper.pyx":334
 *         cdef int lenSeq     = c.l_qseq
 * 
 *         if lenSeq == 0:             # <<<<<<<<<<<<<<
 *             return NULL
 * 
 */
  }

  /* "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;

    /* "htslibWrapper.pyx":337
 *             return NULL
 * 
 *         if q[0] == 0xff:             # <<<<<<<<<<<<<<
 *             return NULL
 * 
 */
  }

  /* "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(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_theRead != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(0, 344, __pyx_L1_error)
    }
  }
  #endif

  /* "htslibWrapper.pyx":345
 * 
 *         assert theRead != NULL
 *         assert seq     != NULL             # <<<<<<<<<<<<<<
 *         assert qual    != NULL
 * 
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_seq != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(0, 345, __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(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_qual != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(0, 346, __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, ((char const *)"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
 */
      (void)(strcpy((__pyx_v_rgID[0]), __pyx_v_tempRgID));

      /* "htslibWrapper.pyx":355
 *         if storeRgID:
 *             v = bam_aux_get(self.b, "RG")
 *             if (v != NULL):             # <<<<<<<<<<<<<<
 *                 tempRgID = bam_aux2Z(v)
 *                 lenRgID  = strlen(tempRgID)
 */
      goto __pyx_L6;
    }

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

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

  /* "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(!Py_OptimizeFlag)) {
      if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) <= 93) != 0))) {
        PyErr_SetNone(PyExc_AssertionError);
        __PYX_ERR(0, 367, __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(!Py_OptimizeFlag)) {
      if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) >= 0) != 0))) {
        PyErr_SetNone(PyExc_AssertionError);
        __PYX_ERR(0, 368, __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_From_int32_t(__pyx_v_c->pos); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 372, __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(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_cigarOps != NULL) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(0, 374, __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 = __Pyx_PyInt_From_int(bam_cigar_oplen((__pyx_v_cigar[__pyx_v_i]))); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 378, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_4);
    __Pyx_XDECREF_SET(__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_As_short(__pyx_v_cigarFlagLen); if (unlikely((__pyx_t_6 == (short)-1) && PyErr_Occurred())) __PYX_ERR(0, 380, __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_7 = ((__pyx_v_i == 0) != 0);
    if (__pyx_t_7) {
    } else {
      __pyx_t_2 = __pyx_t_7;
      goto __pyx_L12_bool_binop_done;
    }
    __pyx_t_7 = ((__pyx_v_cigarFlag == 4) != 0);
    __pyx_t_2 = __pyx_t_7;
    __pyx_L12_bool_binop_done:;
    if (__pyx_t_2) {

      /* "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_ERR(0, 387, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_4);
      __Pyx_DECREF_SET(__pyx_v_readStart, __pyx_t_4);
      __pyx_t_4 = 0;

      /* "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
 * 
 */
    }
  }

  /* "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_As_int(__pyx_v_readStart); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 397, __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;

  /* "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)
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_WriteUnraisable("htslibWrapper.ReadIterator.get", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __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;

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

  /* function exit code */
  __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 = ((char *)"=ACMGRSVTWYHKDBN");

  /* "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;

  /* "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)]
 */

  /* function exit code */
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_12ReadIterator_5__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_12ReadIterator_5__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_12ReadIterator_4__reduce_cython__(((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_v_self));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_13htslibWrapper_12ReadIterator_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__reduce_cython__", 0);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(1, 2, __pyx_L1_error)

  /* "(tree fragment)":1
 * def __reduce_cython__(self):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.ReadIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

/* Python wrapper */
static PyObject *__pyx_pw_13htslibWrapper_12ReadIterator_7__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/
static PyObject *__pyx_pw_13htslibWrapper_12ReadIterator_7__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
  __pyx_r = __pyx_pf_13htslibWrapper_12ReadIterator_6__setstate_cython__(((struct __pyx_obj_13htslibWrapper_ReadIterator *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state));

  /* function exit code */
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_pf_13htslibWrapper_12ReadIterator_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_13htslibWrapper_ReadIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__setstate_cython__", 0);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_Raise(__pyx_t_1, 0, 0, 0);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __PYX_ERR(1, 4, __pyx_L1_error)

  /* "(tree fragment)":3
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):             # <<<<<<<<<<<<<<
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("htslibWrapper.ReadIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __Pyx_XGIVEREF(__pyx_r);
  __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);

    /* "htslibWrapper.pyx":425
 *     """
 * 
 *     if theRead.seq != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.seq)
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":428
 *         free(theRead.seq)
 * 
 *     if theRead.qual != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.qual)
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":431
 *         free(theRead.qual)
 * 
 *     if theRead.cigarOps != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.cigarOps)
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":434
 *         free(theRead.cigarOps)
 * 
 *     if theRead.hash != NULL:             # <<<<<<<<<<<<<<
 *         free(theRead.hash)
 * 
 */
  }

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

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

  /* function exit code */
  __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;
  short __pyx_t_3;
  int __pyx_t_4;
  int __pyx_t_5;
  __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;
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "htslibWrapper.pyx":456
 * 
 *         # Ref match. Store count if > 40
 *         if seq[i] == refSeq[i]:             # <<<<<<<<<<<<<<
 *             totalMatches += 1
 * 
 */
    __pyx_t_5 = (((__pyx_v_seq[__pyx_v_i]) == (__pyx_v_refSeq[__pyx_v_i])) != 0);
    if (__pyx_t_5) {

      /* "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_5 = ((__pyx_v_nMatches == 40) != 0);
      if (__pyx_t_5) {

        /* "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);

        /* "htslibWrapper.pyx":459
 *             totalMatches += 1
 * 
 *             if nMatches == 40:             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 */
      }

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

      /* "htslibWrapper.pyx":456
 * 
 *         # Ref match. Store count if > 40
 *         if seq[i] == refSeq[i]:             # <<<<<<<<<<<<<<
 *             totalMatches += 1
 * 
 */
      goto __pyx_L5;
    }

    /* "htslibWrapper.pyx":468
 *         # Ref mis-match. Store base.
 *         else:
 *             if nMatches > 0:             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 */
    /*else*/ {
      __pyx_t_5 = ((__pyx_v_nMatches > 0) != 0);
      if (__pyx_t_5) {

        /* "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);

        /* "htslibWrapper.pyx":468
 *         # Ref mis-match. Store base.
 *         else:
 *             if nMatches > 0:             # <<<<<<<<<<<<<<
 *                 newSeq[newSeqIndex] = nMatches
 *                 nMatches = 0
 */
      }

      /* "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_5 = ((__pyx_v_nMatches > 0) != 0);
  if (__pyx_t_5) {

    /* "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);

    /* "htslibWrapper.pyx":477
 * 
 *     # If we finish off with a load of matches, catch those
 *     if nMatches > 0:             # <<<<<<<<<<<<<<
 *         newSeq[newSeqIndex] = nMatches
 *         nMatches = 0
 */
  }

  /* "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)
 */
  (void)(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;

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

  /* function exit code */
  __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;
  short __pyx_t_4;
  int __pyx_t_5;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  __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;
    __pyx_t_4 = __pyx_t_3;
    for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
      __pyx_v_i = __pyx_t_5;

      /* "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);
    }

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

  /* "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;
  __pyx_t_4 = __pyx_t_3;
  for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
    __pyx_v_i = __pyx_t_5;

    /* "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(!Py_OptimizeFlag)) {
      if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) >= 0) != 0))) {
        __pyx_t_6 = __Pyx_PyInt_From_char((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 511, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_6);
        __pyx_t_7 = __Pyx_PyString_Format(__pyx_kp_s_Shit_3_Qual_s, __pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 511, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        PyErr_SetObject(PyExc_AssertionError, __pyx_t_7);
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        __PYX_ERR(0, 511, __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(!Py_OptimizeFlag)) {
      if (unlikely(!(((__pyx_v_qual[__pyx_v_i]) <= 93) != 0))) {
        __pyx_t_7 = __Pyx_PyInt_From_char((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 512, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_7);
        __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_Shit_4_Qual_s, __pyx_t_7); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 512, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_6);
        __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
        PyErr_SetObject(PyExc_AssertionError, __pyx_t_6);
        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
        __PYX_ERR(0, 512, __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;

      /* "htslibWrapper.pyx":514
 *         assert qual[i] <= 93, "Shit 4!. Qual = %s" %(qual[i])
 * 
 *         if i == 0:             # <<<<<<<<<<<<<<
 *             newQual[newQualIndex] = qual[i] + 33
 *             newQualIndex += 1
 */
      goto __pyx_L8;
    }

    /* "htslibWrapper.pyx":520
 *             lastCount = 1
 *         else:
 *             if qual[i] == lastChar:             # <<<<<<<<<<<<<<
 *                 lastCount += 1
 *             else:
 */
    /*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);

        /* "htslibWrapper.pyx":520
 *             lastCount = 1
 *         else:
 *             if qual[i] == lastChar:             # <<<<<<<<<<<<<<
 *                 lastCount += 1
 *             else:
 */
        goto __pyx_L9;
      }

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

    /* "htslibWrapper.pyx":530
 *                 lastCount = 1
 * 
 *     if lastCount > 0:             # <<<<<<<<<<<<<<
 *         newQual[newQualIndex] = lastCount
 *         newQualIndex += 1
 */
  }

  /* "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)
 */
  (void)(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;

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

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_6);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_WriteUnraisable("htslibWrapper.compressQual", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __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;
  int __pyx_t_5;
  char __pyx_t_6;
  char __pyx_t_7;
  int __pyx_t_8;
  __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;
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
    __pyx_v_i = __pyx_t_4;

    /* "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_5 = (((__pyx_v_seq[__pyx_v_i]) <= 40) != 0);
    if (__pyx_t_5) {

      /* "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_6 = (__pyx_v_seq[__pyx_v_i]);
      __pyx_t_7 = __pyx_t_6;
      for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
        __pyx_v_j = __pyx_t_8;

        /* "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]));

      /* "htslibWrapper.pyx":557
 * 
 *     for i in range(seqLen):
 *         if seq[i] <= 40:             # <<<<<<<<<<<<<<
 *             for j in range(seq[i]):
 *                 newSeq[newSeqIndex] = refSeq[j + refIndex]
 */
      goto __pyx_L5;
    }

    /* "htslibWrapper.pyx":563
 *             refIndex += seq[i]
 *         else:
 *             newSeq[newSeqIndex] = seq[i]             # <<<<<<<<<<<<<<
 *             refIndex += 1
 *             newSeqIndex += 1
 */
    /*else*/ {
      (__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;

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

  /* function exit code */
  __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;
  long __pyx_t_3;
  int __pyx_t_4;
  char __pyx_t_5;
  char __pyx_t_6;
  int __pyx_t_7;
  PyObject *__pyx_t_8 = NULL;
  PyObject *__pyx_t_9 = NULL;
  PyObject *__pyx_t_10 = NULL;
  __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);
  __pyx_t_3 = __pyx_t_2;
  for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=2) {
    __pyx_v_i = __pyx_t_4;

    /* "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_5 = (__pyx_v_qual[(__pyx_v_i + 1)]);
    __pyx_t_6 = __pyx_t_5;
    for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
      __pyx_v_j = __pyx_t_7;

      /* "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(!Py_OptimizeFlag)) {
        if (unlikely(!((((__pyx_v_qual[__pyx_v_i]) - 33) >= 0) != 0))) {
          __pyx_t_8 = __Pyx_PyInt_From_char((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 591, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_8);
          __pyx_t_9 = __Pyx_PyInt_From_char((__pyx_v_qual[(__pyx_v_i + 1)])); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 591, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_9);
          __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 591, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_10);
          __Pyx_GIVEREF(__pyx_t_8);
          PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_8);
          __Pyx_GIVEREF(__pyx_t_9);
          PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
          __pyx_t_8 = 0;
          __pyx_t_9 = 0;
          __pyx_t_9 = __Pyx_PyString_Format(__pyx_kp_s_Shit_1_Qual_s_Count_s, __pyx_t_10); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 591, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_9);
          __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
          PyErr_SetObject(PyExc_AssertionError, __pyx_t_9);
          __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
          __PYX_ERR(0, 591, __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(!Py_OptimizeFlag)) {
        if (unlikely(!((((__pyx_v_qual[__pyx_v_i]) - 33) <= 93) != 0))) {
          __pyx_t_9 = __Pyx_PyInt_From_char((__pyx_v_qual[__pyx_v_i])); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 592, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_9);
          __pyx_t_10 = __Pyx_PyInt_From_char((__pyx_v_qual[(__pyx_v_i + 1)])); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 592, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_10);
          __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 592, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_8);
          __Pyx_GIVEREF(__pyx_t_9);
          PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
          __Pyx_GIVEREF(__pyx_t_10);
          PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_10);
          __pyx_t_9 = 0;
          __pyx_t_10 = 0;
          __pyx_t_10 = __Pyx_PyString_Format(__pyx_kp_s_Shit_2_Qual_s_Count_s, __pyx_t_8); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 592, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_10);
          __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
          PyErr_SetObject(PyExc_AssertionError, __pyx_t_10);
          __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
          __PYX_ERR(0, 592, __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(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_read->rlen == __pyx_v_newQualIndex) != 0))) {
      PyErr_SetNone(PyExc_AssertionError);
      __PYX_ERR(0, 595, __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;

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

  /* function exit code */
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_XDECREF(__pyx_t_9);
  __Pyx_XDECREF(__pyx_t_10);
  __Pyx_WriteUnraisable("htslibWrapper.uncompressQual", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
  __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;

    /* "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
 * 
 */
  }

  /* "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)));

    /* "htslibWrapper.pyx":613
 *         return
 * 
 *     if read.seq != NULL:             # <<<<<<<<<<<<<<
 *         compressSeq(read, refSeq + (read.pos - refStart))
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":616
 *         compressSeq(read, refSeq + (read.pos - refStart))
 * 
 *     if read.qual != NULL:             # <<<<<<<<<<<<<<
 *         compressQual(read, qualBinSize)
 * 
 */
  }

  /* "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;

    /* "htslibWrapper.pyx":623
 *     #    read.cigarOps = NULL
 * 
 *     if read.hash != NULL:             # <<<<<<<<<<<<<<
 *         free(read.hash)
 *         read.hash = NULL
 */
  }

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

  /* "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
 */

  /* function exit code */
  __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;

    /* "htslibWrapper.pyx":635
 *     Un-compress the read.
 *     """
 *     if not Read_IsCompressed(read):             # <<<<<<<<<<<<<<
 *         return
 * 
 */
  }

  /* "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)));

    /* "htslibWrapper.pyx":638
 *         return
 * 
 *     if read.seq != NULL:             # <<<<<<<<<<<<<<
 *         uncompressSeq(read, refSeq + (read.pos - refStart))
 * 
 */
  }

  /* "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);

    /* "htslibWrapper.pyx":641
 *         uncompressSeq(read, refSeq + (read.pos - refStart))
 * 
 *     if read.qual != NULL:             # <<<<<<<<<<<<<<
 *         uncompressQual(read)
 * 
 */
  }

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

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

  /* function exit code */
  __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;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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;

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

  /* function exit code */
  __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;

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

  /* function exit code */
  __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;

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

  /* function exit code */
  __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 & 0x200) != 0);
  goto __pyx_L0;

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

  /* function exit code */
  __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;

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

  /* function exit code */
  __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 & 0x100) != 0);
  goto __pyx_L0;

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

  /* function exit code */
  __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 & 0x800) != 0);
  goto __pyx_L0;

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

  /* function exit code */
  __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));

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

  /* function exit code */
  __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);

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

  /* function exit code */
  __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 | 0x200);

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

  /* function exit code */
}

/* "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 | 0x800);

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

  /* function exit code */
}

/* "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 & (~0x800));

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

  /* function exit code */
}
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;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 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)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_13htslibWrapper_Samfile(PyObject *o) {
  struct __pyx_obj_13htslibWrapper_Samfile *p = (struct __pyx_obj_13htslibWrapper_Samfile *)o;
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_13htslibWrapper_7Samfile_3__dealloc__(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) {
  PyObject* tmp;
  struct __pyx_obj_13htslibWrapper_Samfile *p = (struct __pyx_obj_13htslibWrapper_Samfile *)o;
  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[] = {
  {"_open", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_13htslibWrapper_7Samfile_5_open, METH_VARARGS|METH_KEYWORDS, __pyx_doc_13htslibWrapper_7Samfile_4_open},
  {"fetch", (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_7fetch, METH_O, __pyx_doc_13htslibWrapper_7Samfile_6fetch},
  {"close", (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_9close, METH_NOARGS, __pyx_doc_13htslibWrapper_7Samfile_8close},
  {"__reduce_cython__", (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_11__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_13htslibWrapper_7Samfile_13__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_13htslibWrapper_Samfile[] = {
  {(char *)"nreferences", __pyx_getprop_13htslibWrapper_7Samfile_nreferences, 0, (char *)"number of :term:`reference` sequences in the file.", 0},
  {(char *)"references", __pyx_getprop_13htslibWrapper_7Samfile_references, 0, (char *)"tuple with the names of :term:`reference` sequences.", 0},
  {(char *)"lengths", __pyx_getprop_13htslibWrapper_7Samfile_lengths, 0, (char *)"tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as :attr:`pysam.Samfile.reference`\n        ", 0},
  {(char *)"text", __pyx_getprop_13htslibWrapper_7Samfile_text, 0, (char *)"full contents of the :term:`sam file` header as a string.", 0},
  {(char *)"header", __pyx_getprop_13htslibWrapper_7Samfile_header, 0, (char *)"header information within the :term:`sam file`. The records and fields are returned as\n        a two-level dictionary.\n        ", 0},
  {0, 0, 0, 0, 0}
};

static PyTypeObject __pyx_type_13htslibWrapper_Samfile = {
  PyVarObject_HEAD_INIT(0, 0)
  "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*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #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*/
  "\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*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #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;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 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)) goto bad;
  return o;
  bad:
  Py_DECREF(o); o = 0;
  return NULL;
}

static void __pyx_tp_dealloc_13htslibWrapper_ReadIterator(PyObject *o) {
  #if CYTHON_USE_TP_FINALIZE
  if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pw_13htslibWrapper_12ReadIterator_3__dealloc__(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  (*Py_TYPE(o)->tp_free)(o);
}

static PyMethodDef __pyx_methods_13htslibWrapper_ReadIterator[] = {
  {"__reduce_cython__", (PyCFunction)__pyx_pw_13htslibWrapper_12ReadIterator_5__reduce_cython__, METH_NOARGS, 0},
  {"__setstate_cython__", (PyCFunction)__pyx_pw_13htslibWrapper_12ReadIterator_7__setstate_cython__, METH_O, 0},
  {0, 0, 0, 0}
};

static PyTypeObject __pyx_type_13htslibWrapper_ReadIterator = {
  PyVarObject_HEAD_INIT(0, 0)
  "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*/
  #endif
  #if PY_MAJOR_VERSION >= 3
  0, /*tp_as_async*/
  #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*/
  "\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*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
};

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

#if PY_MAJOR_VERSION >= 3
#if CYTHON_PEP489_MULTI_PHASE_INIT
static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
static int __pyx_pymod_exec_htslibWrapper(PyObject* module); /*proto*/
static PyModuleDef_Slot __pyx_moduledef_slots[] = {
  {Py_mod_create, (void*)__pyx_pymod_create},
  {Py_mod_exec, (void*)__pyx_pymod_exec_htslibWrapper},
  {0, NULL}
};
#endif

static struct PyModuleDef __pyx_moduledef = {
    PyModuleDef_HEAD_INIT,
    "htslibWrapper",
    0, /* m_doc */
  #if CYTHON_PEP489_MULTI_PHASE_INIT
    0, /* m_size */
  #else
    -1, /* m_size */
  #endif
    __pyx_methods /* m_methods */,
  #if CYTHON_PEP489_MULTI_PHASE_INIT
    __pyx_moduledef_slots, /* m_slots */
  #else
    NULL, /* m_reload */
  #endif
    NULL, /* m_traverse */
    NULL, /* m_clear */
    NULL /* m_free */
};
#endif
#ifndef CYTHON_SMALL_CODE
#if defined(__clang__)
    #define CYTHON_SMALL_CODE
#elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))
    #define CYTHON_SMALL_CODE __attribute__((cold))
#else
    #define CYTHON_SMALL_CODE
#endif
#endif

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 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_kp_s_BAM_file_is_read_only, __pyx_k_BAM_file_is_read_only, sizeof(__pyx_k_BAM_file_is_read_only), 0, 0, 1, 0},
  {&__pyx_n_s_CL, __pyx_k_CL, sizeof(__pyx_k_CL), 0, 0, 1, 1},
  {&__pyx_kp_s_CLEARING_INDEX, __pyx_k_CLEARING_INDEX, sizeof(__pyx_k_CLEARING_INDEX), 0, 0, 1, 0},
  {&__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_kp_s_Cannot_retrieve_random_region_fr, __pyx_k_Cannot_retrieve_random_region_fr, sizeof(__pyx_k_Cannot_retrieve_random_region_fr), 0, 0, 1, 0},
  {&__pyx_kp_s_Could_not_open_file_s_Check_that, __pyx_k_Could_not_open_file_s_Check_that, sizeof(__pyx_k_Could_not_open_file_s_Check_that), 0, 0, 1, 0},
  {&__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_kp_s_Error_while_opening_index_for_fi, __pyx_k_Error_while_opening_index_for_fi, sizeof(__pyx_k_Error_while_opening_index_for_fi), 0, 0, 1, 0},
  {&__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_kp_s_Header_line_without_s_Total_head, __pyx_k_Header_line_without_s_Total_head, sizeof(__pyx_k_Header_line_without_s_Total_head), 0, 0, 1, 0},
  {&__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_kp_s_Random_access_query_only_allowed, __pyx_k_Random_access_query_only_allowed, sizeof(__pyx_k_Random_access_query_only_allowed), 0, 0, 1, 0},
  {&__pyx_n_s_ReadIterator, __pyx_k_ReadIterator, sizeof(__pyx_k_ReadIterator), 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_Samfile, __pyx_k_Samfile, sizeof(__pyx_k_Samfile), 0, 0, 1, 1},
  {&__pyx_kp_s_Samfile_s_is_not_open_Cannot_rea, __pyx_k_Samfile_s_is_not_open_Cannot_rea, sizeof(__pyx_k_Samfile_s_is_not_open_Cannot_rea), 0, 0, 1, 0},
  {&__pyx_kp_s_Shit_1_Qual_s_Count_s, __pyx_k_Shit_1_Qual_s_Count_s, sizeof(__pyx_k_Shit_1_Qual_s_Count_s), 0, 0, 1, 0},
  {&__pyx_kp_s_Shit_2_Qual_s_Count_s, __pyx_k_Shit_2_Qual_s_Count_s, sizeof(__pyx_k_Shit_2_Qual_s_Count_s), 0, 0, 1, 0},
  {&__pyx_kp_s_Shit_3_Qual_s, __pyx_k_Shit_3_Qual_s, sizeof(__pyx_k_Shit_3_Qual_s), 0, 0, 1, 0},
  {&__pyx_kp_s_Shit_4_Qual_s, __pyx_k_Shit_4_Qual_s, sizeof(__pyx_k_Shit_4_Qual_s), 0, 0, 1, 0},
  {&__pyx_n_s_StandardError, __pyx_k_StandardError, sizeof(__pyx_k_StandardError), 0, 0, 1, 1},
  {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 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_kp_s__2, __pyx_k__2, sizeof(__pyx_k__2), 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_n_s_append, __pyx_k_append, sizeof(__pyx_k_append), 0, 0, 1, 1},
  {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 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_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1},
  {&__pyx_kp_s_header_line_with_invalid_type_s, __pyx_k_header_line_with_invalid_type_s, sizeof(__pyx_k_header_line_with_invalid_type_s), 0, 0, 1, 0},
  {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
  {&__pyx_kp_s_invalid_file_opening_mode_s, __pyx_k_invalid_file_opening_mode_s, sizeof(__pyx_k_invalid_file_opening_mode_s), 0, 0, 1, 0},
  {&__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_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_mode, __pyx_k_mode, sizeof(__pyx_k_mode), 0, 0, 1, 1},
  {&__pyx_kp_s_multiple_s_lines_are_not_permitt, __pyx_k_multiple_s_lines_are_not_permitt, sizeof(__pyx_k_multiple_s_lines_are_not_permitt), 0, 0, 1, 0},
  {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
  {&__pyx_kp_s_no_default___reduce___due_to_non, __pyx_k_no_default___reduce___due_to_non, sizeof(__pyx_k_no_default___reduce___due_to_non), 0, 0, 1, 0},
  {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 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_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 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_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1},
  {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1},
  {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 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_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
  {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 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_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_text, __pyx_k_text, sizeof(__pyx_k_text), 0, 0, 1, 1},
  {&__pyx_kp_s_tid_s_out_of_range_0_tid_i, __pyx_k_tid_s_out_of_range_0_tid_i, sizeof(__pyx_k_tid_s_out_of_range_0_tid_i), 0, 0, 1, 0},
  {&__pyx_n_s_types, __pyx_k_types, sizeof(__pyx_k_types), 0, 0, 1, 1},
  {&__pyx_kp_s_unknown_field_code_s_in_record_s, __pyx_k_unknown_field_code_s_in_record_s, sizeof(__pyx_k_unknown_field_code_s_in_record_s), 0, 0, 1, 0},
  {&__pyx_n_s_zlib, __pyx_k_zlib, sizeof(__pyx_k_zlib), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_StandardError = __Pyx_GetBuiltinName(__pyx_n_s_StandardError); if (!__pyx_builtin_StandardError) __PYX_ERR(0, 151, __pyx_L1_error)
  __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 157, __pyx_L1_error)
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 180, __pyx_L1_error)
  __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
  __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 453, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

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

  /* "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_slice__3 = PySlice_New(__pyx_int_1, Py_None, Py_None); if (unlikely(!__pyx_slice__3)) __PYX_ERR(0, 263, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_slice__3);
  __Pyx_GIVEREF(__pyx_slice__3);

  /* "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_tuple__6 = PyTuple_Pack(2, __pyx_kp_s__5, __pyx_int_1); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 276, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__6);
  __Pyx_GIVEREF(__pyx_tuple__6);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__7)) __PYX_ERR(1, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__7);
  __Pyx_GIVEREF(__pyx_tuple__7);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__8)) __PYX_ERR(1, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__8);
  __Pyx_GIVEREF(__pyx_tuple__8);

  /* "(tree fragment)":2
 * def __reduce_cython__(self):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 */
  __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(1, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__9);
  __Pyx_GIVEREF(__pyx_tuple__9);

  /* "(tree fragment)":4
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")
 * def __setstate_cython__(self, __pyx_state):
 *     raise TypeError("no default __reduce__ due to non-trivial __cinit__")             # <<<<<<<<<<<<<<
 */
  __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_no_default___reduce___due_to_non); if (unlikely(!__pyx_tuple__10)) __PYX_ERR(1, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__10);
  __Pyx_GIVEREF(__pyx_tuple__10);

  /* "htslibWrapper.pyx":11
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __pyx_tuple__11 = PyTuple_Pack(1, __pyx_n_s_Log); if (unlikely(!__pyx_tuple__11)) __PYX_ERR(0, 11, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__11);
  __Pyx_GIVEREF(__pyx_tuple__11);

  /* "htslibWrapper.pyx":23
 * 
 * # order of records within sam headers
 * VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" )             # <<<<<<<<<<<<<<
 * 
 * # type conversions within sam header records
 */
  __pyx_tuple__12 = PyTuple_Pack(5, __pyx_n_s_HD, __pyx_n_s_SQ, __pyx_n_s_RG, __pyx_n_s_PG, __pyx_n_s_CO); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 23, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__12);
  __Pyx_GIVEREF(__pyx_tuple__12);

  /* "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_tuple__13 = PyTuple_Pack(3, __pyx_n_s_VN, __pyx_n_s_SO, __pyx_n_s_GO); if (unlikely(!__pyx_tuple__13)) __PYX_ERR(0, 32, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__13);
  __Pyx_GIVEREF(__pyx_tuple__13);

  /* "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_tuple__14 = PyTuple_Pack(7, __pyx_n_s_SN, __pyx_n_s_LN, __pyx_n_s_AH, __pyx_n_s_AS, __pyx_n_s_M5, __pyx_n_s_UR, __pyx_n_s_SP); if (unlikely(!__pyx_tuple__14)) __PYX_ERR(0, 33, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__14);
  __Pyx_GIVEREF(__pyx_tuple__14);

  /* "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_tuple__15 = PyTuple_Pack(10, __pyx_n_s_ID, __pyx_n_s_SM, __pyx_n_s_LB, __pyx_n_s_DS, __pyx_n_s_PU, __pyx_n_s_PI, __pyx_n_s_CN, __pyx_n_s_DT, __pyx_n_s_PL, __pyx_n_s_PG); if (unlikely(!__pyx_tuple__15)) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__15);
  __Pyx_GIVEREF(__pyx_tuple__15);

  /* "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_tuple__16 = PyTuple_Pack(3, __pyx_n_s_ID, __pyx_n_s_VN, __pyx_n_s_CL); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_tuple__16);
  __Pyx_GIVEREF(__pyx_tuple__16);
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) {
  if (__Pyx_InitStrings(__pyx_string_tab) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/
static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/

static int __Pyx_modinit_global_init_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0);
  /*--- Global init code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_variable_export_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0);
  /*--- Variable export code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_function_export_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0);
  /*--- Function export code ---*/
  if (__Pyx_ExportFunction("destroyRead", (void (*)(void))__pyx_f_13htslibWrapper_destroyRead, "void (__pyx_t_13htslibWrapper_cAlignedRead *)") < 0) __PYX_ERR(0, 1, __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_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ExportFunction("uncompressRead", (void (*)(void))__pyx_f_13htslibWrapper_uncompressRead, "void (__pyx_t_13htslibWrapper_cAlignedRead *, char *, int, int, int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_type_init_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
  /*--- 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_ERR(0, 41, __pyx_L1_error)
  __pyx_type_13htslibWrapper_Samfile.tp_print = 0;
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_13htslibWrapper_Samfile.tp_dictoffset && __pyx_type_13htslibWrapper_Samfile.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_13htslibWrapper_Samfile.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (__Pyx_SetVtable(__pyx_type_13htslibWrapper_Samfile.tp_dict, __pyx_vtabptr_13htslibWrapper_Samfile) < 0) __PYX_ERR(0, 41, __pyx_L1_error)
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Samfile, (PyObject *)&__pyx_type_13htslibWrapper_Samfile) < 0) __PYX_ERR(0, 41, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_13htslibWrapper_Samfile) < 0) __PYX_ERR(0, 41, __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_ERR(0, 291, __pyx_L1_error)
  __pyx_type_13htslibWrapper_ReadIterator.tp_print = 0;
  if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_13htslibWrapper_ReadIterator.tp_dictoffset && __pyx_type_13htslibWrapper_ReadIterator.tp_getattro == PyObject_GenericGetAttr)) {
    __pyx_type_13htslibWrapper_ReadIterator.tp_getattro = __Pyx_PyObject_GenericGetAttr;
  }
  if (__Pyx_SetVtable(__pyx_type_13htslibWrapper_ReadIterator.tp_dict, __pyx_vtabptr_13htslibWrapper_ReadIterator) < 0) __PYX_ERR(0, 291, __pyx_L1_error)
  if (PyObject_SetAttr(__pyx_m, __pyx_n_s_ReadIterator, (PyObject *)&__pyx_type_13htslibWrapper_ReadIterator) < 0) __PYX_ERR(0, 291, __pyx_L1_error)
  if (__Pyx_setup_reduce((PyObject*)&__pyx_type_13htslibWrapper_ReadIterator) < 0) __PYX_ERR(0, 291, __pyx_L1_error)
  __pyx_ptype_13htslibWrapper_ReadIterator = &__pyx_type_13htslibWrapper_ReadIterator;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_type_import_code(void) {
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
  /*--- Type import code ---*/
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 9, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", 
  #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000
  sizeof(PyTypeObject),
  #else
  sizeof(PyHeapTypeObject),
  #endif
  __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(2, 9, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 8, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(3, 8, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 15, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __Pyx_ImportType_CheckSize_Warn);
   if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(4, 15, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_RefNannyFinishContext();
  return -1;
}

static int __Pyx_modinit_variable_import_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0);
  /*--- Variable import code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}

static int __Pyx_modinit_function_import_code(void) {
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0);
  /*--- Function import code ---*/
  __Pyx_RefNannyFinishContext();
  return 0;
}


#if PY_MAJOR_VERSION < 3
#ifdef CYTHON_NO_PYINIT_EXPORT
#define __Pyx_PyMODINIT_FUNC void
#else
#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
#endif
#else
#ifdef CYTHON_NO_PYINIT_EXPORT
#define __Pyx_PyMODINIT_FUNC PyObject *
#else
#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
#endif
#endif


#if PY_MAJOR_VERSION < 3
__Pyx_PyMODINIT_FUNC inithtslibWrapper(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC inithtslibWrapper(void)
#else
__Pyx_PyMODINIT_FUNC PyInit_htslibWrapper(void) CYTHON_SMALL_CODE; /*proto*/
__Pyx_PyMODINIT_FUNC PyInit_htslibWrapper(void)
#if CYTHON_PEP489_MULTI_PHASE_INIT
{
  return PyModuleDef_Init(&__pyx_moduledef);
}
static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) {
    #if PY_VERSION_HEX >= 0x030700A1
    static PY_INT64_T main_interpreter_id = -1;
    PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp);
    if (main_interpreter_id == -1) {
        main_interpreter_id = current_id;
        return (unlikely(current_id == -1)) ? -1 : 0;
    } else if (unlikely(main_interpreter_id != current_id))
    #else
    static PyInterpreterState *main_interpreter = NULL;
    PyInterpreterState *current_interpreter = PyThreadState_Get()->interp;
    if (!main_interpreter) {
        main_interpreter = current_interpreter;
    } else if (unlikely(main_interpreter != current_interpreter))
    #endif
    {
        PyErr_SetString(
            PyExc_ImportError,
            "Interpreter change detected - this module can only be loaded into one interpreter per process.");
        return -1;
    }
    return 0;
}
static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *moddict, const char* from_name, const char* to_name, int allow_none) {
    PyObject *value = PyObject_GetAttrString(spec, from_name);
    int result = 0;
    if (likely(value)) {
        if (allow_none || value != Py_None) {
            result = PyDict_SetItemString(moddict, to_name, value);
        }
        Py_DECREF(value);
    } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) {
        PyErr_Clear();
    } else {
        result = -1;
    }
    return result;
}
static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, CYTHON_UNUSED PyModuleDef *def) {
    PyObject *module = NULL, *moddict, *modname;
    if (__Pyx_check_single_interpreter())
        return NULL;
    if (__pyx_m)
        return __Pyx_NewRef(__pyx_m);
    modname = PyObject_GetAttrString(spec, "name");
    if (unlikely(!modname)) goto bad;
    module = PyModule_NewObject(modname);
    Py_DECREF(modname);
    if (unlikely(!module)) goto bad;
    moddict = PyModule_GetDict(module);
    if (unlikely(!moddict)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad;
    if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad;
    return module;
bad:
    Py_XDECREF(module);
    return NULL;
}


static CYTHON_SMALL_CODE int __pyx_pymod_exec_htslibWrapper(PyObject *__pyx_pyinit_module)
#endif
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  __Pyx_RefNannyDeclarations
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  if (__pyx_m) {
    if (__pyx_m == __pyx_pyinit_module) return 0;
    PyErr_SetString(PyExc_RuntimeError, "Module 'htslibWrapper' has already been imported. Re-initialisation is not supported.");
    return -1;
  }
  #elif PY_MAJOR_VERSION >= 3
  if (__pyx_m) return __Pyx_NewRef(__pyx_m);
  #endif
  #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("__Pyx_PyMODINIT_FUNC PyInit_htslibWrapper(void)", 0);
  if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #ifdef __Pxy_PyFrame_Initialize_Offsets
  __Pxy_PyFrame_Initialize_Offsets();
  #endif
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
  #ifdef __Pyx_CyFunction_USED
  if (__pyx_CyFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Coroutine_USED
  if (__pyx_Coroutine_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_AsyncGen_USED
  if (__pyx_AsyncGen_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_StopAsyncIteration_USED
  if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(0, 1, __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 CYTHON_PEP489_MULTI_PHASE_INIT
  __pyx_m = __pyx_pyinit_module;
  Py_INCREF(__pyx_m);
  #else
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4("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_ERR(0, 1, __pyx_L1_error)
  #endif
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_cython_runtime = PyImport_AddModule((char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error)
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  /*--- Initialize various global constants etc. ---*/
  if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __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_ERR(0, 1, __pyx_L1_error)
  #endif
  if (__pyx_module_is_main_htslibWrapper) {
    if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
    if (!PyDict_GetItemString(modules, "htslibWrapper")) {
      if (unlikely(PyDict_SetItemString(modules, "htslibWrapper", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Constants init code ---*/
  if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Global type/function init code ---*/
  (void)__Pyx_modinit_global_init_code();
  (void)__Pyx_modinit_variable_export_code();
  if (unlikely(__Pyx_modinit_function_export_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_type_init_code() != 0)) goto __pyx_L1_error;
  if (unlikely(__Pyx_modinit_type_import_code() != 0)) goto __pyx_L1_error;
  (void)__Pyx_modinit_variable_import_code();
  (void)__Pyx_modinit_function_import_code();
  /*--- Execution code ---*/
  #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
  if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif

  /* "htslibWrapper.pyx":1
 * import os             # <<<<<<<<<<<<<<
 * import types
 * import itertools
 */
  __pyx_t_1 = __Pyx_Import(__pyx_n_s_os, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_os, __pyx_t_1) < 0) __PYX_ERR(0, 1, __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(__pyx_n_s_types, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_types, __pyx_t_1) < 0) __PYX_ERR(0, 2, __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(__pyx_n_s_itertools, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 3, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_itertools, __pyx_t_1) < 0) __PYX_ERR(0, 3, __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(__pyx_n_s_logging, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_logging, __pyx_t_1) < 0) __PYX_ERR(0, 4, __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(__pyx_n_s_zlib, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 6, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_zlib, __pyx_t_1) < 0) __PYX_ERR(0, 6, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":11
 * ###################################################################################################
 * 
 * logger = logging.getLogger("Log")             # <<<<<<<<<<<<<<
 * 
 * ###################################################################################################
 */
  __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_logging); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 11, __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_ERR(0, 11, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 11, __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_ERR(0, 11, __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 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 16, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_HD, ((PyObject *)(&PyDict_Type))) < 0) __PYX_ERR(0, 16, __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, __pyx_n_s_SQ, ((PyObject *)(&PyList_Type))) < 0) __PYX_ERR(0, 16, __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, __pyx_n_s_RG, ((PyObject *)(&PyList_Type))) < 0) __PYX_ERR(0, 16, __pyx_L1_error)

  /* "htslibWrapper.pyx":19
 *                        "SQ" : list,
 *                        "RG" : list,
 *                        "PG" : list,             # <<<<<<<<<<<<<<
 *                        "CO" : list }
 * 
 */
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_PG, ((PyObject *)(&PyList_Type))) < 0) __PYX_ERR(0, 16, __pyx_L1_error)

  /* "htslibWrapper.pyx":20
 *                        "RG" : list,
 *                        "PG" : list,
 *                        "CO" : list }             # <<<<<<<<<<<<<<
 * 
 * # order of records within sam headers
 */
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_CO, ((PyObject *)(&PyList_Type))) < 0) __PYX_ERR(0, 16, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_VALID_HEADER_TYPES, __pyx_t_1) < 0) __PYX_ERR(0, 16, __pyx_L1_error)
  __Pyx_DECREF(__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, __pyx_tuple__12) < 0) __PYX_ERR(0, 23, __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 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyDict_NewPresized(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_VN, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SO, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_GO, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_HD, __pyx_t_2) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_DECREF(__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 = __Pyx_PyDict_NewPresized(7); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 27, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SN, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_LN, ((PyObject *)(&PyInt_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_AH, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_AS, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_M5, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_UR, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SP, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 27, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_SQ, __pyx_t_2) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_DECREF(__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 = __Pyx_PyDict_NewPresized(10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 28, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_ID, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SM, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_LB, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_DS, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PU, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PI, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_CN, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_DT, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PL, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PG, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 28, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_RG, __pyx_t_2) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_DECREF(__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 = __Pyx_PyDict_NewPresized(6); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 29, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_ID, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_VN, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_CL, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PN, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_PP, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_DS, ((PyObject *)(&PyString_Type))) < 0) __PYX_ERR(0, 29, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_PG, __pyx_t_2) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_VALID_HEADER_FIELDS, __pyx_t_1) < 0) __PYX_ERR(0, 26, __pyx_L1_error)
  __Pyx_DECREF(__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 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 32, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_HD, __pyx_tuple__13) < 0) __PYX_ERR(0, 32, __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, __pyx_n_s_SQ, __pyx_tuple__14) < 0) __PYX_ERR(0, 32, __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, __pyx_n_s_RG, __pyx_tuple__15) < 0) __PYX_ERR(0, 32, __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, __pyx_n_s_PG, __pyx_tuple__16) < 0) __PYX_ERR(0, 32, __pyx_L1_error)
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_VALID_HEADER_ORDER, __pyx_t_1) < 0) __PYX_ERR(0, 32, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "htslibWrapper.pyx":1
 * import os             # <<<<<<<<<<<<<<
 * import types
 * import itertools
 */
  __pyx_t_1 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_DECREF(__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)
 * 
 */

  /*--- Wrapped vars code ---*/

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init htslibWrapper", __pyx_clineno, __pyx_lineno, __pyx_filename);
    }
    Py_CLEAR(__pyx_m);
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init htslibWrapper");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if CYTHON_PEP489_MULTI_PHASE_INIT
  return (__pyx_m != NULL) ? 0 : -1;
  #elif PY_MAJOR_VERSION >= 3
  return __pyx_m;
  #else
  return;
  #endif
}

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

/* PyObjectGetAttrStr */
#if CYTHON_USE_TYPE_SLOTS
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);
}
#endif

/* GetBuiltinName */
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 '%.200s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

/* RaiseDoubleKeywords */
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
}

/* ParseKeywords */
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,
        "%.200s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

/* RaiseArgTupleInvalid */
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,
                 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                 func_name, more_or_less, num_expected,
                 (num_expected == 1) ? "" : "s", num_found);
}

/* PyErrFetchRestore */
#if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    tmp_type = tstate->curexc_type;
    tmp_value = tstate->curexc_value;
    tmp_tb = tstate->curexc_traceback;
    tstate->curexc_type = type;
    tstate->curexc_value = value;
    tstate->curexc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
}
static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
    *type = tstate->curexc_type;
    *value = tstate->curexc_value;
    *tb = tstate->curexc_traceback;
    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
}
#endif

/* WriteUnraisableException */
static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
                                  int full_traceback, CYTHON_UNUSED int nogil) {
    PyObject *old_exc, *old_val, *old_tb;
    PyObject *ctx;
    __Pyx_PyThreadState_declare
#ifdef WITH_THREAD
    PyGILState_STATE state;
    if (nogil)
        state = PyGILState_Ensure();
#ifdef _MSC_VER
    else state = (PyGILState_STATE)-1;
#endif
#endif
    __Pyx_PyThreadState_assign
    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
    if (full_traceback) {
        Py_XINCREF(old_exc);
        Py_XINCREF(old_val);
        Py_XINCREF(old_tb);
        __Pyx_ErrRestore(old_exc, old_val, old_tb);
        PyErr_PrintEx(1);
    }
    #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);
    }
#ifdef WITH_THREAD
    if (nogil)
        PyGILState_Release(state);
#endif
}

/* GetModuleGlobalName */
#if CYTHON_USE_DICT_VERSIONS
static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
#else
static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
#endif
{
    PyObject *result;
#if !CYTHON_AVOID_BORROWED_REFS
#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1
    result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    } else if (unlikely(PyErr_Occurred())) {
        return NULL;
    }
#else
    result = PyDict_GetItem(__pyx_d, name);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    }
#endif
#else
    result = PyObject_GetItem(__pyx_d, name);
    __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
    if (likely(result)) {
        return __Pyx_NewRef(result);
    }
    PyErr_Clear();
#endif
    return __Pyx_GetBuiltinName(name);
}

/* PyCFunctionFastCall */
#if CYTHON_FAST_PYCCALL
static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) {
    PyCFunctionObject *func = (PyCFunctionObject*)func_obj;
    PyCFunction meth = PyCFunction_GET_FUNCTION(func);
    PyObject *self = PyCFunction_GET_SELF(func);
    int flags = PyCFunction_GET_FLAGS(func);
    assert(PyCFunction_Check(func));
    assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS)));
    assert(nargs >= 0);
    assert(nargs == 0 || args != NULL);
    /* _PyCFunction_FastCallDict() must not be called with an exception set,
       because it may clear it (directly or indirectly) and so the
       caller loses its exception */
    assert(!PyErr_Occurred());
    if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) {
        return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL);
    } else {
        return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs);
    }
}
#endif

/* PyFunctionFastCall */
#if CYTHON_FAST_PYCALL
static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
                                               PyObject *globals) {
    PyFrameObject *f;
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    PyObject **fastlocals;
    Py_ssize_t i;
    PyObject *result;
    assert(globals != NULL);
    /* XXX Perhaps we should create a specialized
       PyFrame_New() that doesn't take locals, but does
       take builtins without sanity checking them.
       */
    assert(tstate != NULL);
    f = PyFrame_New(tstate, co, globals, NULL);
    if (f == NULL) {
        return NULL;
    }
    fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
    for (i = 0; i < na; i++) {
        Py_INCREF(*args);
        fastlocals[i] = *args++;
    }
    result = PyEval_EvalFrameEx(f,0);
    ++tstate->recursion_depth;
    Py_DECREF(f);
    --tstate->recursion_depth;
    return result;
}
#if 1 || PY_VERSION_HEX < 0x030600B1
static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) {
    PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
    PyObject *globals = PyFunction_GET_GLOBALS(func);
    PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
    PyObject *closure;
#if PY_MAJOR_VERSION >= 3
    PyObject *kwdefs;
#endif
    PyObject *kwtuple, **k;
    PyObject **d;
    Py_ssize_t nd;
    Py_ssize_t nk;
    PyObject *result;
    assert(kwargs == NULL || PyDict_Check(kwargs));
    nk = kwargs ? PyDict_Size(kwargs) : 0;
    if (Py_EnterRecursiveCall((char*)" while calling a Python object")) {
        return NULL;
    }
    if (
#if PY_MAJOR_VERSION >= 3
            co->co_kwonlyargcount == 0 &&
#endif
            likely(kwargs == NULL || nk == 0) &&
            co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
        if (argdefs == NULL && co->co_argcount == nargs) {
            result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
            goto done;
        }
        else if (nargs == 0 && argdefs != NULL
                 && co->co_argcount == Py_SIZE(argdefs)) {
            /* function called with no arguments, but all parameters have
               a default value: use default values as arguments .*/
            args = &PyTuple_GET_ITEM(argdefs, 0);
            result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
            goto done;
        }
    }
    if (kwargs != NULL) {
        Py_ssize_t pos, i;
        kwtuple = PyTuple_New(2 * nk);
        if (kwtuple == NULL) {
            result = NULL;
            goto done;
        }
        k = &PyTuple_GET_ITEM(kwtuple, 0);
        pos = i = 0;
        while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
            Py_INCREF(k[i]);
            Py_INCREF(k[i+1]);
            i += 2;
        }
        nk = i / 2;
    }
    else {
        kwtuple = NULL;
        k = NULL;
    }
    closure = PyFunction_GET_CLOSURE(func);
#if PY_MAJOR_VERSION >= 3
    kwdefs = PyFunction_GET_KW_DEFAULTS(func);
#endif
    if (argdefs != NULL) {
        d = &PyTuple_GET_ITEM(argdefs, 0);
        nd = Py_SIZE(argdefs);
    }
    else {
        d = NULL;
        nd = 0;
    }
#if PY_MAJOR_VERSION >= 3
    result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
                               args, nargs,
                               k, (int)nk,
                               d, (int)nd, kwdefs, closure);
#else
    result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
                               args, nargs,
                               k, (int)nk,
                               d, (int)nd, closure);
#endif
    Py_XDECREF(kwtuple);
done:
    Py_LeaveRecursiveCall();
    return result;
}
#endif
#endif

/* PyObjectCall */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
    PyObject *result;
    ternaryfunc call = func->ob_type->tp_call;
    if (unlikely(!call))
        return PyObject_Call(func, arg, kw);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = (*call)(func, arg, kw);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCall2Args */
static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) {
    PyObject *args, *result = NULL;
    #if CYTHON_FAST_PYCALL
    if (PyFunction_Check(function)) {
        PyObject *args[2] = {arg1, arg2};
        return __Pyx_PyFunction_FastCall(function, args, 2);
    }
    #endif
    #if CYTHON_FAST_PYCCALL
    if (__Pyx_PyFastCFunction_Check(function)) {
        PyObject *args[2] = {arg1, arg2};
        return __Pyx_PyCFunction_FastCall(function, args, 2);
    }
    #endif
    args = PyTuple_New(2);
    if (unlikely(!args)) goto done;
    Py_INCREF(arg1);
    PyTuple_SET_ITEM(args, 0, arg1);
    Py_INCREF(arg2);
    PyTuple_SET_ITEM(args, 1, arg2);
    Py_INCREF(function);
    result = __Pyx_PyObject_Call(function, args, NULL);
    Py_DECREF(args);
    Py_DECREF(function);
done:
    return result;
}

/* PyObjectCallMethO */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
    PyObject *self, *result;
    PyCFunction cfunc;
    cfunc = PyCFunction_GET_FUNCTION(func);
    self = PyCFunction_GET_SELF(func);
    if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
        return NULL;
    result = cfunc(self, arg);
    Py_LeaveRecursiveCall();
    if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
        PyErr_SetString(
            PyExc_SystemError,
            "NULL result without error in PyObject_Call");
    }
    return result;
}
#endif

/* PyObjectCallOneArg */
#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_New(1);
    if (unlikely(!args)) return NULL;
    Py_INCREF(arg);
    PyTuple_SET_ITEM(args, 0, arg);
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
#if CYTHON_FAST_PYCALL
    if (PyFunction_Check(func)) {
        return __Pyx_PyFunction_FastCall(func, &arg, 1);
    }
#endif
    if (likely(PyCFunction_Check(func))) {
        if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
            return __Pyx_PyObject_CallMethO(func, arg);
#if CYTHON_FAST_PYCCALL
        } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) {
            return __Pyx_PyCFunction_FastCall(func, &arg, 1);
#endif
        }
    }
    return __Pyx__PyObject_CallOneArg(func, arg);
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_Pack(1, arg);
    if (unlikely(!args)) return NULL;
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
#endif

/* BytesEquals */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
#if CYTHON_COMPILING_IN_PYPY
    return PyObject_RichCompareBool(s1, s2, equals);
#else
    if (s1 == s2) {
        return (equals == Py_EQ);
    } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
        const char *ps1, *ps2;
        Py_ssize_t length = PyBytes_GET_SIZE(s1);
        if (length != PyBytes_GET_SIZE(s2))
            return (equals == Py_NE);
        ps1 = PyBytes_AS_STRING(s1);
        ps2 = PyBytes_AS_STRING(s2);
        if (ps1[0] != ps2[0]) {
            return (equals == Py_NE);
        } else if (length == 1) {
            return (equals == Py_EQ);
        } else {
            int result;
#if CYTHON_USE_UNICODE_INTERNALS
            Py_hash_t hash1, hash2;
            hash1 = ((PyBytesObject*)s1)->ob_shash;
            hash2 = ((PyBytesObject*)s2)->ob_shash;
            if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
                return (equals == Py_NE);
            }
#endif
            result = memcmp(ps1, ps2, (size_t)length);
            return (equals == Py_EQ) ? (result == 0) : (result != 0);
        }
    } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
        return (equals == Py_NE);
    } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
        return (equals == Py_NE);
    } else {
        int result;
        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
        if (!py_result)
            return -1;
        result = __Pyx_PyObject_IsTrue(py_result);
        Py_DECREF(py_result);
        return result;
    }
#endif
}

/* UnicodeEquals */
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
#if CYTHON_COMPILING_IN_PYPY
    return PyObject_RichCompareBool(s1, s2, equals);
#else
#if PY_MAJOR_VERSION < 3
    PyObject* owned_ref = NULL;
#endif
    int s1_is_unicode, s2_is_unicode;
    if (s1 == s2) {
        goto return_eq;
    }
    s1_is_unicode = PyUnicode_CheckExact(s1);
    s2_is_unicode = PyUnicode_CheckExact(s2);
#if PY_MAJOR_VERSION < 3
    if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
        owned_ref = PyUnicode_FromObject(s2);
        if (unlikely(!owned_ref))
            return -1;
        s2 = owned_ref;
        s2_is_unicode = 1;
    } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
        owned_ref = PyUnicode_FromObject(s1);
        if (unlikely(!owned_ref))
            return -1;
        s1 = owned_ref;
        s1_is_unicode = 1;
    } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
        return __Pyx_PyBytes_Equals(s1, s2, equals);
    }
#endif
    if (s1_is_unicode & s2_is_unicode) {
        Py_ssize_t length;
        int kind;
        void *data1, *data2;
        if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
            return -1;
        length = __Pyx_PyUnicode_GET_LENGTH(s1);
        if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
            goto return_ne;
        }
#if CYTHON_USE_UNICODE_INTERNALS
        {
            Py_hash_t hash1, hash2;
        #if CYTHON_PEP393_ENABLED
            hash1 = ((PyASCIIObject*)s1)->hash;
            hash2 = ((PyASCIIObject*)s2)->hash;
        #else
            hash1 = ((PyUnicodeObject*)s1)->hash;
            hash2 = ((PyUnicodeObject*)s2)->hash;
        #endif
            if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
                goto return_ne;
            }
        }
#endif
        kind = __Pyx_PyUnicode_KIND(s1);
        if (kind != __Pyx_PyUnicode_KIND(s2)) {
            goto return_ne;
        }
        data1 = __Pyx_PyUnicode_DATA(s1);
        data2 = __Pyx_PyUnicode_DATA(s2);
        if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
            goto return_ne;
        } else if (length == 1) {
            goto return_eq;
        } else {
            int result = memcmp(data1, data2, (size_t)(length * kind));
            #if PY_MAJOR_VERSION < 3
            Py_XDECREF(owned_ref);
            #endif
            return (equals == Py_EQ) ? (result == 0) : (result != 0);
        }
    } else if ((s1 == Py_None) & s2_is_unicode) {
        goto return_ne;
    } else if ((s2 == Py_None) & s1_is_unicode) {
        goto return_ne;
    } else {
        int result;
        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
        #if PY_MAJOR_VERSION < 3
        Py_XDECREF(owned_ref);
        #endif
        if (!py_result)
            return -1;
        result = __Pyx_PyObject_IsTrue(py_result);
        Py_DECREF(py_result);
        return result;
    }
return_eq:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(owned_ref);
    #endif
    return (equals == Py_EQ);
return_ne:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(owned_ref);
    #endif
    return (equals == Py_NE);
#endif
}

/* RaiseException */
#if PY_MAJOR_VERSION < 3
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                        CYTHON_UNUSED PyObject *cause) {
    __Pyx_PyThreadState_declare
    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 (PyType_Check(type)) {
#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;
        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;
        }
    }
    __Pyx_PyThreadState_assign
    __Pyx_ErrRestore(type, value, tb);
    return;
raise_error:
    Py_XDECREF(value);
    Py_XDECREF(type);
    Py_XDECREF(tb);
    return;
}
#else
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 *instance_class = NULL;
        if (value && PyExceptionInstance_Check(value)) {
            instance_class = (PyObject*) Py_TYPE(value);
            if (instance_class != type) {
                int is_subclass = PyObject_IsSubclass(instance_class, type);
                if (!is_subclass) {
                    instance_class = NULL;
                } else if (unlikely(is_subclass == -1)) {
                    goto bad;
                } else {
                    type = instance_class;
                }
            }
        }
        if (!instance_class) {
            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 = PyObject_Call(type, args, NULL);
            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 (cause) {
        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) {
#if CYTHON_COMPILING_IN_PYPY
        PyObject *tmp_type, *tmp_value, *tmp_tb;
        PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
        Py_INCREF(tb);
        PyErr_Restore(tmp_type, tmp_value, tb);
        Py_XDECREF(tmp_tb);
#else
        PyThreadState *tstate = __Pyx_PyThreadState_Current;
        PyObject* tmp_tb = tstate->curexc_traceback;
        if (tb != tmp_tb) {
            Py_INCREF(tb);
            tstate->curexc_traceback = tb;
            Py_XDECREF(tmp_tb);
        }
#endif
    }
bad:
    Py_XDECREF(owned_instance);
    return;
}
#endif

/* GetItemInt */
static 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,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    Py_ssize_t wrapped_i = i;
    if (wraparound & unlikely(i < 0)) {
        wrapped_i += PyList_GET_SIZE(o);
    }
    if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
        PyObject *r = PyList_GET_ITEM(o, wrapped_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,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
    Py_ssize_t wrapped_i = i;
    if (wraparound & unlikely(i < 0)) {
        wrapped_i += PyTuple_GET_SIZE(o);
    }
    if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
        PyObject *r = PyTuple_GET_ITEM(o, wrapped_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,
                                                     CYTHON_NCP_UNUSED int wraparound,
                                                     CYTHON_NCP_UNUSED int boundscheck) {
#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
    if (is_list || PyList_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
        if ((!boundscheck) || (likely(__Pyx_is_valid_index(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(__Pyx_is_valid_index(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))
                        return NULL;
                    PyErr_Clear();
                }
            }
            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));
}

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

/* PyObjectCallNoArg */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
#if CYTHON_FAST_PYCALL
    if (PyFunction_Check(func)) {
        return __Pyx_PyFunction_FastCall(func, NULL, 0);
    }
#endif
#ifdef __Pyx_CyFunction_USED
    if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func)))
#else
    if (likely(PyCFunction_Check(func)))
#endif
    {
        if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) {
            return __Pyx_PyObject_CallMethO(func, NULL);
        }
    }
    return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL);
}
#endif

/* SliceObject */
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_USE_TYPE_SLOTS
    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))
                    goto bad;
                PyErr_Clear();
            }
        }
        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_USE_TYPE_SLOTS
        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;
}

/* PyObjectGetMethod */
static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) {
    PyObject *attr;
#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP
    PyTypeObject *tp = Py_TYPE(obj);
    PyObject *descr;
    descrgetfunc f = NULL;
    PyObject **dictptr, *dict;
    int meth_found = 0;
    assert (*method == NULL);
    if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) {
        attr = __Pyx_PyObject_GetAttrStr(obj, name);
        goto try_unpack;
    }
    if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) {
        return 0;
    }
    descr = _PyType_Lookup(tp, name);
    if (likely(descr != NULL)) {
        Py_INCREF(descr);
#if PY_MAJOR_VERSION >= 3
        #ifdef __Pyx_CyFunction_USED
        if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr)))
        #else
        if (likely(PyFunction_Check(descr) || (Py_TYPE(descr) == &PyMethodDescr_Type)))
        #endif
#else
        #ifdef __Pyx_CyFunction_USED
        if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr)))
        #else
        if (likely(PyFunction_Check(descr)))
        #endif
#endif
        {
            meth_found = 1;
        } else {
            f = Py_TYPE(descr)->tp_descr_get;
            if (f != NULL && PyDescr_IsData(descr)) {
                attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
                Py_DECREF(descr);
                goto try_unpack;
            }
        }
    }
    dictptr = _PyObject_GetDictPtr(obj);
    if (dictptr != NULL && (dict = *dictptr) != NULL) {
        Py_INCREF(dict);
        attr = __Pyx_PyDict_GetItemStr(dict, name);
        if (attr != NULL) {
            Py_INCREF(attr);
            Py_DECREF(dict);
            Py_XDECREF(descr);
            goto try_unpack;
        }
        Py_DECREF(dict);
    }
    if (meth_found) {
        *method = descr;
        return 1;
    }
    if (f != NULL) {
        attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
        Py_DECREF(descr);
        goto try_unpack;
    }
    if (descr != NULL) {
        *method = descr;
        return 0;
    }
    PyErr_Format(PyExc_AttributeError,
#if PY_MAJOR_VERSION >= 3
                 "'%.50s' object has no attribute '%U'",
                 tp->tp_name, name);
#else
                 "'%.50s' object has no attribute '%.400s'",
                 tp->tp_name, PyString_AS_STRING(name));
#endif
    return 0;
#else
    attr = __Pyx_PyObject_GetAttrStr(obj, name);
    goto try_unpack;
#endif
try_unpack:
#if CYTHON_UNPACK_METHODS
    if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) {
        PyObject *function = PyMethod_GET_FUNCTION(attr);
        Py_INCREF(function);
        Py_DECREF(attr);
        *method = function;
        return 1;
    }
#endif
    *method = attr;
    return 0;
}

/* PyObjectCallMethod1 */
static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) {
    PyObject *result = __Pyx_PyObject_CallOneArg(method, arg);
    Py_DECREF(method);
    return result;
}
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
    PyObject *method = NULL, *result;
    int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
    if (likely(is_method)) {
        result = __Pyx_PyObject_Call2Args(method, obj, arg);
        Py_DECREF(method);
        return result;
    }
    if (unlikely(!method)) return NULL;
    return __Pyx__PyObject_CallMethod1(method, arg);
}

/* append */
static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
    if (likely(PyList_CheckExact(L))) {
        if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
    } else {
        PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
        if (unlikely(!retval))
            return -1;
        Py_DECREF(retval);
    }
    return 0;
}

/* DictGetItem */
#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
    PyObject *value;
    value = PyDict_GetItemWithError(d, key);
    if (unlikely(!value)) {
        if (!PyErr_Occurred()) {
            if (unlikely(PyTuple_Check(key))) {
                PyObject* args = PyTuple_Pack(1, key);
                if (likely(args)) {
                    PyErr_SetObject(PyExc_KeyError, args);
                    Py_DECREF(args);
                }
            } else {
                PyErr_SetObject(PyExc_KeyError, key);
            }
        }
        return NULL;
    }
    Py_INCREF(value);
    return value;
}
#endif

/* StringJoin */
#if !CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
    return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL);
}
#endif

/* RaiseTooManyValuesToUnpack */
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);
}

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

/* IterFinish */
static CYTHON_INLINE int __Pyx_IterFinish(void) {
#if CYTHON_FAST_THREAD_STATE
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    PyObject* exc_type = tstate->curexc_type;
    if (unlikely(exc_type)) {
        if (likely(__Pyx_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
}

/* UnpackItemEndCheck */
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;
}

/* ObjectGetItem */
#if CYTHON_USE_TYPE_SLOTS
static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) {
    PyObject *runerr;
    Py_ssize_t key_value;
    PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence;
    if (unlikely(!(m && m->sq_item))) {
        PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name);
        return NULL;
    }
    key_value = __Pyx_PyIndex_AsSsize_t(index);
    if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) {
        return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1);
    }
    if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) {
        PyErr_Clear();
        PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name);
    }
    return NULL;
}
static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) {
    PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping;
    if (likely(m && m->mp_subscript)) {
        return m->mp_subscript(obj, key);
    }
    return __Pyx_PyObject_GetIndex(obj, key);
}
#endif

/* ArgTypeTest */
static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact)
{
    if (unlikely(!type)) {
        PyErr_SetString(PyExc_SystemError, "Missing type object");
        return 0;
    }
    else if (exact) {
        #if PY_MAJOR_VERSION == 2
        if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
        #endif
    }
    else {
        if (likely(__Pyx_TypeCheck(obj, type))) return 1;
    }
    PyErr_Format(PyExc_TypeError,
        "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)",
        name, type->tp_name, Py_TYPE(obj)->tp_name);
    return 0;
}

/* PyObject_GenericGetAttrNoDict */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) {
    PyErr_Format(PyExc_AttributeError,
#if PY_MAJOR_VERSION >= 3
                 "'%.50s' object has no attribute '%U'",
                 tp->tp_name, attr_name);
#else
                 "'%.50s' object has no attribute '%.400s'",
                 tp->tp_name, PyString_AS_STRING(attr_name));
#endif
    return NULL;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) {
    PyObject *descr;
    PyTypeObject *tp = Py_TYPE(obj);
    if (unlikely(!PyString_Check(attr_name))) {
        return PyObject_GenericGetAttr(obj, attr_name);
    }
    assert(!tp->tp_dictoffset);
    descr = _PyType_Lookup(tp, attr_name);
    if (unlikely(!descr)) {
        return __Pyx_RaiseGenericGetAttributeError(tp, attr_name);
    }
    Py_INCREF(descr);
    #if PY_MAJOR_VERSION < 3
    if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS)))
    #endif
    {
        descrgetfunc f = Py_TYPE(descr)->tp_descr_get;
        if (unlikely(f)) {
            PyObject *res = f(descr, obj, (PyObject *)tp);
            Py_DECREF(descr);
            return res;
        }
    }
    return descr;
}
#endif

/* PyObject_GenericGetAttr */
#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) {
    if (unlikely(Py_TYPE(obj)->tp_dictoffset)) {
        return PyObject_GenericGetAttr(obj, attr_name);
    }
    return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name);
}
#endif

/* SetVTable */
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000
    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;
}

/* SetupReduce */
static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
  int ret;
  PyObject *name_attr;
  name_attr = __Pyx_PyObject_GetAttrStr(meth, __pyx_n_s_name);
  if (likely(name_attr)) {
      ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
  } else {
      ret = -1;
  }
  if (unlikely(ret < 0)) {
      PyErr_Clear();
      ret = 0;
  }
  Py_XDECREF(name_attr);
  return ret;
}
static int __Pyx_setup_reduce(PyObject* type_obj) {
    int ret = 0;
    PyObject *object_reduce = NULL;
    PyObject *object_reduce_ex = NULL;
    PyObject *reduce = NULL;
    PyObject *reduce_ex = NULL;
    PyObject *reduce_cython = NULL;
    PyObject *setstate = NULL;
    PyObject *setstate_cython = NULL;
#if CYTHON_USE_PYTYPE_LOOKUP
    if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD;
#else
    if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD;
#endif
#if CYTHON_USE_PYTYPE_LOOKUP
    object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
#else
    object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD;
#endif
    reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD;
    if (reduce_ex == object_reduce_ex) {
#if CYTHON_USE_PYTYPE_LOOKUP
        object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD;
#else
        object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD;
#endif
        reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD;
        if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
            reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD;
            ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD;
            ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD;
            setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate);
            if (!setstate) PyErr_Clear();
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
                setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD;
                ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD;
                ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD;
            }
            PyType_Modified((PyTypeObject*)type_obj);
        }
    }
    goto GOOD;
BAD:
    if (!PyErr_Occurred())
        PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name);
    ret = -1;
GOOD:
#if !CYTHON_USE_PYTYPE_LOOKUP
    Py_XDECREF(object_reduce);
    Py_XDECREF(object_reduce_ex);
#endif
    Py_XDECREF(reduce);
    Py_XDECREF(reduce_ex);
    Py_XDECREF(reduce_cython);
    Py_XDECREF(setstate);
    Py_XDECREF(setstate_cython);
    return ret;
}

/* TypeImport */
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(PyObject *module, const char *module_name, const char *class_name,
    size_t size, enum __Pyx_ImportType_CheckSize check_size)
{
    PyObject *result = 0;
    char warning[200];
    Py_ssize_t basicsize;
#ifdef Py_LIMITED_API
    PyObject *py_basicsize;
#endif
    result = PyObject_GetAttrString(module, class_name);
    if (!result)
        goto bad;
    if (!PyType_Check(result)) {
        PyErr_Format(PyExc_TypeError,
            "%.200s.%.200s 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 ((size_t)basicsize < size) {
        PyErr_Format(PyExc_ValueError,
            "%.200s.%.200s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        goto bad;
    }
    if (check_size == __Pyx_ImportType_CheckSize_Error && (size_t)basicsize != size) {
        PyErr_Format(PyExc_ValueError,
            "%.200s.%.200s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        goto bad;
    }
    else if (check_size == __Pyx_ImportType_CheckSize_Warn && (size_t)basicsize > size) {
        PyOS_snprintf(warning, sizeof(warning),
            "%s.%s size changed, may indicate binary incompatibility. "
            "Expected %zd from C header, got %zd from PyObject",
            module_name, class_name, size, basicsize);
        if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
    }
    return (PyTypeObject *)result;
bad:
    Py_XDECREF(result);
    return NULL;
}
#endif

/* Import */
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_MAJOR_VERSION < 3
    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_MAJOR_VERSION >= 3
        if (level == -1) {
            if (strchr(__Pyx_MODULE_NAME, '.')) {
                module = PyImport_ImportModuleLevelObject(
                    name, global_dict, empty_dict, list, 1);
                if (!module) {
                    if (!PyErr_ExceptionMatches(PyExc_ImportError))
                        goto bad;
                    PyErr_Clear();
                }
            }
            level = 0;
        }
        #endif
        if (!module) {
            #if PY_MAJOR_VERSION < 3
            PyObject *py_level = PyInt_FromLong(level);
            if (!py_level)
                goto bad;
            module = PyObject_CallFunctionObjArgs(py_import,
                name, global_dict, empty_dict, list, py_level, (PyObject *)NULL);
            Py_DECREF(py_level);
            #else
            module = PyImport_ImportModuleLevelObject(
                name, global_dict, empty_dict, list, level);
            #endif
        }
    }
bad:
    #if PY_MAJOR_VERSION < 3
    Py_XDECREF(py_import);
    #endif
    Py_XDECREF(empty_list);
    Py_XDECREF(empty_dict);
    return module;
}

/* CLineInTraceback */
#ifndef CYTHON_CLINE_IN_TRACEBACK
static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) {
    PyObject *use_cline;
    PyObject *ptype, *pvalue, *ptraceback;
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject **cython_runtime_dict;
#endif
    if (unlikely(!__pyx_cython_runtime)) {
        return c_line;
    }
    __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
#if CYTHON_COMPILING_IN_CPYTHON
    cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
    if (likely(cython_runtime_dict)) {
        __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            use_cline, *cython_runtime_dict,
            __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
    } else
#endif
    {
      PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
      if (use_cline_obj) {
        use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
        Py_DECREF(use_cline_obj);
      } else {
        PyErr_Clear();
        use_cline = NULL;
      }
    }
    if (!use_cline) {
        c_line = 0;
        PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
    }
    else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
        c_line = 0;
    }
    __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
    return c_line;
}
#endif

/* CodeObjectCache */
static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
    int start = 0, mid = 0, end = count - 1;
    if (end >= 0 && code_line > entries[end].code_line) {
        return count;
    }
    while (start < end) {
        mid = start + (end - start) / 2;
        if (code_line < entries[mid].code_line) {
            end = mid;
        } else if (code_line > entries[mid].code_line) {
             start = mid + 1;
        } else {
            return mid;
        }
    }
    if (code_line <= entries[mid].code_line) {
        return mid;
    } else {
        return mid + 1;
    }
}
static PyCodeObject *__pyx_find_code_object(int code_line) {
    PyCodeObject* code_object;
    int pos;
    if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
        return NULL;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
        return NULL;
    }
    code_object = __pyx_code_cache.entries[pos].code_object;
    Py_INCREF(code_object);
    return code_object;
}
static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
    int pos, i;
    __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
    if (unlikely(!code_line)) {
        return;
    }
    if (unlikely(!entries)) {
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
        if (likely(entries)) {
            __pyx_code_cache.entries = entries;
            __pyx_code_cache.max_count = 64;
            __pyx_code_cache.count = 1;
            entries[0].code_line = code_line;
            entries[0].code_object = code_object;
            Py_INCREF(code_object);
        }
        return;
    }
    pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
    if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
        PyCodeObject* tmp = entries[pos].code_object;
        entries[pos].code_object = code_object;
        Py_DECREF(tmp);
        return;
    }
    if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
        int new_max = __pyx_code_cache.max_count + 64;
        entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
            __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
        if (unlikely(!entries)) {
            return;
        }
        __pyx_code_cache.entries = entries;
        __pyx_code_cache.max_count = new_max;
    }
    for (i=__pyx_code_cache.count; i>pos; i--) {
        entries[i] = entries[i-1];
    }
    entries[pos].code_line = code_line;
    entries[pos].code_object = code_object;
    __pyx_code_cache.count++;
    Py_INCREF(code_object);
}

/* AddTraceback */
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
            const char *funcname, int c_line,
            int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyObject *py_srcfile = 0;
    PyObject *py_funcname = 0;
    #if PY_MAJOR_VERSION < 3
    py_srcfile = PyString_FromString(filename);
    #else
    py_srcfile = PyUnicode_FromString(filename);
    #endif
    if (!py_srcfile) goto bad;
    if (c_line) {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #else
        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
        #endif
    }
    else {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromString(funcname);
        #else
        py_funcname = PyUnicode_FromString(funcname);
        #endif
    }
    if (!py_funcname) goto bad;
    py_code = __Pyx_PyCode_New(
        0,
        0,
        0,
        0,
        0,
        __pyx_empty_bytes, /*PyObject *code,*/
        __pyx_empty_tuple, /*PyObject *consts,*/
        __pyx_empty_tuple, /*PyObject *names,*/
        __pyx_empty_tuple, /*PyObject *varnames,*/
        __pyx_empty_tuple, /*PyObject *freevars,*/
        __pyx_empty_tuple, /*PyObject *cellvars,*/
        py_srcfile,   /*PyObject *filename,*/
        py_funcname,  /*PyObject *name,*/
        py_line,
        __pyx_empty_bytes  /*PyObject *lnotab*/
    );
    Py_DECREF(py_srcfile);
    Py_DECREF(py_funcname);
    return py_code;
bad:
    Py_XDECREF(py_srcfile);
    Py_XDECREF(py_funcname);
    return NULL;
}
static void __Pyx_AddTraceback(const char *funcname, int c_line,
                               int py_line, const char *filename) {
    PyCodeObject *py_code = 0;
    PyFrameObject *py_frame = 0;
    PyThreadState *tstate = __Pyx_PyThreadState_Current;
    if (c_line) {
        c_line = __Pyx_CLineForTraceback(tstate, c_line);
    }
    py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
    if (!py_code) {
        py_code = __Pyx_CreateCodeObjectForTraceback(
            funcname, c_line, py_line, filename);
        if (!py_code) goto bad;
        __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
    }
    py_frame = PyFrame_New(
        tstate,            /*PyThreadState *tstate,*/
        py_code,           /*PyCodeObject *code,*/
        __pyx_d,    /*PyObject *globals,*/
        0                  /*PyObject *locals*/
    );
    if (!py_frame) goto bad;
    __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
    PyTraceBack_Here(py_frame);
bad:
    Py_XDECREF(py_code);
    Py_XDECREF(py_frame);
}

/* Print */
#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) {
                switch (s[len-1]) {
                    case ' ': break;
                    case '\f': case '\r': case '\n': case '\t': case '\v':
                        PyFile_SoftSpace(f, 0);
                        break;
                    default:  break;
                }
            }
        }
    }
    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
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

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
    const long neg_one = (long) ((long) 0 - (long) 1), const_zero = (long) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(long) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(long) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(long) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(long),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
    const int neg_one = (int) ((int) 0 - (int) 1), const_zero = (int) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(int) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(int) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(int) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(int),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) {
    const int32_t neg_one = (int32_t) ((int32_t) 0 - (int32_t) 1), const_zero = (int32_t) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(int32_t) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(int32_t) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(int32_t) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(int32_t),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
    const uint32_t neg_one = (uint32_t) ((uint32_t) 0 - (uint32_t) 1), const_zero = (uint32_t) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(uint32_t) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(uint32_t) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
                                     little, !is_unsigned);
    }
}

/* CIntFromPyVerify */
#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
    __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
    {\
        func_type value = func_value;\
        if (sizeof(target_type) < sizeof(func_type)) {\
            if (unlikely(value != (func_type) (target_type) value)) {\
                func_type zero = 0;\
                if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
                    return (target_type) -1;\
                if (is_unsigned && unlikely(value < zero))\
                    goto raise_neg_overflow;\
                else\
                    goto raise_overflow;\
            }\
        }\
        return (target_type) value;\
    }

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value) {
    const short neg_one = (short) ((short) 0 - (short) 1), const_zero = (short) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(short) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(short) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(short) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(short) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(short) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(short),
                                     little, !is_unsigned);
    }
}

/* CIntToPy */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value) {
    const char neg_one = (char) ((char) 0 - (char) 1), const_zero = (char) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(char) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(char) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
#endif
        }
    } else {
        if (sizeof(char) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
#ifdef HAVE_LONG_LONG
        } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_LONG_LONG) value);
#endif
        }
    }
    {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&value;
        return _PyLong_FromByteArray(bytes, sizeof(char),
                                     little, !is_unsigned);
    }
}

/* PrintOne */
#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
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

/* CIntFromPy */
static CYTHON_INLINE short __Pyx_PyInt_As_short(PyObject *x) {
    const short neg_one = (short) ((short) 0 - (short) 1), const_zero = (short) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(short) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(short, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (short) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (short) 0;
                case  1: __PYX_VERIFY_RETURN_INT(short, digit, digits[0])
                case 2:
                    if (8 * sizeof(short) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) >= 2 * PyLong_SHIFT) {
                            return (short) (((((short)digits[1]) << PyLong_SHIFT) | (short)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(short) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) >= 3 * PyLong_SHIFT) {
                            return (short) (((((((short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(short) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) >= 4 * PyLong_SHIFT) {
                            return (short) (((((((((short)digits[3]) << PyLong_SHIFT) | (short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (short) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(short) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(short, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(short) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(short, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (short) 0;
                case -1: __PYX_VERIFY_RETURN_INT(short, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(short,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(short) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 2 * PyLong_SHIFT) {
                            return (short) (((short)-1)*(((((short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(short) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 2 * PyLong_SHIFT) {
                            return (short) ((((((short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(short) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 3 * PyLong_SHIFT) {
                            return (short) (((short)-1)*(((((((short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(short) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 3 * PyLong_SHIFT) {
                            return (short) ((((((((short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(short) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 4 * PyLong_SHIFT) {
                            return (short) (((short)-1)*(((((((((short)digits[3]) << PyLong_SHIFT) | (short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(short) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(short, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(short) - 1 > 4 * PyLong_SHIFT) {
                            return (short) ((((((((((short)digits[3]) << PyLong_SHIFT) | (short)digits[2]) << PyLong_SHIFT) | (short)digits[1]) << PyLong_SHIFT) | (short)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(short) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(short, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(short) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(short, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            short val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (short) -1;
        }
    } else {
        short val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (short) -1;
        val = __Pyx_PyInt_As_short(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to short");
    return (short) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to short");
    return (short) -1;
}

/* CIntFromPy */
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
    const int neg_one = (int) ((int) 0 - (int) 1), const_zero = (int) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(int) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (int) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case  1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0])
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) {
                            return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) {
                            return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) {
                            return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (int) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(int) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (int) 0;
                case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(int,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(int) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                            return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(int) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                            return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(int) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) {
                            return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(int) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            int val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (int) -1;
        }
    } else {
        int val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (int) -1;
        val = __Pyx_PyInt_As_int(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to int");
    return (int) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to int");
    return (int) -1;
}

/* CIntFromPy */
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
    const long neg_one = (long) ((long) 0 - (long) 1), const_zero = (long) 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
    if (likely(PyInt_Check(x))) {
        if (sizeof(long) < sizeof(long)) {
            __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
        } else {
            long val = PyInt_AS_LONG(x);
            if (is_unsigned && unlikely(val < 0)) {
                goto raise_neg_overflow;
            }
            return (long) val;
        }
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case  1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0])
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) {
                            return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) {
                            return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) {
                            return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
                        }
                    }
                    break;
            }
#endif
#if CYTHON_COMPILING_IN_CPYTHON
            if (unlikely(Py_SIZE(x) < 0)) {
                goto raise_neg_overflow;
            }
#else
            {
                int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
                if (unlikely(result < 0))
                    return (long) -1;
                if (unlikely(result == 1))
                    goto raise_neg_overflow;
            }
#endif
            if (sizeof(long) <= sizeof(unsigned long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
#endif
            }
        } else {
#if CYTHON_USE_PYLONG_INTERNALS
            const digit* digits = ((PyLongObject*)x)->ob_digit;
            switch (Py_SIZE(x)) {
                case  0: return (long) 0;
                case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0]))
                case  1: __PYX_VERIFY_RETURN_INT(long,  digit, +digits[0])
                case -2:
                    if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 2:
                    if (8 * sizeof(long) > 1 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                            return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -3:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 3:
                    if (8 * sizeof(long) > 2 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                            return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case -4:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
                case 4:
                    if (8 * sizeof(long) > 3 * PyLong_SHIFT) {
                        if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
                            __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
                        } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                            return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
                        }
                    }
                    break;
            }
#endif
            if (sizeof(long) <= sizeof(long)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
#ifdef HAVE_LONG_LONG
            } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
                __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
#endif
            }
        }
        {
#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
            PyErr_SetString(PyExc_RuntimeError,
                            "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
#else
            long val;
            PyObject *v = __Pyx_PyNumber_IntOrLong(x);
 #if PY_MAJOR_VERSION < 3
            if (likely(v) && !PyLong_Check(v)) {
                PyObject *tmp = v;
                v = PyNumber_Long(tmp);
                Py_DECREF(tmp);
            }
 #endif
            if (likely(v)) {
                int one = 1; int is_little = (int)*(unsigned char *)&one;
                unsigned char *bytes = (unsigned char *)&val;
                int ret = _PyLong_AsByteArray((PyLongObject *)v,
                                              bytes, sizeof(val),
                                              is_little, !is_unsigned);
                Py_DECREF(v);
                if (likely(!ret))
                    return val;
            }
#endif
            return (long) -1;
        }
    } else {
        long val;
        PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
        if (!tmp) return (long) -1;
        val = __Pyx_PyInt_As_long(tmp);
        Py_DECREF(tmp);
        return val;
    }
raise_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "value too large to convert to long");
    return (long) -1;
raise_neg_overflow:
    PyErr_SetString(PyExc_OverflowError,
        "can't convert negative value to long");
    return (long) -1;
}

/* FastTypeChecks */
#if CYTHON_COMPILING_IN_CPYTHON
static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
    while (a) {
        a = a->tp_base;
        if (a == b)
            return 1;
    }
    return b == &PyBaseObject_Type;
}
static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
    PyObject *mro;
    if (a == b) return 1;
    mro = a->tp_mro;
    if (likely(mro)) {
        Py_ssize_t i, n;
        n = PyTuple_GET_SIZE(mro);
        for (i = 0; i < n; i++) {
            if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
                return 1;
        }
        return 0;
    }
    return __Pyx_InBases(a, b);
}
#if PY_MAJOR_VERSION == 2
static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
    PyObject *exception, *value, *tb;
    int res;
    __Pyx_PyThreadState_declare
    __Pyx_PyThreadState_assign
    __Pyx_ErrFetch(&exception, &value, &tb);
    res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
    if (unlikely(res == -1)) {
        PyErr_WriteUnraisable(err);
        res = 0;
    }
    if (!res) {
        res = PyObject_IsSubclass(err, exc_type2);
        if (unlikely(res == -1)) {
            PyErr_WriteUnraisable(err);
            res = 0;
        }
    }
    __Pyx_ErrRestore(exception, value, tb);
    return res;
}
#else
static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
    int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0;
    if (!res) {
        res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
    }
    return res;
}
#endif
static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
    Py_ssize_t i, n;
    assert(PyExceptionClass_Check(exc_type));
    n = PyTuple_GET_SIZE(tuple);
#if PY_MAJOR_VERSION >= 3
    for (i=0; i<n; i++) {
        if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
    }
#endif
    for (i=0; i<n; i++) {
        PyObject *t = PyTuple_GET_ITEM(tuple, i);
        #if PY_MAJOR_VERSION < 3
        if (likely(exc_type == t)) return 1;
        #endif
        if (likely(PyExceptionClass_Check(t))) {
            if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
        } else {
        }
    }
    return 0;
}
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
    if (likely(err == exc_type)) return 1;
    if (likely(PyExceptionClass_Check(err))) {
        if (likely(PyExceptionClass_Check(exc_type))) {
            return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
        } else if (likely(PyTuple_Check(exc_type))) {
            return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
        } else {
        }
    }
    return PyErr_GivenExceptionMatches(err, exc_type);
}
static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
    assert(PyExceptionClass_Check(exc_type1));
    assert(PyExceptionClass_Check(exc_type2));
    if (likely(err == exc_type1 || err == exc_type2)) return 1;
    if (likely(PyExceptionClass_Check(err))) {
        return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
    }
    return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
}
#endif

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

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

/* InitStrings */
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
    while (t->p) {
        #if PY_MAJOR_VERSION < 3
        if (t->is_unicode) {
            *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
        } else if (t->intern) {
            *t->p = PyString_InternFromString(t->s);
        } else {
            *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
        }
        #else
        if (t->is_unicode | t->is_str) {
            if (t->intern) {
                *t->p = PyUnicode_InternFromString(t->s);
            } else if (t->encoding) {
                *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
            } else {
                *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
            }
        } else {
            *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
        }
        #endif
        if (!*t->p)
            return -1;
        if (PyObject_Hash(*t->p) == -1)
            return -1;
        ++t;
    }
    return 0;
}

static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
}
static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
    Py_ssize_t ignore;
    return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
#if !CYTHON_PEP393_ENABLED
static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
    char* defenc_c;
    PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
    if (!defenc) return NULL;
    defenc_c = PyBytes_AS_STRING(defenc);
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
    {
        char* end = defenc_c + PyBytes_GET_SIZE(defenc);
        char* c;
        for (c = defenc_c; c < end; c++) {
            if ((unsigned char) (*c) >= 128) {
                PyUnicode_AsASCIIString(o);
                return NULL;
            }
        }
    }
#endif
    *length = PyBytes_GET_SIZE(defenc);
    return defenc_c;
}
#else
static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
    if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
    if (likely(PyUnicode_IS_ASCII(o))) {
        *length = PyUnicode_GET_LENGTH(o);
        return PyUnicode_AsUTF8(o);
    } else {
        PyUnicode_AsASCIIString(o);
        return NULL;
    }
#else
    return PyUnicode_AsUTF8AndSize(o, length);
#endif
}
#endif
#endif
static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
    if (
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
            __Pyx_sys_getdefaultencoding_not_ascii &&
#endif
            PyUnicode_Check(o)) {
        return __Pyx_PyUnicode_AsStringAndSize(o, length);
    } else
#endif
#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
    if (PyByteArray_Check(o)) {
        *length = PyByteArray_GET_SIZE(o);
        return PyByteArray_AS_STRING(o);
    } else
#endif
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (unlikely(r < 0)) {
            return NULL;
        } else {
            return result;
        }
    }
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
    int retval;
    if (unlikely(!x)) return -1;
    retval = __Pyx_PyObject_IsTrue(x);
    Py_DECREF(x);
    return retval;
}
static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
#if PY_MAJOR_VERSION >= 3
    if (PyLong_Check(result)) {
        if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
                "__int__ returned non-int (type %.200s).  "
                "The ability to return an instance of a strict subclass of int "
                "is deprecated, and may be removed in a future version of Python.",
                Py_TYPE(result)->tp_name)) {
            Py_DECREF(result);
            return NULL;
        }
        return result;
    }
#endif
    PyErr_Format(PyExc_TypeError,
                 "__%.4s__ returned non-%.4s (type %.200s)",
                 type_name, type_name, Py_TYPE(result)->tp_name);
    Py_DECREF(result);
    return NULL;
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
#if CYTHON_USE_TYPE_SLOTS
  PyNumberMethods *m;
#endif
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_Check(x) || PyLong_Check(x)))
#else
  if (likely(PyLong_Check(x)))
#endif
    return __Pyx_NewRef(x);
#if CYTHON_USE_TYPE_SLOTS
  m = Py_TYPE(x)->tp_as_number;
  #if PY_MAJOR_VERSION < 3
  if (m && m->nb_int) {
    name = "int";
    res = m->nb_int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = m->nb_long(x);
  }
  #else
  if (likely(m && m->nb_int)) {
    name = "int";
    res = m->nb_int(x);
  }
  #endif
#else
  if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
    res = PyNumber_Int(x);
  }
#endif
  if (likely(res)) {
#if PY_MAJOR_VERSION < 3
    if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
#else
    if (unlikely(!PyLong_CheckExact(res))) {
#endif
        return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
    }
  }
  else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_TypeError,
                    "an integer is required");
  }
  return res;
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
  Py_ssize_t ival;
  PyObject *x;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_CheckExact(b))) {
    if (sizeof(Py_ssize_t) >= sizeof(long))
        return PyInt_AS_LONG(b);
    else
        return PyInt_AsSsize_t(b);
  }
#endif
  if (likely(PyLong_CheckExact(b))) {
    #if CYTHON_USE_PYLONG_INTERNALS
    const digit* digits = ((PyLongObject*)b)->ob_digit;
    const Py_ssize_t size = Py_SIZE(b);
    if (likely(__Pyx_sst_abs(size) <= 1)) {
        ival = likely(size) ? digits[0] : 0;
        if (size == -1) ival = -ival;
        return ival;
    } else {
      switch (size) {
         case 2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
      }
    }
    #endif
    return PyLong_AsSsize_t(b);
  }
  x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
  return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
    return PyInt_FromSize_t(ival);
}


#endif /* Py_PYTHON_H */
