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#define _USE_MATH_DEFINES
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#include <math.h>
#define __PYX_HAVE_API__csamtools
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "stdio.h"
#include "ctype.h"
#include "unistd.h"
#include "fileobject.h"
#include "razf.h"
#include "stdint.h"
#include "bam.h"
#include "sam.h"
#include "glf.h"
#include "bam_maqcns.h"
#include "faidx.h"
#include "pysam_util.h"
#include "pythread.h"

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static const char *__pyx_f[] = {
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};

/* Type declarations */

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":366
 *      counter[0] += 1;
 * 
 * ctypedef struct MateData:             # <<<<<<<<<<<<<<
 *      char * name
 *      bam1_t * mate
 */

typedef struct {
  char *name;
  bam1_t *mate;
  uint32_t flag;
} __pyx_t_9csamtools_MateData;

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1332
 * ##-------------------------------------------------------------------
 * ##-------------------------------------------------------------------
 * ctypedef struct __iterdata:             # <<<<<<<<<<<<<<
 *     samfile_t * samfile
 *     bam_iter_t iter
 */

typedef struct {
  samfile_t *samfile;
  bam_iter_t iter;
  faidx_t *fastafile;
  int tid;
  char *seq;
  int seq_len;
} __pyx_t_9csamtools___iterdata;

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1510
 *         bam_plp_set_mask( self.pileup_iter, self.mask )
 * 
 *     cdef setupIteratorData( self,             # <<<<<<<<<<<<<<
 *                             int tid,
 *                             int start,
 */

struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
  int __pyx_n;
  int reopen;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":80
 *      return dest
 * 
 * cdef class PileupRead             # <<<<<<<<<<<<<<
 * cdef makePileupRead( bam_pileup1_t * src ):
 *     '''fill a  PileupRead object from a bam_pileup1_t * object.'''
 */

struct __pyx_obj_9csamtools_PileupRead {
  PyObject_HEAD
  struct __pyx_obj_9csamtools_AlignedRead *_alignment;
  int32_t _qpos;
  int _indel;
  int _level;
  uint32_t _is_del;
  uint32_t _is_head;
  uint32_t _is_tail;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1125
 * ##-------------------------------------------------------------------
 * ##-------------------------------------------------------------------
 * cdef class IteratorRow:             # <<<<<<<<<<<<<<
 *     '''abstract base class for iterators over mapped reads.
 * 
 */

struct __pyx_obj_9csamtools_IteratorRow {
  PyObject_HEAD
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1283
 * 
 * 
 * cdef class IteratorRowAllRefs(IteratorRow):             # <<<<<<<<<<<<<<
 *     """iterates over all mapped reads by chaining iterators over each reference
 *     """
 */

struct __pyx_obj_9csamtools_IteratorRowAllRefs {
  struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
  struct __pyx_obj_9csamtools_Samfile *samfile;
  int tid;
  struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":71
 *     return dest
 * 
 * cdef class PileupProxy             # <<<<<<<<<<<<<<
 * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
 *      cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
 */

struct __pyx_obj_9csamtools_PileupProxy {
  PyObject_HEAD
  bam_pileup1_t *plp;
  int tid;
  int pos;
  int n_pu;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1144
 *     pass
 * 
 * cdef class IteratorRowRegion(IteratorRow):             # <<<<<<<<<<<<<<
 *     """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
 * 
 */

struct __pyx_obj_9csamtools_IteratorRowRegion {
  struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
  struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
  bam_iter_t iter;
  bam1_t *b;
  int retval;
  struct __pyx_obj_9csamtools_Samfile *samfile;
  samfile_t *fp;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":222
 * ## Public methods
 * ######################################################################
 * cdef class Fastafile:             # <<<<<<<<<<<<<<
 *     '''*(filename)*
 * 
 */

struct __pyx_obj_9csamtools_Fastafile {
  PyObject_HEAD
  struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
  char *_filename;
  faidx_t *fastafile;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2892
 *         return call
 * 
 * cdef class IndelCall:             # <<<<<<<<<<<<<<
 *     '''the results of an indel call.'''
 *     cdef int _tid
 */

struct __pyx_obj_9csamtools_IndelCall {
  PyObject_HEAD
  int _tid;
  int _pos;
  int _coverage;
  int _rms_mapping_quality;
  bam_maqindel_ret_t *_r;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2981
 *         bam_maqindel_ret_destroy(self._r)
 * 
 * cdef class IndelCallerBase:             # <<<<<<<<<<<<<<
 *     '''Base class for SNP callers.
 * 
 */

struct __pyx_obj_9csamtools_IndelCallerBase {
  PyObject_HEAD
  bam_maqindel_opt_t *options;
  struct __pyx_obj_9csamtools_IteratorColumn *iter;
  int cap_mapQ;
  int max_depth;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":3119
 *         return self._call()
 * 
 * cdef class IteratorIndelCalls( IndelCallerBase ):             # <<<<<<<<<<<<<<
 *     """*(IteratorColumn iterator)*
 * 
 */

struct __pyx_obj_9csamtools_IteratorIndelCalls {
  struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2662
 * 
 * 
 * cdef class SNPCallerBase:             # <<<<<<<<<<<<<<
 *     '''Base class for SNP callers.
 * 
 */

struct __pyx_obj_9csamtools_SNPCallerBase {
  PyObject_HEAD
  struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab;
  bam_maqcns_t *c;
  struct __pyx_obj_9csamtools_IteratorColumn *iter;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2735
 *         sys.stdout.flush()
 * 
 * cdef class IteratorSNPCalls( SNPCallerBase ):             # <<<<<<<<<<<<<<
 *     """*(IteratorColumn iterator)*
 * 
 */

struct __pyx_obj_9csamtools_IteratorSNPCalls {
  struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1397
 *     return ret
 * 
 * cdef class IteratorColumn:             # <<<<<<<<<<<<<<
 *     '''abstract base class for iterators over columns.
 * 
 */

struct __pyx_obj_9csamtools_IteratorColumn {
  PyObject_HEAD
  struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
  struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
  int tid;
  int pos;
  int n_plp;
  int mask;
  const bam_pileup1_t * plp;
  bam_plp_t pileup_iter;
  __pyx_t_9csamtools___iterdata iterdata;
  struct __pyx_obj_9csamtools_Samfile *samfile;
  struct __pyx_obj_9csamtools_Fastafile *fastafile;
  PyObject *stepper;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1567
 *             self.iterdata.seq = NULL
 * 
 * cdef class IteratorColumnRegion(IteratorColumn):             # <<<<<<<<<<<<<<
 *     '''iterates over a region only.
 *     '''
 */

struct __pyx_obj_9csamtools_IteratorColumnRegion {
  struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2810
 *         return call
 * 
 * cdef class SNPCaller( SNPCallerBase ):             # <<<<<<<<<<<<<<
 *     '''*(IteratorColumn iterator_column )*
 * 
 */

struct __pyx_obj_9csamtools_SNPCaller {
  struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1596
 *                                      self.n_plp )
 * 
 * cdef class IteratorColumnAllRefs(IteratorColumn):             # <<<<<<<<<<<<<<
 *     """iterates over all columns by chaining iterators over each reference
 *     """
 */

struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
  struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":3076
 *         return call
 * 
 * cdef class IndelCaller( IndelCallerBase ):             # <<<<<<<<<<<<<<
 *     '''*(IteratorColumn iterator_column )*
 * 
 */

struct __pyx_obj_9csamtools_IndelCaller {
  struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":393
 * 
 * 
 * cdef class Samfile:             # <<<<<<<<<<<<<<
 *     '''*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
 * 
 */

struct __pyx_obj_9csamtools_Samfile {
  PyObject_HEAD
  struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
  char *_filename;
  samfile_t *samfile;
  bam_index_t *index;
  int isbam;
  int isremote;
  bam1_t *b;
  char *mode;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2605
 *     return retval, out_stderr, out_stdout
 * 
 * cdef class SNPCall:             # <<<<<<<<<<<<<<
 *     '''the results of a SNP call.'''
 *     cdef int _tid
 */

struct __pyx_obj_9csamtools_SNPCall {
  PyObject_HEAD
  int _tid;
  int _pos;
  char _reference_base;
  char _genotype;
  int _consensus_quality;
  int _snp_quality;
  int _rms_mapping_quality;
  int _coverage;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1224
 *         samclose( self.fp )
 * 
 * cdef class IteratorRowAll(IteratorRow):             # <<<<<<<<<<<<<<
 *     """*(Samfile samfile, int reopen = True)*
 * 
 */

struct __pyx_obj_9csamtools_IteratorRowAll {
  struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
  struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
  bam1_t *b;
  samfile_t *fp;
};

/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":64
 * ## private factory methods
 * #####################################################################
 * cdef class AlignedRead             # <<<<<<<<<<<<<<
 * cdef makeAlignedRead(bam1_t * src):
 *     '''enter src into AlignedRead.'''
 */

struct __pyx_obj_9csamtools_AlignedRead {
  PyObject_HEAD
  bam1_t *_delegate;
};


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1397
 *     return ret
 * 
 * cdef class IteratorColumn:             # <<<<<<<<<<<<<<
 *     '''abstract base class for iterators over columns.
 * 
 */

struct __pyx_vtabstruct_9csamtools_IteratorColumn {
  int (*cnext)(struct __pyx_obj_9csamtools_IteratorColumn *);
  char *(*getSequence)(struct __pyx_obj_9csamtools_IteratorColumn *);
  PyObject *(*setMask)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *);
  PyObject *(*setupIteratorData)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
  PyObject *(*reset)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
};
static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1567
 *             self.iterdata.seq = NULL
 * 
 * cdef class IteratorColumnRegion(IteratorColumn):             # <<<<<<<<<<<<<<
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 */

struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion {
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static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2662
 * 
 * 
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 * 
 */

struct __pyx_vtabstruct_9csamtools_SNPCallerBase {
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};
static struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtabptr_9csamtools_SNPCallerBase;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2810
 *         return call
 * 
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 */

struct __pyx_vtabstruct_9csamtools_SNPCaller {
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};
static struct __pyx_vtabstruct_9csamtools_SNPCaller *__pyx_vtabptr_9csamtools_SNPCaller;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1144
 *     pass
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 * cdef class IteratorRowRegion(IteratorRow):             # <<<<<<<<<<<<<<
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 */

struct __pyx_vtabstruct_9csamtools_IteratorRowRegion {
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static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1596
 *                                      self.n_plp )
 * 
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struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs {
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static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":393
 * 
 * 
 * cdef class Samfile:             # <<<<<<<<<<<<<<
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 */

struct __pyx_vtabstruct_9csamtools_Samfile {
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  bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *);
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};
static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":222
 * ## Public methods
 * ######################################################################
 * cdef class Fastafile:             # <<<<<<<<<<<<<<
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 * 
 */

struct __pyx_vtabstruct_9csamtools_Fastafile {
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};
static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1224
 *         samclose( self.fp )
 * 
 * cdef class IteratorRowAll(IteratorRow):             # <<<<<<<<<<<<<<
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 * 
 */

struct __pyx_vtabstruct_9csamtools_IteratorRowAll {
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};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;


/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":2735
 *         sys.stdout.flush()
 * 
 * cdef class IteratorSNPCalls( SNPCallerBase ):             # <<<<<<<<<<<<<<
 *     """*(IteratorColumn iterator)*
 * 
 */

struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls {
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/* 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.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 csamtools */

static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCallerBase = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorSNPCalls = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCaller = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndelCall = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0;
static char *__pyx_v_9csamtools_bam_nt16_rev_table;
static int __pyx_v_9csamtools_max_pos;
static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *, int, int, int); /*proto*/
static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/
static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/
static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
#define __Pyx_MODULE_NAME "csamtools"
int __pyx_module_is_main_csamtools = 0;

/* Implementation of csamtools */
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_cmp;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_range;
static char __pyx_k_1[] = "\t";
static char __pyx_k_2[] = "\n";
static char __pyx_k_3[] = "calling len() on closed file";
static char __pyx_k_5[] = "could not open file `%s`";
static char __pyx_k_6[] = "I/O operation on closed file";
static char __pyx_k_9[] = "no sequence/region supplied.";
static char __pyx_k_11[] = "invalid region: start (%i) > end (%i)";
static char __pyx_k_12[] = "";
static char __pyx_k_13[] = "start out of range (%i)";
static char __pyx_k_14[] = "end out of range (%i)";
static char __pyx_k_15[] = "%s:%i-%i";
static char __pyx_k_16[] = "invalid file opening mode `%s`";
static char __pyx_k_17[] = "http:";
static char __pyx_k_18[] = "ftp:";
static char __pyx_k_19[] = "either supply options `template`, `header` or  both `referencenames` and `referencelengths` for writing";
static char __pyx_k_20[] = "unequal names and lengths of reference sequences";
static char __pyx_k_21[] = "-";
static char __pyx_k_22[] = "file `%s` not found";
static char __pyx_k_23[] = "could not open file - is it SAM/BAM format?";
static char __pyx_k_27[] = ".bai";
static char __pyx_k_28[] = "error while opening index `%s` ";
static char __pyx_k_30[] = "tid out of range 0<=tid<%i";
static char __pyx_k_32[] = "[:-]";
static char __pyx_k_34[] = "invalid reference `%s`";
static char __pyx_k_35[] = "invalid coordinates: start (%i) > end (%i)";
static char __pyx_k_37[] = "seek only available in bam files";
static char __pyx_k_43[] = "fetch called on bamfile without index";
static char __pyx_k_45[] = "callback functionality requires a region/reference";
static char __pyx_k_47[] = "no index available for fetch";
static char __pyx_k_49[] = "fetch called for samfile without header";
static char __pyx_k_51[] = "fetch for a region is not available for sam files";
static char __pyx_k_53[] = "callback not implemented yet";
static char __pyx_k_55[] = "read is unpaired";
static char __pyx_k_57[] = "mate is unmapped";
static char __pyx_k_59[] = "mate not found";
static char __pyx_k_64[] = "counting functionality requires a region/reference";
static char __pyx_k_67[] = "count for a region is not available for sam files";
static char __pyx_k_70[] = "no index available for pileup";
static char __pyx_k_73[] = "pileup of samfiles not implemented yet";
static char __pyx_k_83[] = "@";
static char __pyx_k_85[] = "header line without '@': '%s'";
static char __pyx_k_87[] = "header line with invalid type '%s': '%s'";
static char __pyx_k_88[] = ":";
static char __pyx_k_90[] = "unknown field code '%s' in record '%s'";
static char __pyx_k_91[] = "multiple '%s' lines are not permitted";
static char __pyx_k_92[] = "@%s";
static char __pyx_k_93[] = "%s:%s";
static char __pyx_k_94[] = "invalid type for record %s: %s, expected %s";
static char __pyx_k_95[] = "incomplete sequence information in '%s'";
static char __pyx_k_98[] = "no index available for iteration";
static char __pyx_k__A[] = "A";
static char __pyx_k__C[] = "C";
static char __pyx_k__D[] = "D";
static char __pyx_k__F[] = "F";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
static char __pyx_k__f[] = "f";
static char __pyx_k__i[] = "i";
static char __pyx_k__n[] = "n";
static char __pyx_k__r[] = "r";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
static char __pyx_k__x[] = "x";
static char __pyx_k_102[] = "reference sequence for '%s' (tid=%i) not found";
static char __pyx_k_103[] = "unknown stepper option `%s` in IteratorColumn";
static char __pyx_k_105[] = "error during iteration";
static char __pyx_k_108[] = "Invalid clipping in CIGAR string";
static char __pyx_k_109[] = "quality and sequence mismatch: %i != %i";
static char __pyx_k_110[] = "%c";
static char __pyx_k_111[] = "create_string_buffer";
static char __pyx_k_112[] = "<cccf";
static char __pyx_k_113[] = "<cccb";
static char __pyx_k_114[] = "<ccch";
static char __pyx_k_115[] = "integer %i out of range of BAM/SAM specification";
static char __pyx_k_116[] = "<ccci";
static char __pyx_k_117[] = "<cccB";
static char __pyx_k_118[] = "<cccH";
static char __pyx_k_119[] = "<cccI";
static char __pyx_k_120[] = "<cccc";
static char __pyx_k_121[] = "<ccc%is";
static char __pyx_k_122[] = "tags field too large";
static char __pyx_k_124[] = "tag '%s' not present";
static char __pyx_k_125[] = "Contig index";
static char __pyx_k_126[] = "Mapped position on contig";
static char __pyx_k_127[] = "Contig index for mate pair";
static char __pyx_k_128[] = "Position of mate pair";
static char __pyx_k_129[] = "Insert size";
static char __pyx_k_130[] = "Binary flag";
static char __pyx_k_131[] = "Count of cigar entries";
static char __pyx_k_132[] = "Cigar entries";
static char __pyx_k_133[] = "Mapping quality";
static char __pyx_k_134[] = "Bam index bin number";
static char __pyx_k_135[] = "Length of query name";
static char __pyx_k_136[] = "Query name";
static char __pyx_k_137[] = "Length of query sequence";
static char __pyx_k_138[] = "Query sequence";
static char __pyx_k_139[] = "Quality scores";
static char __pyx_k_140[] = "Length of auxilary data";
static char __pyx_k_141[] = "Maximum data length";
static char __pyx_k_142[] = "Current data length";
static char __pyx_k_143[] = "%-30s %-10s= %s";
static char __pyx_k_144[] = "(";
static char __pyx_k_145[] = ")";
static char __pyx_k_146[] = "This class cannot be instantiated from Python";
static char __pyx_k_151[] = "No such file or directory: '%s'";
static char __pyx_k_152[] = "-o";
static char __pyx_k_153[] = "option -o is forbidden in samtools view";
static char __pyx_k_155[] = "_rms_mapping_quality";
static char __pyx_k_156[] = "--> read %i %s %i";
static char __pyx_k_157[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
static char __pyx_k_158[] = "-------------------------------------\n";
static char __pyx_k_159[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
static char __pyx_k_161[] = "position %i out of bounds on reference sequence (len=%i)";
static char __pyx_k_163[] = "no reads in region - no call";
static char __pyx_k_165[] = "%s/%s";
static char __pyx_k_166[] = "IndelCallerBase requires an pileup iterator with reference sequence";
static char __pyx_k_170[] = "the query name (None if not present)";
static char __pyx_k_171[] = "the :term:`cigar` alignment (None if not present).\n        ";
static char __pyx_k_172[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
static char __pyx_k_173[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
static char __pyx_k_174[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n        SAM/BAM files may included extra flanking bases sequences that were\n        not part of the alignment.  These bases may be the result of the\n        Smith-Waterman or other algorithms, which may not require alignments\n        that begin at the first residue or end at the last.  In addition,\n        extra sequencing adapters, multiplex identifiers, and low-quality bases that\n        were not considered for alignment may have been retained.";
static char __pyx_k_175[] = "aligned query sequence quality values (None if not present)";
static char __pyx_k_176[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
static char __pyx_k_177[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
static char __pyx_k_178[] = "Length of the aligned query sequence";
static char __pyx_k_179[] = "the tags in the AUX field.\n\n        This property permits convenience access to \n        the tags. Changes it the returned list will\n        not update the tags automatically. Instead,\n        the following is required for adding a \n        new tag::\n\n            read.tags = read.tags + [(\"RG\",0)]\n\n        ";
static char __pyx_k_180[] = "properties flag";
static char __pyx_k_181[] = "\n        :term:`target` ID\n\n        DEPRECATED from pysam-0.4 - use tid in the future.\n        The rname field caused a lot of confusion as it returns\n        the :term:`target` ID instead of the reference sequence\n        name.\n\n        .. note::\n\n            This field contains the index of the reference sequence \n            in the sequence dictionary. To obtain the name\n            of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n            \n        ";
static char __pyx_k_182[] = "\n        :term:`target` ID\n\n        .. note::\n\n            This field contains the index of the reference sequence \n            in the sequence dictionary. To obtain the name\n            of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n            \n        ";
static char __pyx_k_183[] = "0-based leftmost coordinate";
static char __pyx_k_184[] = "properties bin";
static char __pyx_k_185[] = "length of the read (read only). Returns 0 if not given.";
static char __pyx_k_186[] = "aligned end position of the read (read only).  Returns\n        None if not available.";
static char __pyx_k_187[] = "aligned length of the read (read only).  Returns None if\n        not available.";
static char __pyx_k_188[] = "mapping quality";
static char __pyx_k_189[] = "the :term:`reference` id of the mate ";
static char __pyx_k_190[] = "the position of the mate";
static char __pyx_k_191[] = "the insert size";
static char __pyx_k_192[] = "true if read is paired in sequencing";
static char __pyx_k_193[] = "true if read is mapped in a proper pair";
static char __pyx_k_194[] = "true if read itself is unmapped";
static char __pyx_k_195[] = "true if the mate is unmapped";
static char __pyx_k_196[] = "true if read is mapped to reverse strand";
static char __pyx_k_197[] = "true is read is mapped to reverse strand";
static char __pyx_k_198[] = "true if this is read1";
static char __pyx_k_199[] = "true if this is read2";
static char __pyx_k_200[] = "true if not primary alignment";
static char __pyx_k_201[] = "true if QC failure";
static char __pyx_k_202[] = " true if optical or PCR duplicate";
static char __pyx_k_203[] = "the chromosome ID as is defined in the header";
static char __pyx_k_204[] = "number of reads mapping to this column.";
static char __pyx_k_205[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
static char __pyx_k_206[] = "a :class:`pysam.AlignedRead` object of the aligned read";
static char __pyx_k_207[] = "position of the read base at the pileup site, 0-based";
static char __pyx_k_208[] = "indel length; 0 for no indel, positive for ins and negative for del";
static char __pyx_k_209[] = "1 iff the base on the padded read is a deletion";
static char __pyx_k_210[] = "number of :term:`filename` associated with this object.";
static char __pyx_k_211[] = "number of :term:`reference` sequences in the file.";
static char __pyx_k_212[] = "tuple with the names of :term:`reference` sequences.";
static char __pyx_k_213[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n        :attr:`pysam.Samfile.references`\n        ";
static char __pyx_k_214[] = "full contents of the :term:`sam file` header as a string.";
static char __pyx_k_215[] = "header information within the :term:`sam file`. The records and fields are returned as \n        a two-level dictionary.\n        ";
static char __pyx_k_216[] = "current sequence length.";
static char __pyx_k_217[] = "nucleotide position of SNP.";
static char __pyx_k_218[] = "reference base at pos. ``N`` if no reference sequence supplied.";
static char __pyx_k_219[] = "the genotype called.";
static char __pyx_k_220[] = "the genotype quality (Phred-scaled).";
static char __pyx_k_221[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
static char __pyx_k_222[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
static char __pyx_k_223[] = "coverage or read depth - the number of reads involved in the call.";
static char __pyx_k_224[] = "sequence of first allele.";
static char __pyx_k_225[] = "sequence of second allele.";
static char __pyx_k_226[] = "reads supporting first allele.";
static char __pyx_k_227[] = "=ACMGRSVTWYHKDBN";
static char __pyx_k_228[] = "/dev/null";
static char __pyx_k_230[] = "A pileup column. A pileup column contains  \n    all the reads that map to a certain target base.\n\n    tid      \n        chromosome ID as is defined in the header      \n    pos      \n        the target base coordinate (0-based)    \n    n \n        number of reads mapping to this column  \n    pileups  \n        list of reads (:class:`pysam.PileupRead`) aligned to this column    \n    ";
static char __pyx_k_231[] = "\n    stderr is captured. \n    ";
static char __pyx_k_237[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__CO[] = "CO";
static char __pyx_k__DS[] = "DS";
static char __pyx_k__DT[] = "DT";
static char __pyx_k__GO[] = "GO";
static char __pyx_k__HD[] = "HD";
static char __pyx_k__ID[] = "ID";
static char __pyx_k__LB[] = "LB";
static char __pyx_k__LN[] = "LN";
static char __pyx_k__M5[] = "M5";
static char __pyx_k__PG[] = "PG";
static char __pyx_k__PI[] = "PI";
static char __pyx_k__PL[] = "PL";
static char __pyx_k__PN[] = "PN";
static char __pyx_k__PU[] = "PU";
static char __pyx_k__RG[] = "RG";
static char __pyx_k__SM[] = "SM";
static char __pyx_k__SN[] = "SN";
static char __pyx_k__SO[] = "SO";
static char __pyx_k__SP[] = "SP";
static char __pyx_k__SQ[] = "SQ";
static char __pyx_k__UR[] = "UR";
static char __pyx_k__VN[] = "VN";
static char __pyx_k___r[] = "_r";
static char __pyx_k__fd[] = "fd";
static char __pyx_k__fp[] = "fp";
static char __pyx_k__gt[] = "gt";
static char __pyx_k__id[] = "id";
static char __pyx_k__os[] = "os";
static char __pyx_k__rb[] = "rb";
static char __pyx_k__re[] = "re";
static char __pyx_k__wb[] = "wb";
static char __pyx_k__wh[] = "wh";
static char __pyx_k__all[] = "all";
static char __pyx_k__bam[] = "bam";
static char __pyx_k__beg[] = "beg";
static char __pyx_k__bin[] = "bin";
static char __pyx_k__chr[] = "chr";
static char __pyx_k__cmp[] = "cmp";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
static char __pyx_k__map[] = "map";
static char __pyx_k__plp[] = "plp";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__q_r[] = "q_r";
static char __pyx_k__raw[] = "raw";
static char __pyx_k__seq[] = "seq";
static char __pyx_k__sys[] = "sys";
static char __pyx_k__tid[] = "tid";
static char __pyx_k__wbu[] = "wbu";
static char __pyx_k__Outs[] = "Outs";
static char __pyx_k___pos[] = "_pos";
static char __pyx_k___tid[] = "_tid";
static char __pyx_k__args[] = "args";
static char __pyx_k__cnt1[] = "cnt1";
static char __pyx_k__cnt2[] = "cnt2";
static char __pyx_k__core[] = "core";
static char __pyx_k__data[] = "data";
static char __pyx_k__dup2[] = "dup2";
static char __pyx_k__flag[] = "flag";
static char __pyx_k__hash[] = "hash";
static char __pyx_k__iter[] = "iter";
static char __pyx_k__join[] = "join";
static char __pyx_k__mapq[] = "mapq";
static char __pyx_k__mask[] = "mask";
static char __pyx_k__mate[] = "mate";
static char __pyx_k__mode[] = "mode";
static char __pyx_k__mpos[] = "mpos";
static char __pyx_k__mtid[] = "mtid";
static char __pyx_k__n_pu[] = "n_pu";
static char __pyx_k__name[] = "name";
static char __pyx_k__open[] = "open";
static char __pyx_k__path[] = "path";
static char __pyx_k__port[] = "port";
static char __pyx_k__qpos[] = "qpos";
static char __pyx_k__qseq[] = "qseq";
static char __pyx_k__qual[] = "qual";
static char __pyx_k__self[] = "self";
static char __pyx_k__tags[] = "tags";
static char __pyx_k__text[] = "text";
static char __pyx_k__view[] = "view";
static char __pyx_k___call[] = "_call";
static char __pyx_k___open[] = "_open";
static char __pyx_k___qpos[] = "_qpos";
static char __pyx_k__bqual[] = "bqual";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__cnext[] = "cnext";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__indel[] = "indel";
static char __pyx_k__index[] = "index";
static char __pyx_k__isbam[] = "isbam";
static char __pyx_k__isize[] = "isize";
static char __pyx_k__l_aux[] = "l_aux";
static char __pyx_k__level[] = "level";
static char __pyx_k__n_hap[] = "n_hap";
static char __pyx_k__n_plp[] = "n_plp";
static char __pyx_k__q_cns[] = "q_cns";
static char __pyx_k__q_ref[] = "q_ref";
static char __pyx_k__qname[] = "qname";
static char __pyx_k__range[] = "range";
static char __pyx_k__reset[] = "reset";
static char __pyx_k__rname[] = "rname";
static char __pyx_k__setfd[] = "setfd";
static char __pyx_k__split[] = "split";
static char __pyx_k__start[] = "start";
static char __pyx_k__strip[] = "strip";
static char __pyx_k__theta[] = "theta";
static char __pyx_k__types[] = "types";
static char __pyx_k__where[] = "where";
static char __pyx_k___indel[] = "_indel";
static char __pyx_k___level[] = "_level";
static char __pyx_k__append[] = "append";
static char __pyx_k__ctypes[] = "ctypes";
static char __pyx_k__errmod[] = "errmod";
static char __pyx_k__exists[] = "exists";
static char __pyx_k__fields[] = "fields";
static char __pyx_k__fileno[] = "fileno";
static char __pyx_k__gettid[] = "gettid";
static char __pyx_k__header[] = "header";
static char __pyx_k__indel1[] = "indel1";
static char __pyx_k__indel2[] = "indel2";
static char __pyx_k__is_del[] = "is_del";
static char __pyx_k__l_qseq[] = "l_qseq";
static char __pyx_k__l_text[] = "l_text";
static char __pyx_k__m_data[] = "m_data";
static char __pyx_k__method[] = "method";
static char __pyx_k__object[] = "object";
static char __pyx_k__offset[] = "offset";
static char __pyx_k__record[] = "record";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
static char __pyx_k__retval[] = "retval";
static char __pyx_k__rg2lib[] = "rg2lib";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
static char __pyx_k__struct[] = "struct";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__IntType[] = "IntType";
static char __pyx_k__O_CREAT[] = "O_CREAT";
static char __pyx_k__Samfile[] = "Samfile";
static char __pyx_k____all__[] = "__all__";
static char __pyx_k____del__[] = "__del__";
static char __pyx_k____str__[] = "__str__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k___is_del[] = "_is_del";
static char __pyx_k__is_head[] = "is_head";
static char __pyx_k__is_tail[] = "is_tail";
static char __pyx_k__l_qname[] = "l_qname";
static char __pyx_k__mkstemp[] = "mkstemp";
static char __pyx_k__n_cigar[] = "n_cigar";
static char __pyx_k__options[] = "options";
static char __pyx_k__pileups[] = "pileups";
static char __pyx_k__q_indel[] = "q_indel";
static char __pyx_k__r_indel[] = "r_indel";
static char __pyx_k__release[] = "release";
static char __pyx_k__restore[] = "restore";
static char __pyx_k__rowiter[] = "rowiter";
static char __pyx_k__samfile[] = "samfile";
static char __pyx_k__seq_len[] = "seq_len";
static char __pyx_k__setfile[] = "setfile";
static char __pyx_k__stepper[] = "stepper";
static char __pyx_k__streams[] = "streams";
static char __pyx_k__DictType[] = "DictType";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_WRONLY[] = "O_WRONLY";
static char __pyx_k____dict__[] = "__dict__";
static char __pyx_k____init__[] = "__init__";
static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k___is_head[] = "_is_head";
static char __pyx_k___is_tail[] = "_is_tail";
static char __pyx_k___logfile[] = "_logfile";
static char __pyx_k__calcsize[] = "calcsize";
static char __pyx_k__callback[] = "callback";
static char __pyx_k__cap_mapQ[] = "cap_mapQ";
static char __pyx_k__cnt_anti[] = "cnt_anti";
static char __pyx_k__coverage[] = "coverage";
static char __pyx_k__data_len[] = "data_len";
static char __pyx_k__exc_type[] = "exc_type";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__genotype[] = "genotype";
static char __pyx_k__het_rate[] = "het_rate";
static char __pyx_k__isremote[] = "isremote";
static char __pyx_k__iterdata[] = "iterdata";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__samtools[] = "samtools";
static char __pyx_k__stderr_f[] = "stderr_f";
static char __pyx_k__stderr_h[] = "stderr_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
static char __pyx_k__Fastafile[] = "Fastafile";
static char __pyx_k__FloatType[] = "FloatType";
static char __pyx_k__SNPCaller[] = "SNPCaller";
static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k___coverage[] = "_coverage";
static char __pyx_k___delegate[] = "_delegate";
static char __pyx_k___filename[] = "_filename";
static char __pyx_k___genotype[] = "_genotype";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
static char __pyx_k__csamtools[] = "csamtools";
static char __pyx_k__exc_value[] = "exc_value";
static char __pyx_k__fastafile[] = "fastafile";
static char __pyx_k__is_paired[] = "is_paired";
static char __pyx_k__max_depth[] = "max_depth";
static char __pyx_k__min_baseQ[] = "min_baseQ";
static char __pyx_k__n_targets[] = "n_targets";
static char __pyx_k__pack_into[] = "pack_into";
static char __pyx_k__readlines[] = "readlines";
static char __pyx_k__reference[] = "reference";
static char __pyx_k__setdevice[] = "setdevice";
static char __pyx_k__traceback[] = "traceback";
static char __pyx_k__until_eof[] = "until_eof";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___alignment[] = "_alignment";
static char __pyx_k___buildLine[] = "_buildLine";
static char __pyx_k__reads_diff[] = "reads_diff";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__target_len[] = "target_len";
static char __pyx_k__AlignedRead[] = "AlignedRead";
static char __pyx_k__IndelCaller[] = "IndelCaller";
static char __pyx_k__IteratorRow[] = "IteratorRow";
static char __pyx_k__PileupProxy[] = "PileupProxy";
static char __pyx_k__StderrStore[] = "StderrStore";
static char __pyx_k__collections[] = "collections";
static char __pyx_k__getSequence[] = "getSequence";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__pileup_iter[] = "pileup_iter";
static char __pyx_k__reads_first[] = "reads_first";
static char __pyx_k__snp_quality[] = "snp_quality";
static char __pyx_k__stderr_save[] = "stderr_save";
static char __pyx_k__target_name[] = "target_name";
static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___buildHeader[] = "_buildHeader";
static char __pyx_k___parseRegion[] = "_parseRegion";
static char __pyx_k___snp_quality[] = "_snp_quality";
static char __pyx_k__catch_stderr[] = "catch_stderr";
static char __pyx_k__catch_stdout[] = "catch_stdout";
static char __pyx_k__first_allele[] = "first_allele";
static char __pyx_k__hasReference[] = "hasReference";
static char __pyx_k__n_haplotypes[] = "n_haplotypes";
static char __pyx_k__reads_second[] = "reads_second";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS";
static char __pyx_k__second_allele[] = "second_allele";
static char __pyx_k__IteratorColumn[] = "IteratorColumn";
static char __pyx_k__readAndRelease[] = "readAndRelease";
static char __pyx_k__reference_base[] = "reference_base";
static char __pyx_k__referencenames[] = "referencenames";
static char __pyx_k___reference_base[] = "_reference_base";
static char __pyx_k__iterator_column[] = "iterator_column";
static char __pyx_k__mapping_quality[] = "mapping_quality";
static char __pyx_k__IteratorSNPCalls[] = "IteratorSNPCalls";
static char __pyx_k____getattribute__[] = "__getattribute__";
static char __pyx_k__mate_is_unmapped[] = "mate_is_unmapped";
static char __pyx_k__referencelengths[] = "referencelengths";
static char __pyx_k__consensus_quality[] = "consensus_quality";
static char __pyx_k__setupIteratorData[] = "setupIteratorData";
static char __pyx_k__IteratorIndelCalls[] = "IteratorIndelCalls";
static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
static char __pyx_k___consensus_quality[] = "_consensus_quality";
static char __pyx_k___samtools_dispatch[] = "_samtools_dispatch";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
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static PyObject *__pyx_n_s__O_CREAT;
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/* "/home/andreas/pysam/pysam/pysam/csamtools.pyx":1637
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
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static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
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PyTypeObject __pyx_type_9csamtools_PileupRead = {
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static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
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static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
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static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
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static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
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static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
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PyTypeObject __pyx_type_9csamtools_Samfile = {
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  __Pyx_DOCSTR("*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*\n              \n    A :term:`SAM`/:term:`BAM` formatted 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    Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n    a :term:`BAM` formatted file for reading, type::\n\n        import pysam\n        f = pysam.Samfile('ex1.bam','rb')\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\n    For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n    sources (see also the samtools format specification):\n\n        1. If *template* is given, the header is copied from a another *Samfile* \n           (*template* must be of type *Samfile*).\n\n        2. If *header* is given, the header is built from a multi-level dictionary. The first level \n           are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n           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    "), /*tp_doc*/
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static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
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  __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n    Various iterators implement different behaviours for wrapping around\n    contig boundaries. Examples include:\n\n    :class:`pysam.IteratorRowRegion`\n        iterate within a single contig and a defined region.\n\n    :class:`pysam.IteratorRowAll`\n        iterate until EOF. This iterator will also include unmapped reads.\n\n    :class:`pysam.IteratorRowAllRefs`\n        iterate over all reads in all reference sequences.\n        \n    The method :meth:`Samfile.fetch` returns an IteratorRow.\n    "), /*tp_doc*/
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static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
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  PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
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}

static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
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    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
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    PyErr_Restore(etype, eval, etb);
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  Py_XDECREF(((PyObject *)p->samfile));
  __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}

static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
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}

static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
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  return 0;
}

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};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;

static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_IteratorRowAll *p;
  PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
  p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
  if (__pyx_pf_9csamtools_14IteratorRowAll_0__cinit__(o, a, k) < 0) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}

static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
  {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
  {0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
  0, /*nb_add*/
  0, /*nb_subtract*/
  0, /*nb_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
  #endif
  0, /*nb_remainder*/
  0, /*nb_divmod*/
  0, /*nb_power*/
  0, /*nb_negative*/
  0, /*nb_positive*/
  0, /*nb_absolute*/
  0, /*nb_nonzero*/
  0, /*nb_invert*/
  0, /*nb_lshift*/
  0, /*nb_rshift*/
  0, /*nb_and*/
  0, /*nb_xor*/
  0, /*nb_or*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_coerce*/
  #endif
  0, /*nb_int*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_long*/
  #else
  0, /*reserved*/
  #endif
  0, /*nb_float*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_oct*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*nb_hex*/
  #endif
  0, /*nb_inplace_add*/
  0, /*nb_inplace_subtract*/
  0, /*nb_inplace_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_inplace_divide*/
  #endif
  0, /*nb_inplace_remainder*/
  0, /*nb_inplace_power*/
  0, /*nb_inplace_lshift*/
  0, /*nb_inplace_rshift*/
  0, /*nb_inplace_and*/
  0, /*nb_inplace_xor*/
  0, /*nb_inplace_or*/
  0, /*nb_floor_divide*/
  0, /*nb_true_divide*/
  0, /*nb_inplace_floor_divide*/
  0, /*nb_inplace_true_divide*/
  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
  #endif
};

static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
  0, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
  sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
  &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n    iterate over all reads in *samfile*\n\n    By default, the file is re-openend to avoid conflicts if\n    multiple operators work on the same file. Set *reopen* = False\n    to not re-open *samfile*.\n    "), /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
  __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
  __pyx_methods_9csamtools_IteratorRowAll, /*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_9csamtools_IteratorRowAll, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};

static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
  PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
  p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
  p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
  if (__pyx_pf_9csamtools_18IteratorRowAllRefs_0__cinit__(o, a, k) < 0) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
  struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
  Py_XDECREF(((PyObject *)p->samfile));
  Py_XDECREF(((PyObject *)p->rowiter));
  __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}

static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
  if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
    e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
  }
  if (p->samfile) {
    e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
  }
  if (p->rowiter) {
    e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
  struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
  PyObject* tmp;
  if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
    __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
  }
  tmp = ((PyObject*)p->samfile);
  p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->rowiter);
  p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
  {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(0)},
  {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
  {0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
  0, /*nb_add*/
  0, /*nb_subtract*/
  0, /*nb_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
  #endif
  0, /*nb_remainder*/
  0, /*nb_divmod*/
  0, /*nb_power*/
  0, /*nb_negative*/
  0, /*nb_positive*/
  0, /*nb_absolute*/
  0, /*nb_nonzero*/
  0, /*nb_invert*/
  0, /*nb_lshift*/
  0, /*nb_rshift*/
  0, /*nb_and*/
  0, /*nb_xor*/
  0, /*nb_or*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_coerce*/
  #endif
  0, /*nb_int*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_long*/
  #else
  0, /*reserved*/
  #endif
  0, /*nb_float*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_oct*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*nb_hex*/
  #endif
  0, /*nb_inplace_add*/
  0, /*nb_inplace_subtract*/
  0, /*nb_inplace_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_inplace_divide*/
  #endif
  0, /*nb_inplace_remainder*/
  0, /*nb_inplace_power*/
  0, /*nb_inplace_lshift*/
  0, /*nb_inplace_rshift*/
  0, /*nb_inplace_and*/
  0, /*nb_inplace_xor*/
  0, /*nb_inplace_or*/
  0, /*nb_floor_divide*/
  0, /*nb_true_divide*/
  0, /*nb_inplace_floor_divide*/
  0, /*nb_inplace_true_divide*/
  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
  #endif
};

static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
  0, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
  sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
  &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n    "), /*tp_doc*/
  __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
  __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
  __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
  __pyx_methods_9csamtools_IteratorRowAllRefs, /*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_9csamtools_IteratorRowAllRefs, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};
static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;

static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_IteratorColumn *p;
  PyObject *o = (*t->tp_alloc)(t, 0);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
  p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
  p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
  p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
  p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
  p->stepper = Py_None; Py_INCREF(Py_None);
  if (__pyx_pf_9csamtools_14IteratorColumn_0__cinit__(o, a, k) < 0) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
  struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  Py_XDECREF(((PyObject *)p->iter));
  Py_XDECREF(((PyObject *)p->samfile));
  Py_XDECREF(((PyObject *)p->fastafile));
  Py_XDECREF(p->stepper);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
  if (p->iter) {
    e = (*v)(((PyObject*)p->iter), a); if (e) return e;
  }
  if (p->samfile) {
    e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
  }
  if (p->fastafile) {
    e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
  }
  if (p->stepper) {
    e = (*v)(p->stepper, a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
  struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
  PyObject* tmp;
  tmp = ((PyObject*)p->iter);
  p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->samfile);
  p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->fastafile);
  p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  tmp = ((PyObject*)p->stepper);
  p->stepper = Py_None; Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
  return __pyx_pf_9csamtools_14IteratorColumn_7seq_len_0__get__(o);
}

static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
  {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
  {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
  {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_216), 0},
  {0, 0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
  0, /*nb_add*/
  0, /*nb_subtract*/
  0, /*nb_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
  #endif
  0, /*nb_remainder*/
  0, /*nb_divmod*/
  0, /*nb_power*/
  0, /*nb_negative*/
  0, /*nb_positive*/
  0, /*nb_absolute*/
  0, /*nb_nonzero*/
  0, /*nb_invert*/
  0, /*nb_lshift*/
  0, /*nb_rshift*/
  0, /*nb_and*/
  0, /*nb_xor*/
  0, /*nb_or*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_coerce*/
  #endif
  0, /*nb_int*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_long*/
  #else
  0, /*reserved*/
  #endif
  0, /*nb_float*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_oct*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*nb_hex*/
  #endif
  0, /*nb_inplace_add*/
  0, /*nb_inplace_subtract*/
  0, /*nb_inplace_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_inplace_divide*/
  #endif
  0, /*nb_inplace_remainder*/
  0, /*nb_inplace_power*/
  0, /*nb_inplace_lshift*/
  0, /*nb_inplace_rshift*/
  0, /*nb_inplace_and*/
  0, /*nb_inplace_xor*/
  0, /*nb_inplace_or*/
  0, /*nb_floor_divide*/
  0, /*nb_true_divide*/
  0, /*nb_inplace_floor_divide*/
  0, /*nb_inplace_true_divide*/
  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
  #endif
};

static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
  0, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
  PyVarObject_HEAD_INIT(0, 0)
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  __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n    IteratorColumn objects wrap the pileup functionality of samtools.\n    \n    For reasons of efficiency, the iterator points to the current \n    pileup buffer. The pileup buffer is updated at every iteration.\n    This might cause some unexpected behavious. For example,\n    consider the conversion to a list::\n    \n       f = Samfile(\"file.bam\", \"rb\")\n       result = list( f.pileup() )\n\n    Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n    but each object in ``result`` will contain the same information.\n    \n    The desired behaviour can be achieved by list comprehension::\n\n       result = [ x.pileups() for x in f.pileup() ]\n\n    ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n    If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n    method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n    and :meth:`seq_len`.\n\n    Optional kwargs to the iterator\n\n    stepper\n       The stepper controlls how the iterator advances. \n       Possible options for the stepper are \n       \n       all\n           use all reads for pileup.\n       samtools\n           same filter and read processing as in :term:`csamtools` pileup\n    fastafile\n       A :class:`FastaFile` object\n    mask\n       Skip all reads with bits set in mask.\n       \n    \n    "), /*tp_doc*/
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static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
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  PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
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  p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
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  if (__pyx_pf_9csamtools_20IteratorColumnRegion_0__cinit__(o, a, k) < 0) {
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  }
  return o;
}

static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
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static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
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static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
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static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
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PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
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static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
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static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
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static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
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static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
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static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
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static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
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  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
  &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  __pyx_pf_9csamtools_7SNPCall_0__str__, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
  __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
  0, /*tp_traverse*/
  0, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_9csamtools_SNPCall, /*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_9csamtools_SNPCall, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};
static struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_vtable_9csamtools_SNPCallerBase;

static PyObject *__pyx_tp_new_9csamtools_SNPCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_SNPCallerBase *p;
  PyObject *o = (*t->tp_alloc)(t, 0);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_SNPCallerBase *)o);
  p->__pyx_vtab = __pyx_vtabptr_9csamtools_SNPCallerBase;
  p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
  if (__pyx_pf_9csamtools_13SNPCallerBase_0__cinit__(o, a, k) < 0) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_9csamtools_SNPCallerBase(PyObject *o) {
  struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
  {
    PyObject *etype, *eval, *etb;
    PyErr_Fetch(&etype, &eval, &etb);
    ++Py_REFCNT(o);
    __pyx_pf_9csamtools_13SNPCallerBase_1__dealloc__(o);
    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
    --Py_REFCNT(o);
    PyErr_Restore(etype, eval, etb);
  }
  Py_XDECREF(((PyObject *)p->iter));
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_9csamtools_SNPCallerBase(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
  if (p->iter) {
    e = (*v)(((PyObject*)p->iter), a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_9csamtools_SNPCallerBase(PyObject *o) {
  struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
  PyObject* tmp;
  tmp = ((PyObject*)p->iter);
  p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyMethodDef __pyx_methods_9csamtools_SNPCallerBase[] = {
  {0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_SNPCallerBase = {
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  0, /*nb_subtract*/
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  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
  #endif
  0, /*nb_remainder*/
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  0, /*nb_negative*/
  0, /*nb_positive*/
  0, /*nb_absolute*/
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  #if PY_MAJOR_VERSION < 3
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  0, /*nb_true_divide*/
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  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
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};

static PySequenceMethods __pyx_tp_as_sequence_SNPCallerBase = {
  0, /*sq_length*/
  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
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  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_SNPCallerBase = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_SNPCallerBase = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
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  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
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  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_SNPCallerBase = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("csamtools.SNPCallerBase"), /*tp_name*/
  sizeof(struct __pyx_obj_9csamtools_SNPCallerBase), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
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  0, /*reserved*/
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  0, /*tp_repr*/
  &__pyx_tp_as_number_SNPCallerBase, /*tp_as_number*/
  &__pyx_tp_as_sequence_SNPCallerBase, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_SNPCallerBase, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_SNPCallerBase, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  __Pyx_DOCSTR("Base class for SNP callers.\n\n    *min_baseQ*\n       minimum base quality (possibly capped by BAQ)\n    *capQ_threshold*\n       coefficient for adjusting mapQ of poor mappings\n    *theta*\n       theta in maq consensus calling model\n    *n_haplotypes*\n       number of haplotypes in the sample\n    *het_rate*\n       prior of a difference between two haplotypes\n    "), /*tp_doc*/
  __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
  __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_9csamtools_SNPCallerBase, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
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  0, /*tp_dict*/
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  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
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  __pyx_tp_new_9csamtools_SNPCallerBase, /*tp_new*/
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  0, /*tp_weaklist*/
  0, /*tp_del*/
  #if PY_VERSION_HEX >= 0x02060000
  0, /*tp_version_tag*/
  #endif
};
static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls __pyx_vtable_9csamtools_IteratorSNPCalls;

static PyObject *__pyx_tp_new_9csamtools_IteratorSNPCalls(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_IteratorSNPCalls *p;
  PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)o);
  p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_IteratorSNPCalls;
  if (__pyx_pf_9csamtools_16IteratorSNPCalls_0__cinit__(o, a, k) < 0) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static PyMethodDef __pyx_methods_9csamtools_IteratorSNPCalls[] = {
  {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_16IteratorSNPCalls_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_16IteratorSNPCalls_2__next__)},
  {0, 0, 0, 0}
};

static PyNumberMethods __pyx_tp_as_number_IteratorSNPCalls = {
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  0, /*nb_subtract*/
  0, /*nb_multiply*/
  #if PY_MAJOR_VERSION < 3
  0, /*nb_divide*/
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  #if PY_MAJOR_VERSION < 3
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  0, /*nb_floor_divide*/
  0, /*nb_true_divide*/
  0, /*nb_inplace_floor_divide*/
  0, /*nb_inplace_true_divide*/
  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
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};

static PySequenceMethods __pyx_tp_as_sequence_IteratorSNPCalls = {
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  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
  0, /*sq_slice*/
  0, /*sq_ass_item*/
  0, /*sq_ass_slice*/
  0, /*sq_contains*/
  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_IteratorSNPCalls = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_IteratorSNPCalls = {
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_IteratorSNPCalls = {
  PyVarObject_HEAD_INIT(0, 0)
  __Pyx_NAMESTR("csamtools.IteratorSNPCalls"), /*tp_name*/
  sizeof(struct __pyx_obj_9csamtools_IteratorSNPCalls), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
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  &__pyx_tp_as_sequence_IteratorSNPCalls, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_IteratorSNPCalls, /*tp_as_mapping*/
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  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
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  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n    call SNPs within a region.\n\n    *iterator* is a pileup iterator. SNPs will be called\n    on all positions returned by this iterator.\n\n    This caller is fast if SNPs are called over large continuous\n    regions. It is slow, if instantiated frequently and in random\n    order as the sequence will have to be reloaded.\n\n    "), /*tp_doc*/
  __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
  __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  __pyx_pf_9csamtools_16IteratorSNPCalls_1__iter__, /*tp_iter*/
  __pyx_pf_9csamtools_16IteratorSNPCalls_2__next__, /*tp_iternext*/
  __pyx_methods_9csamtools_IteratorSNPCalls, /*tp_methods*/
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  __pyx_tp_new_9csamtools_IteratorSNPCalls, /*tp_new*/
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  #if PY_VERSION_HEX >= 0x02060000
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};
static struct __pyx_vtabstruct_9csamtools_SNPCaller __pyx_vtable_9csamtools_SNPCaller;

static PyObject *__pyx_tp_new_9csamtools_SNPCaller(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_9csamtools_SNPCaller *p;
  PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
  if (!o) return 0;
  p = ((struct __pyx_obj_9csamtools_SNPCaller *)o);
  p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_SNPCaller;
  if (__pyx_pf_9csamtools_9SNPCaller_0__cinit__(o, a, k) < 0) {
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  }
  return o;
}

static PyMethodDef __pyx_methods_9csamtools_SNPCaller[] = {
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};

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  0, /*nb_true_divide*/
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  #if PY_VERSION_HEX >= 0x02050000
  0, /*nb_index*/
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};

static PySequenceMethods __pyx_tp_as_sequence_SNPCaller = {
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  0, /*sq_concat*/
  0, /*sq_repeat*/
  0, /*sq_item*/
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  0, /*sq_inplace_concat*/
  0, /*sq_inplace_repeat*/
};

static PyMappingMethods __pyx_tp_as_mapping_SNPCaller = {
  0, /*mp_length*/
  0, /*mp_subscript*/
  0, /*mp_ass_subscript*/
};

static PyBufferProcs __pyx_tp_as_buffer_SNPCaller = {
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  0, /*bf_getreadbuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getwritebuffer*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getsegcount*/
  #endif
  #if PY_MAJOR_VERSION < 3
  0, /*bf_getcharbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_getbuffer*/
  #endif
  #if PY_VERSION_HEX >= 0x02060000
  0, /*bf_releasebuffer*/
  #endif
};

PyTypeObject __pyx_type_9csamtools_SNPCaller = {
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  __Pyx_NAMESTR("csamtools.SNPCaller"), /*tp_name*/
  sizeof(struct __pyx_obj_9csamtools_SNPCaller), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  &__pyx_tp_as_number_SNPCaller, /*tp_as_number*/
  &__pyx_tp_as_sequence_SNPCaller, /*tp_as_sequence*/
  &__pyx_tp_as_mapping_SNPCaller, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  &__pyx_tp_as_buffer_SNPCaller, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n    The samtools SNP caller.\n\n    This object will call SNPs in *samfile* against the reference\n    sequence in *fasta*.\n\n    This caller is fast for calling few SNPs in selected regions.\n\n    It is slow, if called over large genomic regions.\n    "), /*tp_doc*/
  __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
  __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_9csamtools_SNPCaller, /*tp_methods*/
  0, /*tp_members*/
  0, /*tp_getset*/
  0, /*tp_base*/
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  0, /*tp_descr_get*/
  0, /*tp_descr_set*/
  0, /*tp_dictoffset*/
  0, /*tp_init*/
  0, /*tp_alloc*/
  __pyx_tp_new_9csamtools_SNPCaller, /*tp_new*/
  0, /*tp_free*/
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_consensus_quality(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_snp_quality(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_coverage(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_second_allele(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_first(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_second(PyObject *o, void *x) {
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static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_diff(PyObject *o, void *x) {
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  {
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  {
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  {
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static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
                                   PyFrameObject** frame,
                                   const char *funcname,
                                   const char *srcfile,
                                   int firstlineno) {
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        if (*code == NULL) {
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            PyThreadState_GET(),            /*PyThreadState *tstate*/
            *code,                          /*PyCodeObject *code*/
            PyModule_GetDict(__pyx_m),      /*PyObject *globals*/
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        if (*frame == NULL) return 0;
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    else {
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    return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}

static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
    PyObject *py_srcfile = 0;
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    #if PY_MAJOR_VERSION < 3
    py_funcname = PyString_FromString(funcname);
    py_srcfile = PyString_FromString(srcfile);
    #else
    py_funcname = PyUnicode_FromString(funcname);
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    #endif
    if (!py_funcname | !py_srcfile) goto bad;

    py_code = PyCode_New(
        0,                /*int argcount,*/
        #if PY_MAJOR_VERSION >= 3
        0,                /*int kwonlyargcount,*/
        #endif
        0,                /*int nlocals,*/
        0,                /*int stacksize,*/
        0,                /*int flags,*/
        __pyx_empty_bytes,  /*PyObject *code,*/
        __pyx_empty_tuple,  /*PyObject *consts,*/
        __pyx_empty_tuple,  /*PyObject *names,*/
        __pyx_empty_tuple,  /*PyObject *varnames,*/
        __pyx_empty_tuple,  /*PyObject *freevars,*/
        __pyx_empty_tuple,  /*PyObject *cellvars,*/
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        py_funcname,      /*PyObject *name,*/
        firstlineno,      /*int firstlineno,*/
        __pyx_empty_bytes   /*PyObject *lnotab*/
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bad:
    Py_XDECREF(py_srcfile);
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    return py_code;
}

#endif /* CYTHON_PROFILE */

static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
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        PyErr_Format(PyExc_SystemError, "Missing type object");
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    if (likely(PyObject_TypeCheck(obj, type)))
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    PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
                 Py_TYPE(obj)->tp_name, type->tp_name);
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static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
    PyErr_Format(PyExc_ValueError,
        #if PY_VERSION_HEX < 0x02050000
                 "need more than %d value%s to unpack", (int)index,
        #else
                 "need more than %zd value%s to unpack", index,
        #endif
                 (index == 1) ? "" : "s");
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static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
    PyErr_Format(PyExc_ValueError,
        #if PY_VERSION_HEX < 0x02050000
            "too many values to unpack (expected %d)", (int)expected);
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            "too many values to unpack (expected %zd)", expected);
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static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
    PyObject *item;
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static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
    PyObject *item;
    if ((item = PyIter_Next(iter))) {
        Py_DECREF(item);
        __Pyx_RaiseTooManyValuesError(expected);
        return -1;
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    else if (!PyErr_Occurred())
        return 0;
    else
        return -1;
}

static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
    PyObject *kwdict,
    const char* function_name,
    int kw_allowed)
{
    PyObject* key = 0;
    Py_ssize_t pos = 0;
    while (PyDict_Next(kwdict, &pos, &key, 0)) {
        #if PY_MAJOR_VERSION < 3
        if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
        #else
        if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
        #endif
            goto invalid_keyword_type;
    }
    if ((!kw_allowed) && unlikely(key))
        goto invalid_keyword;
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invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%s() keywords must be strings", function_name);
    return 0;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%s() got an unexpected keyword argument '%s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
    return 0;
}

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_AS_STRING(kw_name));
        #endif
}

static void __Pyx_RaiseArgtupleInvalid(
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    int exact,
    Py_ssize_t num_min,
    Py_ssize_t num_max,
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{
    Py_ssize_t num_expected;
    const char *number, *more_or_less;

    if (num_found < num_min) {
        num_expected = num_min;
        more_or_less = "at least";
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        num_expected = num_max;
        more_or_less = "at most";
    }
    if (exact) {
        more_or_less = "exactly";
    }
    number = (num_expected == 1) ? "" : "s";
    PyErr_Format(PyExc_TypeError,
        #if PY_VERSION_HEX < 0x02050000
            "%s() takes %s %d positional argument%s (%d given)",
        #else
            "%s() takes %s %zd positional argument%s (%zd given)",
        #endif
        func_name, more_or_less, num_expected, number, num_found);
}

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;
        } else {
            #if PY_MAJOR_VERSION < 3
            if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
            #else
            if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
            #endif
                goto invalid_keyword_type;
            } else {
                for (name = first_kw_arg; *name; name++) {
                    #if PY_MAJOR_VERSION >= 3
                    if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
                        PyUnicode_Compare(**name, key) == 0) break;
                    #else
                    if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
                        _PyString_Eq(**name, key)) break;
                    #endif
                }
                if (*name) {
                    values[name-argnames] = value;
                } else {
                    /* unexpected keyword found */
                    for (name=argnames; name != first_kw_arg; name++) {
                        if (**name == key) goto arg_passed_twice;
                        #if PY_MAJOR_VERSION >= 3
                        if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
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                        if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
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                    if (kwds2) {
                        if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
                    } else {
                        goto invalid_keyword;
                    }
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        }
    }
    return 0;
arg_passed_twice:
    __Pyx_RaiseDoubleKeywordsError(function_name, **name);
    goto bad;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%s() got an unexpected keyword argument '%s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
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    tstate->curexc_value = value;
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    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
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static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
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    *tb = tstate->curexc_traceback;

    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
}


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


static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
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}

static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
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    PyObject *tmp_type, *tmp_value, *tmp_tb;
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    tstate->curexc_value = 0;
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    if (unlikely(tstate->curexc_type))
        goto bad;
    #if PY_MAJOR_VERSION >= 3
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    *type = local_type;
    *value = local_value;
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    Py_INCREF(local_type);
    Py_INCREF(local_value);
    Py_INCREF(local_tb);
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    /* Make sure tstate is in a consistent state when we XDECREF
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    Py_XDECREF(tmp_tb);
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bad:
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    return r;
}


static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
    PyThreadState *tstate = PyThreadState_GET();
    *type = tstate->exc_type;
    *value = tstate->exc_value;
    *tb = tstate->exc_traceback;
    Py_XINCREF(*type);
    Py_XINCREF(*value);
    Py_XINCREF(*tb);
}

static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyThreadState *tstate = PyThreadState_GET();
    tmp_type = tstate->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = type;
    tstate->exc_value = value;
    tstate->exc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
}

static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
    PyObject *py_import = 0;
    PyObject *empty_list = 0;
    PyObject *module = 0;
    PyObject *global_dict = 0;
    PyObject *empty_dict = 0;
    PyObject *list;
    py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
    if (!py_import)
        goto bad;
    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;
    module = PyObject_CallFunctionObjArgs(py_import,
        name, global_dict, empty_dict, list, NULL);
bad:
    Py_XDECREF(empty_list);
    Py_XDECREF(py_import);
    Py_XDECREF(empty_dict);
    return module;
}

static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
    PyObject *metaclass;
    /* Default metaclass */
#if PY_MAJOR_VERSION < 3
    if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
        PyObject *base = PyTuple_GET_ITEM(bases, 0);
        metaclass = PyObject_GetAttrString(base, "__class__");
        if (!metaclass) {
            PyErr_Clear();
            metaclass = (PyObject*) Py_TYPE(base);
        }
    } else {
        metaclass = (PyObject *) &PyClass_Type;
    }
#else
    if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
        PyObject *base = PyTuple_GET_ITEM(bases, 0);
        metaclass = (PyObject*) Py_TYPE(base);
    } else {
        metaclass = (PyObject *) &PyType_Type;
    }
#endif
    Py_INCREF(metaclass);
    return metaclass;
}

static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
                                   PyObject *modname) {
    PyObject *result;
    PyObject *metaclass;

    if (PyDict_SetItemString(dict, "__module__", modname) < 0)
        return NULL;

    /* Python2 __metaclass__ */
    metaclass = PyDict_GetItemString(dict, "__metaclass__");
    if (metaclass) {
        Py_INCREF(metaclass);
    } else {
        metaclass = __Pyx_FindPy2Metaclass(bases);
    }
    result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
    Py_DECREF(metaclass);
    return result;
}


PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
	__pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
    if (op == NULL)
        return NULL;
	op->func.m_ml = ml;
	Py_XINCREF(self);
	op->func.m_self = self;
	Py_XINCREF(module);
	op->func.m_module = module;
	PyObject_GC_Track(op);
	return (PyObject *)op;
}

static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
	PyObject_GC_UnTrack(m);
	Py_XDECREF(m->func.m_self);
	Py_XDECREF(m->func.m_module);
    PyObject_GC_Del(m);
}

static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
	if (obj == Py_None)
		obj = NULL;
	return PyMethod_New(func, obj, type);
}

int __pyx_binding_PyCFunctionType_init(void) {
    __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
    __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
    __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
    __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
    if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
        return -1;
    }
    __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
    return 0;

}

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

#if PY_MAJOR_VERSION < 3
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
    Py_XINCREF(type);
    Py_XINCREF(value);
    Py_XINCREF(tb);
    /* First, check the traceback argument, replacing None with NULL. */
    if (tb == Py_None) {
        Py_DECREF(tb);
        tb = 0;
    }
    else if (tb != NULL && !PyTraceBack_Check(tb)) {
        PyErr_SetString(PyExc_TypeError,
            "raise: arg 3 must be a traceback or None");
        goto raise_error;
    }
    /* Next, replace a missing value with None */
    if (value == NULL) {
        value = Py_None;
        Py_INCREF(value);
    }
    #if PY_VERSION_HEX < 0x02050000
    if (!PyClass_Check(type))
    #else
    if (!PyType_Check(type))
    #endif
    {
        /* Raising an instance.  The value should be a dummy. */
        if (value != Py_None) {
            PyErr_SetString(PyExc_TypeError,
                "instance exception may not have a separate value");
            goto raise_error;
        }
        /* Normalize to raise <class>, <instance> */
        Py_DECREF(value);
        value = type;
        #if PY_VERSION_HEX < 0x02050000
            if (PyInstance_Check(type)) {
                type = (PyObject*) ((PyInstanceObject*)type)->in_class;
                Py_INCREF(type);
            }
            else {
                type = 0;
                PyErr_SetString(PyExc_TypeError,
                    "raise: exception must be an old-style class or instance");
                goto raise_error;
            }
        #else
            type = (PyObject*) Py_TYPE(type);
            Py_INCREF(type);
            if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
                PyErr_SetString(PyExc_TypeError,
                    "raise: exception class must be a subclass of BaseException");
                goto raise_error;
            }
        #endif
    }

    __Pyx_ErrRestore(type, value, tb);
    return;
raise_error:
    Py_XDECREF(value);
    Py_XDECREF(type);
    Py_XDECREF(tb);
    return;
}

#else /* Python 3+ */

static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
    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)) {
        PyErr_SetString(PyExc_TypeError,
            "raise: exception class must be a subclass of BaseException");
        goto bad;
    }

    PyErr_SetObject(type, value);

    if (tb) {
        PyThreadState *tstate = PyThreadState_GET();
        PyObject* tmp_tb = tstate->curexc_traceback;
        if (tb != tmp_tb) {
            Py_INCREF(tb);
            tstate->curexc_traceback = tb;
            Py_XDECREF(tmp_tb);
        }
    }

bad:
    return;
}
#endif

static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
    const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
    const int is_unsigned = const_zero < neg_one;
    if (sizeof(uint32_t) == sizeof(char)) {
        if (is_unsigned)
            return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
        else
            return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
    } else if (sizeof(uint32_t) == sizeof(short)) {
        if (is_unsigned)
            return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
        else
            return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
    } else if (sizeof(uint32_t) == sizeof(int)) {
        if (is_unsigned)
            return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
        else
            return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
    } else if (sizeof(uint32_t) == sizeof(long)) {
        if (is_unsigned)
            return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
        else
            return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
    } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
        else
            return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
    }  else {
        uint32_t val;
        PyObject *v = __Pyx_PyNumber_Int(x);
        #if PY_VERSION_HEX < 0x03000000
        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;
        }
        return (uint32_t)-1;
    }
}

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

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
    const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
    const int is_unsigned = const_zero < neg_one;
    if ((sizeof(int64_t) == sizeof(char))  ||
        (sizeof(int64_t) == sizeof(short))) {
        return PyInt_FromLong((long)val);
    } else if ((sizeof(int64_t) == sizeof(int)) ||
               (sizeof(int64_t) == sizeof(long))) {
        if (is_unsigned)
            return PyLong_FromUnsignedLong((unsigned long)val);
        else
            return PyInt_FromLong((long)val);
    } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
        else
            return PyLong_FromLongLong((PY_LONG_LONG)val);
    } else {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&val;
        return _PyLong_FromByteArray(bytes, sizeof(int64_t),
                                     little, !is_unsigned);
    }
}

static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
    const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
    const int is_unsigned = const_zero < neg_one;
    if (sizeof(int32_t) == sizeof(char)) {
        if (is_unsigned)
            return (int32_t)__Pyx_PyInt_AsUnsignedChar(x);
        else
            return (int32_t)__Pyx_PyInt_AsSignedChar(x);
    } else if (sizeof(int32_t) == sizeof(short)) {
        if (is_unsigned)
            return (int32_t)__Pyx_PyInt_AsUnsignedShort(x);
        else
            return (int32_t)__Pyx_PyInt_AsSignedShort(x);
    } else if (sizeof(int32_t) == sizeof(int)) {
        if (is_unsigned)
            return (int32_t)__Pyx_PyInt_AsUnsignedInt(x);
        else
            return (int32_t)__Pyx_PyInt_AsSignedInt(x);
    } else if (sizeof(int32_t) == sizeof(long)) {
        if (is_unsigned)
            return (int32_t)__Pyx_PyInt_AsUnsignedLong(x);
        else
            return (int32_t)__Pyx_PyInt_AsSignedLong(x);
    } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
        else
            return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
    }  else {
        int32_t val;
        PyObject *v = __Pyx_PyNumber_Int(x);
        #if PY_VERSION_HEX < 0x03000000
        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;
        }
        return (int32_t)-1;
    }
}

static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) {
    const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
    const int is_unsigned = const_zero < neg_one;
    if ((sizeof(uint8_t) == sizeof(char))  ||
        (sizeof(uint8_t) == sizeof(short))) {
        return PyInt_FromLong((long)val);
    } else if ((sizeof(uint8_t) == sizeof(int)) ||
               (sizeof(uint8_t) == sizeof(long))) {
        if (is_unsigned)
            return PyLong_FromUnsignedLong((unsigned long)val);
        else
            return PyInt_FromLong((long)val);
    } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
        else
            return PyLong_FromLongLong((PY_LONG_LONG)val);
    } else {
        int one = 1; int little = (int)*(unsigned char *)&one;
        unsigned char *bytes = (unsigned char *)&val;
        return _PyLong_FromByteArray(bytes, sizeof(uint8_t),
                                     little, !is_unsigned);
    }
}

#if 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) {
    PyObject* v;
    int i;

    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
        if (PyFile_SoftSpace(f, 1)) {
            if (PyFile_WriteString(" ", f) < 0)
                return -1;
        }
        v = PyTuple_GET_ITEM(arg_tuple, i);
        if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
            return -1;
        if (PyString_Check(v)) {
            char *s = PyString_AsString(v);
            Py_ssize_t len = PyString_Size(v);
            if (len > 0 &&
                isspace(Py_CHARMASK(s[len-1])) &&
                s[len-1] != ' ')
                    PyFile_SoftSpace(f, 0);
        }
    }
    if (newline) {
        if (PyFile_WriteString("\n", f) < 0)
            return -1;
        PyFile_SoftSpace(f, 0);
    }
    return 0;
}

#else /* Python 3 has a print function */

static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
    PyObject* kwargs = 0;
    PyObject* result = 0;
    PyObject* end_string;
    if (unlikely(!__pyx_print)) {
        __pyx_print = __Pyx_GetAttrString(__pyx_b, "print");
        if (!__pyx_print)
            return -1;
    }
    if (stream) {
        kwargs = PyDict_New();
        if (unlikely(!kwargs))
            return -1;
        if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0))
            goto bad;
        if (!newline) {
            end_string = PyUnicode_FromStringAndSize(" ", 1);
            if (unlikely(!end_string))
                goto bad;
            if (PyDict_SetItemString(kwargs, "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_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
                Py_DECREF(end_string);
                return -1;
            }
            Py_DECREF(end_string);
        }
        kwargs = __pyx_print_kwargs;
    }
    result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
    if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
        Py_DECREF(kwargs);
    if (!result)
        return -1;
    Py_DECREF(result);
    return 0;
bad:
    if (kwargs != __pyx_print_kwargs)
        Py_XDECREF(kwargs);
    return -1;
}

#endif

#if PY_MAJOR_VERSION < 3

static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
    if (!f) {
        if (!(f = __Pyx_GetStdout()))
            return -1;
    }
    if (PyFile_SoftSpace(f, 0)) {
        if (PyFile_WriteString(" ", f) < 0)
            return -1;
    }
    if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
        return -1;
    if (PyFile_WriteString("\n", f) < 0)
        return -1;
    return 0;
    /* the line below is just to avoid compiler
     * compiler warnings about unused functions */
    return __Pyx_Print(f, NULL, 0);
}

#else /* Python 3 has a print function */

static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
    int res;
    PyObject* arg_tuple = PyTuple_New(1);
    if (unlikely(!arg_tuple))
        return -1;
    Py_INCREF(o);
    PyTuple_SET_ITEM(arg_tuple, 0, o);
    res = __Pyx_Print(stream, arg_tuple, 1);
    Py_DECREF(arg_tuple);
    return res;
}

#endif

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

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

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

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

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

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

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

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

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

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

static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
    const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to unsigned long");
            return (unsigned long)-1;
        }
        return (unsigned long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to unsigned long");
                return (unsigned long)-1;
            }
            return PyLong_AsUnsignedLong(x);
        } else {
            return PyLong_AsLong(x);
        }
    } else {
        unsigned long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (unsigned long)-1;
        val = __Pyx_PyInt_AsUnsignedLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
    const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to unsigned PY_LONG_LONG");
            return (unsigned PY_LONG_LONG)-1;
        }
        return (unsigned PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to unsigned PY_LONG_LONG");
                return (unsigned PY_LONG_LONG)-1;
            }
            return PyLong_AsUnsignedLongLong(x);
        } else {
            return PyLong_AsLongLong(x);
        }
    } else {
        unsigned PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (unsigned PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
    const long neg_one = (long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to long");
            return (long)-1;
        }
        return (long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to long");
                return (long)-1;
            }
            return PyLong_AsUnsignedLong(x);
        } else {
            return PyLong_AsLong(x);
        }
    } else {
        long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (long)-1;
        val = __Pyx_PyInt_AsLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
    const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to PY_LONG_LONG");
            return (PY_LONG_LONG)-1;
        }
        return (PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to PY_LONG_LONG");
                return (PY_LONG_LONG)-1;
            }
            return PyLong_AsUnsignedLongLong(x);
        } else {
            return PyLong_AsLongLong(x);
        }
    } else {
        PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
    const signed long neg_one = (signed long)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to signed long");
            return (signed long)-1;
        }
        return (signed long)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to signed long");
                return (signed long)-1;
            }
            return PyLong_AsUnsignedLong(x);
        } else {
            return PyLong_AsLong(x);
        }
    } else {
        signed long val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (signed long)-1;
        val = __Pyx_PyInt_AsSignedLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
    const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
    const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        if (is_unsigned && unlikely(val < 0)) {
            PyErr_SetString(PyExc_OverflowError,
                            "can't convert negative value to signed PY_LONG_LONG");
            return (signed PY_LONG_LONG)-1;
        }
        return (signed PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_Check(x))) {
        if (is_unsigned) {
            if (unlikely(Py_SIZE(x) < 0)) {
                PyErr_SetString(PyExc_OverflowError,
                                "can't convert negative value to signed PY_LONG_LONG");
                return (signed PY_LONG_LONG)-1;
            }
            return PyLong_AsUnsignedLongLong(x);
        } else {
            return PyLong_AsLongLong(x);
        }
    } else {
        signed PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (signed PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsSignedLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

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

static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
    const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
    const int is_unsigned = const_zero < neg_one;
    if (sizeof(uint64_t) == sizeof(char)) {
        if (is_unsigned)
            return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
        else
            return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
    } else if (sizeof(uint64_t) == sizeof(short)) {
        if (is_unsigned)
            return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
        else
            return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
    } else if (sizeof(uint64_t) == sizeof(int)) {
        if (is_unsigned)
            return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
        else
            return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
    } else if (sizeof(uint64_t) == sizeof(long)) {
        if (is_unsigned)
            return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
        else
            return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
    } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
        if (is_unsigned)
            return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
        else
            return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
    }  else {
        uint64_t val;
        PyObject *v = __Pyx_PyNumber_Int(x);
        #if PY_VERSION_HEX < 0x03000000
        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;
        }
        return (uint64_t)-1;
    }
}

#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
    long size, int strict)
{
    PyObject *py_module = 0;
    PyObject *result = 0;
    PyObject *py_name = 0;
    char warning[200];

    py_module = __Pyx_ImportModule(module_name);
    if (!py_module)
        goto bad;
    #if PY_MAJOR_VERSION < 3
    py_name = PyString_FromString(class_name);
    #else
    py_name = PyUnicode_FromString(class_name);
    #endif
    if (!py_name)
        goto bad;
    result = PyObject_GetAttr(py_module, py_name);
    Py_DECREF(py_name);
    py_name = 0;
    Py_DECREF(py_module);
    py_module = 0;
    if (!result)
        goto bad;
    if (!PyType_Check(result)) {
        PyErr_Format(PyExc_TypeError,
            "%s.%s is not a type object",
            module_name, class_name);
        goto bad;
    }
    if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
        PyOS_snprintf(warning, sizeof(warning),
            "%s.%s size changed, may indicate binary incompatibility",
            module_name, class_name);
        #if PY_VERSION_HEX < 0x02050000
        PyErr_Warn(NULL, warning);
        #else
        PyErr_WarnEx(NULL, warning, 0);
        #endif
    }
    else if (((PyTypeObject *)result)->tp_basicsize != size) {
        PyErr_Format(PyExc_ValueError,
            "%s.%s has the wrong size, try recompiling",
            module_name, class_name);
        goto bad;
    }
    return (PyTypeObject *)result;
bad:
    Py_XDECREF(py_module);
    Py_XDECREF(result);
    return 0;
}
#endif

#ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
    PyObject *py_name = 0;
    PyObject *py_module = 0;

    #if PY_MAJOR_VERSION < 3
    py_name = PyString_FromString(name);
    #else
    py_name = PyUnicode_FromString(name);
    #endif
    if (!py_name)
        goto bad;
    py_module = PyImport_Import(py_name);
    Py_DECREF(py_name);
    return py_module;
bad:
    Py_XDECREF(py_name);
    return 0;
}
#endif

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

#include "compile.h"
#include "frameobject.h"
#include "traceback.h"

static void __Pyx_AddTraceback(const char *funcname) {
    PyObject *py_srcfile = 0;
    PyObject *py_funcname = 0;
    PyObject *py_globals = 0;
    PyCodeObject *py_code = 0;
    PyFrameObject *py_frame = 0;

    #if PY_MAJOR_VERSION < 3
    py_srcfile = PyString_FromString(__pyx_filename);
    #else
    py_srcfile = PyUnicode_FromString(__pyx_filename);
    #endif
    if (!py_srcfile) goto bad;
    if (__pyx_clineno) {
        #if PY_MAJOR_VERSION < 3
        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
        #else
        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
        #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_globals = PyModule_GetDict(__pyx_m);
    if (!py_globals) goto bad;
    py_code = PyCode_New(
        0,            /*int argcount,*/
        #if PY_MAJOR_VERSION >= 3
        0,            /*int kwonlyargcount,*/
        #endif
        0,            /*int nlocals,*/
        0,            /*int stacksize,*/
        0,            /*int flags,*/
        __pyx_empty_bytes, /*PyObject *code,*/
        __pyx_empty_tuple,  /*PyObject *consts,*/
        __pyx_empty_tuple,  /*PyObject *names,*/
        __pyx_empty_tuple,  /*PyObject *varnames,*/
        __pyx_empty_tuple,  /*PyObject *freevars,*/
        __pyx_empty_tuple,  /*PyObject *cellvars,*/
        py_srcfile,   /*PyObject *filename,*/
        py_funcname,  /*PyObject *name,*/
        __pyx_lineno,   /*int firstlineno,*/
        __pyx_empty_bytes  /*PyObject *lnotab*/
    );
    if (!py_code) goto bad;
    py_frame = PyFrame_New(
        PyThreadState_GET(), /*PyThreadState *tstate,*/
        py_code,             /*PyCodeObject *code,*/
        py_globals,          /*PyObject *globals,*/
        0                    /*PyObject *locals*/
    );
    if (!py_frame) goto bad;
    py_frame->f_lineno = __pyx_lineno;
    PyTraceBack_Here(py_frame);
bad:
    Py_XDECREF(py_srcfile);
    Py_XDECREF(py_funcname);
    Py_XDECREF(py_code);
    Py_XDECREF(py_frame);
}

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

/* Type Conversion Functions */

static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}

static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
  PyNumberMethods *m;
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_VERSION_HEX < 0x03000000
  if (PyInt_Check(x) || PyLong_Check(x))
#else
  if (PyLong_Check(x))
#endif
    return Py_INCREF(x), x;
  m = Py_TYPE(x)->tp_as_number;
#if PY_VERSION_HEX < 0x03000000
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = PyNumber_Long(x);
  }
#else
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Long(x);
  }
#endif
  if (res) {
#if PY_VERSION_HEX < 0x03000000
    if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
    if (!PyLong_Check(res)) {
#endif
      PyErr_Format(PyExc_TypeError,
                   "__%s__ returned non-%s (type %.200s)",
                   name, name, Py_TYPE(res)->tp_name);
      Py_DECREF(res);
      return NULL;
    }
  }
  else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_TypeError,
                    "an integer is required");
  }
  return res;
}

static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
  Py_ssize_t ival;
  PyObject* x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}

static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
   if (ival <= LONG_MAX)
       return PyInt_FromLong((long)ival);
   else {
       unsigned char *bytes = (unsigned char *) &ival;
       int one = 1; int little = (int)*(unsigned char*)&one;
       return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
   }
#else
   return PyInt_FromSize_t(ival);
#endif
}

static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
   unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
   if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
       return (size_t)-1;
   } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
       PyErr_SetString(PyExc_OverflowError,
                       "value too large to convert to size_t");
       return (size_t)-1;
   }
   return (size_t)val;
}


#endif /* Py_PYTHON_H */
