/* Generated by Cython 0.21 */

#define PY_SSIZE_T_CLEAN
#ifndef CYTHON_USE_PYLONG_INTERNALS
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 0
#else
#include "pyconfig.h"
#ifdef PYLONG_BITS_IN_DIGIT
#define CYTHON_USE_PYLONG_INTERNALS 1
#else
#define CYTHON_USE_PYLONG_INTERNALS 0
#endif
#endif
#endif
#include "Python.h"
#ifndef Py_PYTHON_H
    #error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
    #error Cython requires Python 2.6+ or Python 3.2+.
#else
#define CYTHON_ABI "0_21"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
#if !defined(WIN32) && !defined(MS_WINDOWS)
  #ifndef __stdcall
    #define __stdcall
  #endif
  #ifndef __cdecl
    #define __cdecl
  #endif
  #ifndef __fastcall
    #define __fastcall
  #endif
#endif
#ifndef DL_IMPORT
  #define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
  #define DL_EXPORT(t) t
#endif
#ifndef PY_LONG_LONG
  #define PY_LONG_LONG LONG_LONG
#endif
#ifndef Py_HUGE_VAL
  #define Py_HUGE_VAL HUGE_VAL
#endif
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600
#define Py_OptimizeFlag 0
#endif
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
          PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyClass_Type
#else
  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
          PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyType_Type
#endif
#if PY_MAJOR_VERSION >= 3
  #define Py_TPFLAGS_CHECKTYPES 0
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#if PY_MAJOR_VERSION >= 3
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
  #define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
  #define CYTHON_PEP393_ENABLED 1
  #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ? \
                                              0 : _PyUnicode_Ready((PyObject *)(op)))
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
  #define __Pyx_PyUnicode_KIND(u)         PyUnicode_KIND(u)
  #define __Pyx_PyUnicode_DATA(u)         PyUnicode_DATA(u)
  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
#else
  #define CYTHON_PEP393_ENABLED 0
  #define __Pyx_PyUnicode_READY(op)       (0)
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
  #define __Pyx_PyUnicode_KIND(u)         (sizeof(Py_UNICODE))
  #define __Pyx_PyUnicode_DATA(u)         ((void*)PyUnicode_AS_UNICODE(u))
  #define __Pyx_PyUnicode_READ(k, d, i)   ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
#if CYTHON_COMPILING_IN_PYPY
  #define __Pyx_PyUnicode_Concat(a, b)      PyNumber_Add(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  PyNumber_Add(a, b)
#else
  #define __Pyx_PyUnicode_Concat(a, b)      PyUnicode_Concat(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
      PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
#endif
#define __Pyx_PyString_FormatSafe(a, b)   ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b)  ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyString_Format(a, b)  PyUnicode_Format(a, b)
#else
  #define __Pyx_PyString_Format(a, b)  PyString_Format(a, b)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBaseString_Type            PyUnicode_Type
  #define PyStringObject               PyUnicodeObject
  #define PyString_Type                PyUnicode_Type
  #define PyString_Check               PyUnicode_Check
  #define PyString_CheckExact          PyUnicode_CheckExact
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
  #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
#else
  #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
  #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
#endif
#ifndef PySet_CheckExact
  #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
#if PY_MAJOR_VERSION >= 3
  #define PyIntObject                  PyLongObject
  #define PyInt_Type                   PyLong_Type
  #define PyInt_Check(op)              PyLong_Check(op)
  #define PyInt_CheckExact(op)         PyLong_CheckExact(op)
  #define PyInt_FromString             PyLong_FromString
  #define PyInt_FromUnicode            PyLong_FromUnicode
  #define PyInt_FromLong               PyLong_FromLong
  #define PyInt_FromSize_t             PyLong_FromSize_t
  #define PyInt_FromSsize_t            PyLong_FromSsize_t
  #define PyInt_AsLong                 PyLong_AsLong
  #define PyInt_AS_LONG                PyLong_AS_LONG
  #define PyInt_AsSsize_t              PyLong_AsSsize_t
  #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
  #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
  #define PyNumber_Int                 PyNumber_Long
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBoolObject                 PyLongObject
#endif
#if PY_VERSION_HEX < 0x030200A4
  typedef long Py_hash_t;
  #define __Pyx_PyInt_FromHash_t PyInt_FromLong
  #define __Pyx_PyInt_AsHash_t   PyInt_AsLong
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#ifndef CYTHON_INLINE
  #if defined(__GNUC__)
    #define CYTHON_INLINE __inline__
  #elif defined(_MSC_VER)
    #define CYTHON_INLINE __inline
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_INLINE inline
  #else
    #define CYTHON_INLINE
  #endif
#endif
#ifndef CYTHON_RESTRICT
  #if defined(__GNUC__)
    #define CYTHON_RESTRICT __restrict__
  #elif defined(_MSC_VER) && _MSC_VER >= 1400
    #define CYTHON_RESTRICT __restrict
  #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define CYTHON_RESTRICT restrict
  #else
    #define CYTHON_RESTRICT
  #endif
#endif
#ifdef NAN
#define __PYX_NAN() ((float) NAN)
#else
static CYTHON_INLINE float __PYX_NAN() {
  /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
   a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
   a quiet NaN. */
  float value;
  memset(&value, 0xFF, sizeof(value));
  return value;
}
#endif
#ifdef __cplusplus
template<typename T>
void __Pyx_call_destructor(T* x) {
    x->~T();
}
#endif


#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
#else
  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_Divide(x,y)
  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(x,y)
#endif

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

#if defined(WIN32) || defined(MS_WINDOWS)
#define _USE_MATH_DEFINES
#endif
#include <math.h>
#define __PYX_HAVE__taggd__io__barcode_utils
#define __PYX_HAVE_API__taggd__io__barcode_utils
#include "string.h"
#include "stdio.h"
#include "pythread.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */

#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
#endif

#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
#   if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
#     define CYTHON_UNUSED __attribute__ ((__unused__))
#   else
#     define CYTHON_UNUSED
#   endif
# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
#   define CYTHON_UNUSED __attribute__ ((__unused__))
# else
#   define CYTHON_UNUSED
# endif
#endif
typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;

#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#define __Pyx_fits_Py_ssize_t(v, type, is_signed)  (    \
    (sizeof(type) < sizeof(Py_ssize_t))  ||             \
    (sizeof(type) > sizeof(Py_ssize_t) &&               \
          likely(v < (type)PY_SSIZE_T_MAX ||            \
                 v == (type)PY_SSIZE_T_MAX)  &&         \
          (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||       \
                                v == (type)PY_SSIZE_T_MIN)))  ||  \
    (sizeof(type) == sizeof(Py_ssize_t) &&              \
          (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||        \
                               v == (type)PY_SSIZE_T_MAX)))  )
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
#define __Pyx_PyBytes_FromString        PyBytes_FromString
#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
#if PY_MAJOR_VERSION < 3
    #define __Pyx_PyStr_FromString        __Pyx_PyBytes_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#else
    #define __Pyx_PyStr_FromString        __Pyx_PyUnicode_FromString
    #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
#endif
#define __Pyx_PyObject_AsSString(s)    ((signed char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_AsUString(s)    ((unsigned char*) __Pyx_PyObject_AsString(s))
#define __Pyx_PyObject_FromUString(s)  __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromUString(s)   __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromUString(s)   __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromUString(s)     __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s)
#if PY_MAJOR_VERSION < 3
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
{
    const Py_UNICODE *u_end = u;
    while (*u_end++) ;
    return (size_t)(u_end - u - 1);
}
#else
#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
#endif
#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    const char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    if (strcmp(default_encoding_c, "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        char ascii_chars[128];
        int c;
        for (c = 0; c < 128; c++) {
            ascii_chars[c] = c;
        }
        __Pyx_sys_getdefaultencoding_not_ascii = 1;
        ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
        if (!ascii_chars_u) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
            PyErr_Format(
                PyExc_ValueError,
                "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
        Py_DECREF(ascii_chars_u);
        Py_DECREF(ascii_chars_b);
    }
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return -1;
}
#endif
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
#else
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
    if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
    strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    return -1;
}
#endif
#endif


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

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


static const char *__pyx_f[] = {
  "taggd/io/barcode_utils.pyx",
  "taggd/io/barcode_utils.pxd",
  "type.pxd",
  "bool.pxd",
  "complex.pxd",
};

/*--- Type declarations ---*/
struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode;
struct __pyx_opt_args_5taggd_4misc_16distance_metrics_hamming_distance;
struct __pyx_opt_args_5taggd_4misc_16distance_metrics_levenshtein_distance;

/* "taggd/misc/distance_metrics.pxd":3
 * from cpython cimport bool
 * 
 * cdef int hamming_distance(str seq1, str seq2, int limit=?)             # <<<<<<<<<<<<<<
 * 
 * cdef list subglobal_distance(str, str)
 */
struct __pyx_opt_args_5taggd_4misc_16distance_metrics_hamming_distance {
  int __pyx_n;
  int limit;
};

/* "taggd/misc/distance_metrics.pxd":7
 * cdef list subglobal_distance(str, str)
 * 
 * cdef int levenshtein_distance(str seq1, str seq2, int limit=?)             # <<<<<<<<<<<<<<
 */
struct __pyx_opt_args_5taggd_4misc_16distance_metrics_levenshtein_distance {
  int __pyx_n;
  int limit;
};

/* "taggd/io/barcode_utils.pxd":1
 * cdef class Barcode:             # <<<<<<<<<<<<<<
 *     cdef public str sequence
 *     cdef public list attributes
 */
struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode {
  PyObject_HEAD
  PyObject *sequence;
  PyObject *attributes;
};

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

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

static PyObject *__Pyx_GetBuiltinName(PyObject *name);

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

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

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

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

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

#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000
static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) {
    PyObject *res;
    PyTypeObject *tp = Py_TYPE(obj);
#if PY_MAJOR_VERSION < 3
    if (unlikely(PyInstance_Check(obj)))
        return __Pyx_PyObject_GetAttrStr(obj, attr_name);
#endif
    res = _PyType_Lookup(tp, attr_name);
    if (likely(res)) {
        descrgetfunc f = Py_TYPE(res)->tp_descr_get;
        if (!f) {
            Py_INCREF(res);
        } else {
            res = f(res, obj, (PyObject *)tp);
        }
    } else {
        PyErr_SetObject(PyExc_AttributeError, attr_name);
    }
    return res;
}
#else
#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n)
#endif

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
#endif

static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);

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

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

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

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

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

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
#else
#define __Pyx_PyList_GetSlice(seq, start, stop)   PySequence_GetSlice(seq, start, stop)
#define __Pyx_PyTuple_GetSlice(seq, start, stop)  PySequence_GetSlice(seq, start, stop)
#endif

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

static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);

static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);

static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d);

static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);

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

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

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

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

static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);

static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);

static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);

static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);

static int __Pyx_check_binary_version(void);

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

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

static PyObject *__Pyx_ImportModule(const char *name);

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

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

static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);


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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

/* Module declarations from '__builtin__' */

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* Module declarations from 'cpython' */

/* Module declarations from 'taggd.misc.distance_metrics' */
static int (*__pyx_f_5taggd_4misc_16distance_metrics_hamming_distance)(PyObject *, PyObject *, struct __pyx_opt_args_5taggd_4misc_16distance_metrics_hamming_distance *__pyx_optional_args); /*proto*/

/* Module declarations from 'taggd.io.barcode_utils' */
static PyTypeObject *__pyx_ptype_5taggd_2io_13barcode_utils_Barcode = 0;
static PyObject *__pyx_f_5taggd_2io_13barcode_utils_read_barcode_file(PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_5taggd_2io_13barcode_utils_estimate_min_edit_distance(PyObject *, int, int __pyx_skip_dispatch); /*proto*/
#define __Pyx_MODULE_NAME "taggd.io.barcode_utils"
int __pyx_module_is_main_taggd__io__barcode_utils = 0;

/* Implementation of 'taggd.io.barcode_utils' */
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_xrange;
static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode___cinit__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_seq_, PyObject *__pyx_v_attributes_); /* proto */
static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence___get__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self); /* proto */
static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_2__set__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_4__del__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes___get__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self); /* proto */
static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_2__set__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_4__del__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_read_barcode_file(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile_path); /* proto */
static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_2estimate_min_edit_distance(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_true_barcodes, int __pyx_v_max_iters); /* proto */
static PyObject *__pyx_tp_new_5taggd_2io_13barcode_utils_Barcode(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_seq[] = "seq_";
static char __pyx_k_exit[] = "__exit__";
static char __pyx_k_keys[] = "keys";
static char __pyx_k_main[] = "__main__";
static char __pyx_k_open[] = "open";
static char __pyx_k_test[] = "__test__";
static char __pyx_k_enter[] = "__enter__";
static char __pyx_k_range[] = "range";
static char __pyx_k_split[] = "split";
static char __pyx_k_strip[] = "strip";
static char __pyx_k_import[] = "__import__";
static char __pyx_k_random[] = "random";
static char __pyx_k_xrange[] = "xrange";
static char __pyx_k_shuffle[] = "shuffle";
static char __pyx_k_max_iters[] = "max_iters";
static char __pyx_k_ValueError[] = "ValueError";
static char __pyx_k_attributes[] = "attributes_";
static char __pyx_k_true_barcodes[] = "true_barcodes";
static char __pyx_k_Contains_utilities_for_handling[] = "\nContains utilities for handling barcodes.\n";
static char __pyx_k_Barcode_file_incorrect_duplicate[] = "Barcode file incorrect, duplicate barcode: ";
static char __pyx_k_Barcode_file_incorrect_varying_l[] = "Barcode file incorrect, varying lengths among barcodes";
static PyObject *__pyx_kp_s_Barcode_file_incorrect_duplicate;
static PyObject *__pyx_kp_s_Barcode_file_incorrect_varying_l;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_n_s_attributes;
static PyObject *__pyx_n_s_enter;
static PyObject *__pyx_n_s_exit;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_keys;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_max_iters;
static PyObject *__pyx_n_s_open;
static PyObject *__pyx_n_s_random;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_seq;
static PyObject *__pyx_n_s_shuffle;
static PyObject *__pyx_n_s_split;
static PyObject *__pyx_n_s_strip;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_true_barcodes;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_tuple__2;

/* "taggd/io/barcode_utils.pyx":13
 *     """
 * 
 *     def __cinit__(self, str seq_, list attributes_):             # <<<<<<<<<<<<<<
 *         self.sequence = seq_
 *         self.attributes = attributes_
 */

/* Python wrapper */
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_seq_ = 0;
  PyObject *__pyx_v_attributes_ = 0;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_seq,&__pyx_n_s_attributes,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_seq)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_attributes)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_seq_ = ((PyObject*)values[0]);
    __pyx_v_attributes_ = ((PyObject*)values[1]);
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("taggd.io.barcode_utils.Barcode.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return -1;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_seq_), (&PyString_Type), 1, "seq_", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_attributes_), (&PyList_Type), 1, "attributes_", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode___cinit__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self), __pyx_v_seq_, __pyx_v_attributes_);

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

static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode___cinit__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_seq_, PyObject *__pyx_v_attributes_) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__cinit__", 0);

  /* "taggd/io/barcode_utils.pyx":14
 * 
 *     def __cinit__(self, str seq_, list attributes_):
 *         self.sequence = seq_             # <<<<<<<<<<<<<<
 *         self.attributes = attributes_
 * 
 */
  __Pyx_INCREF(__pyx_v_seq_);
  __Pyx_GIVEREF(__pyx_v_seq_);
  __Pyx_GOTREF(__pyx_v_self->sequence);
  __Pyx_DECREF(__pyx_v_self->sequence);
  __pyx_v_self->sequence = __pyx_v_seq_;

  /* "taggd/io/barcode_utils.pyx":15
 *     def __cinit__(self, str seq_, list attributes_):
 *         self.sequence = seq_
 *         self.attributes = attributes_             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_INCREF(__pyx_v_attributes_);
  __Pyx_GIVEREF(__pyx_v_attributes_);
  __Pyx_GOTREF(__pyx_v_self->attributes);
  __Pyx_DECREF(__pyx_v_self->attributes);
  __pyx_v_self->attributes = __pyx_v_attributes_;

  /* "taggd/io/barcode_utils.pyx":13
 *     """
 * 
 *     def __cinit__(self, str seq_, list attributes_):             # <<<<<<<<<<<<<<
 *         self.sequence = seq_
 *         self.attributes = attributes_
 */

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "taggd/io/barcode_utils.pxd":2
 * cdef class Barcode:
 *     cdef public str sequence             # <<<<<<<<<<<<<<
 *     cdef public list attributes
 * 
 */

/* Python wrapper */
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence___get__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self));

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

static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence___get__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__", 0);
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_self->sequence);
  __pyx_r = __pyx_v_self->sequence;
  goto __pyx_L0;

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

/* Python wrapper */
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_2__set__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self), ((PyObject *)__pyx_v_value));

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

static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_2__set__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_value) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__set__", 0);
  if (!(likely(PyString_CheckExact(__pyx_v_value))||((__pyx_v_value) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_v_value)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_t_1 = __pyx_v_value;
  __Pyx_INCREF(__pyx_t_1);
  __Pyx_GIVEREF(__pyx_t_1);
  __Pyx_GOTREF(__pyx_v_self->sequence);
  __Pyx_DECREF(__pyx_v_self->sequence);
  __pyx_v_self->sequence = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("taggd.io.barcode_utils.Barcode.sequence.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_5__del__(PyObject *__pyx_v_self); /*proto*/
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_5__del__(PyObject *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_4__del__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self));

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

static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_8sequence_4__del__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__del__", 0);
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  __Pyx_GOTREF(__pyx_v_self->sequence);
  __Pyx_DECREF(__pyx_v_self->sequence);
  __pyx_v_self->sequence = ((PyObject*)Py_None);

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "taggd/io/barcode_utils.pxd":3
 * cdef class Barcode:
 *     cdef public str sequence
 *     cdef public list attributes             # <<<<<<<<<<<<<<
 * 
 * cpdef dict read_barcode_file(str infile_path)
 */

/* Python wrapper */
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_1__get__(PyObject *__pyx_v_self); /*proto*/
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_1__get__(PyObject *__pyx_v_self) {
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes___get__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self));

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

static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes___get__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__get__", 0);
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_self->attributes);
  __pyx_r = __pyx_v_self->attributes;
  goto __pyx_L0;

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

/* Python wrapper */
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_2__set__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self), ((PyObject *)__pyx_v_value));

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

static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_2__set__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self, PyObject *__pyx_v_value) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("__set__", 0);
  if (!(likely(PyList_CheckExact(__pyx_v_value))||((__pyx_v_value) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_v_value)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_t_1 = __pyx_v_value;
  __Pyx_INCREF(__pyx_t_1);
  __Pyx_GIVEREF(__pyx_t_1);
  __Pyx_GOTREF(__pyx_v_self->attributes);
  __Pyx_DECREF(__pyx_v_self->attributes);
  __pyx_v_self->attributes = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* function exit code */
  __pyx_r = 0;
  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("taggd.io.barcode_utils.Barcode.attributes.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = -1;
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_5__del__(PyObject *__pyx_v_self); /*proto*/
static int __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_5__del__(PyObject *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_4__del__(((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)__pyx_v_self));

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

static int __pyx_pf_5taggd_2io_13barcode_utils_7Barcode_10attributes_4__del__(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *__pyx_v_self) {
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("__del__", 0);
  __Pyx_INCREF(Py_None);
  __Pyx_GIVEREF(Py_None);
  __Pyx_GOTREF(__pyx_v_self->attributes);
  __Pyx_DECREF(__pyx_v_self->attributes);
  __pyx_v_self->attributes = ((PyObject*)Py_None);

  /* function exit code */
  __pyx_r = 0;
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "taggd/io/barcode_utils.pyx":18
 * 
 * 
 * cpdef dict read_barcode_file(str infile_path):             # <<<<<<<<<<<<<<
 *     """
 *     Reads a barcode ("chip") file and returns the barcodes.
 */

static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_1read_barcode_file(PyObject *__pyx_self, PyObject *__pyx_v_infile_path); /*proto*/
static PyObject *__pyx_f_5taggd_2io_13barcode_utils_read_barcode_file(PyObject *__pyx_v_infile_path, CYTHON_UNUSED int __pyx_skip_dispatch) {
  PyObject *__pyx_v_res_dict = 0;
  PyObject *__pyx_v_line = 0;
  PyObject *__pyx_v_tmp = 0;
  PyObject *__pyx_v_seq = 0;
  int __pyx_v_length;
  PyObject *__pyx_v_infile = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  PyObject *__pyx_t_5 = NULL;
  PyObject *__pyx_t_6 = NULL;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  Py_ssize_t __pyx_t_9;
  PyObject *(*__pyx_t_10)(PyObject *);
  PyObject *__pyx_t_11 = NULL;
  int __pyx_t_12;
  Py_ssize_t __pyx_t_13;
  int __pyx_t_14;
  PyObject *__pyx_t_15 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("read_barcode_file", 0);

  /* "taggd/io/barcode_utils.pyx":24
 *     :return: a dictionary with barcode sequences as keys and Barcode instances as values.
 *     """
 *     cdef dict res_dict = {}             # <<<<<<<<<<<<<<
 *     cdef str line
 *     cdef list tmp
 */
  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v_res_dict = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "taggd/io/barcode_utils.pyx":28
 *     cdef list tmp
 *     cdef str seq
 *     cdef int length = 0             # <<<<<<<<<<<<<<
 *     with open(infile_path) as infile:
 *         for line in infile:
 */
  __pyx_v_length = 0;

  /* "taggd/io/barcode_utils.pyx":29
 *     cdef str seq
 *     cdef int length = 0
 *     with open(infile_path) as infile:             # <<<<<<<<<<<<<<
 *         for line in infile:
 *             tmp = line.strip().split()
 */
  /*with:*/ {
    __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_INCREF(__pyx_v_infile_path);
    PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_infile_path);
    __Pyx_GIVEREF(__pyx_v_infile_path);
    __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_open, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_3 = __Pyx_PyObject_LookupSpecial(__pyx_t_2, __pyx_n_s_exit); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_3);
    __pyx_t_4 = __Pyx_PyObject_LookupSpecial(__pyx_t_2, __pyx_n_s_enter); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
    __Pyx_GOTREF(__pyx_t_4);
    __pyx_t_5 = NULL;
    if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) {
      __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4);
      if (likely(__pyx_t_5)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
        __Pyx_INCREF(__pyx_t_5);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_4, function);
      }
    }
    if (__pyx_t_5) {
      __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
    } else {
      __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
    }
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
    __pyx_t_4 = __pyx_t_1;
    __pyx_t_1 = 0;
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    /*try:*/ {
      {
        __Pyx_ExceptionSave(&__pyx_t_6, &__pyx_t_7, &__pyx_t_8);
        __Pyx_XGOTREF(__pyx_t_6);
        __Pyx_XGOTREF(__pyx_t_7);
        __Pyx_XGOTREF(__pyx_t_8);
        /*try:*/ {
          __pyx_v_infile = __pyx_t_4;
          __pyx_t_4 = 0;

          /* "taggd/io/barcode_utils.pyx":30
 *     cdef int length = 0
 *     with open(infile_path) as infile:
 *         for line in infile:             # <<<<<<<<<<<<<<
 *             tmp = line.strip().split()
 *             seq = tmp[0]
 */
          if (likely(PyList_CheckExact(__pyx_v_infile)) || PyTuple_CheckExact(__pyx_v_infile)) {
            __pyx_t_4 = __pyx_v_infile; __Pyx_INCREF(__pyx_t_4); __pyx_t_9 = 0;
            __pyx_t_10 = NULL;
          } else {
            __pyx_t_9 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_infile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_4);
            __pyx_t_10 = Py_TYPE(__pyx_t_4)->tp_iternext; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
          }
          for (;;) {
            if (likely(!__pyx_t_10)) {
              if (likely(PyList_CheckExact(__pyx_t_4))) {
                if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_4)) break;
                #if CYTHON_COMPILING_IN_CPYTHON
                __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_9); __Pyx_INCREF(__pyx_t_2); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                #else
                __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                #endif
              } else {
                if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
                #if CYTHON_COMPILING_IN_CPYTHON
                __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_9); __Pyx_INCREF(__pyx_t_2); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                #else
                __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                #endif
              }
            } else {
              __pyx_t_2 = __pyx_t_10(__pyx_t_4);
              if (unlikely(!__pyx_t_2)) {
                PyObject* exc_type = PyErr_Occurred();
                if (exc_type) {
                  if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
                  else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                }
                break;
              }
              __Pyx_GOTREF(__pyx_t_2);
            }
            if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_XDECREF_SET(__pyx_v_line, ((PyObject*)__pyx_t_2));
            __pyx_t_2 = 0;

            /* "taggd/io/barcode_utils.pyx":31
 *     with open(infile_path) as infile:
 *         for line in infile:
 *             tmp = line.strip().split()             # <<<<<<<<<<<<<<
 *             seq = tmp[0]
 *             if length == 0:
 */
            __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_5);
            __pyx_t_11 = NULL;
            if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
              __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_5);
              if (likely(__pyx_t_11)) {
                PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
                __Pyx_INCREF(__pyx_t_11);
                __Pyx_INCREF(function);
                __Pyx_DECREF_SET(__pyx_t_5, function);
              }
            }
            if (__pyx_t_11) {
              __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
            } else {
              __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __Pyx_GOTREF(__pyx_t_1);
            __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
            __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_split); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_5);
            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
            __pyx_t_1 = NULL;
            if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
              __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_5);
              if (likely(__pyx_t_1)) {
                PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
                __Pyx_INCREF(__pyx_t_1);
                __Pyx_INCREF(function);
                __Pyx_DECREF_SET(__pyx_t_5, function);
              }
            }
            if (__pyx_t_1) {
              __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
            } else {
              __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __Pyx_GOTREF(__pyx_t_2);
            __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
            if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_XDECREF_SET(__pyx_v_tmp, ((PyObject*)__pyx_t_2));
            __pyx_t_2 = 0;

            /* "taggd/io/barcode_utils.pyx":32
 *         for line in infile:
 *             tmp = line.strip().split()
 *             seq = tmp[0]             # <<<<<<<<<<<<<<
 *             if length == 0:
 *                 length = len(seq)
 */
            if (unlikely(__pyx_v_tmp == Py_None)) {
              PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __pyx_t_2 = __Pyx_GetItemInt_List(__pyx_v_tmp, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
            __Pyx_GOTREF(__pyx_t_2);
            if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_XDECREF_SET(__pyx_v_seq, ((PyObject*)__pyx_t_2));
            __pyx_t_2 = 0;

            /* "taggd/io/barcode_utils.pyx":33
 *             tmp = line.strip().split()
 *             seq = tmp[0]
 *             if length == 0:             # <<<<<<<<<<<<<<
 *                 length = len(seq)
 *             if len(seq) != length:
 */
            __pyx_t_12 = ((__pyx_v_length == 0) != 0);
            if (__pyx_t_12) {

              /* "taggd/io/barcode_utils.pyx":34
 *             seq = tmp[0]
 *             if length == 0:
 *                 length = len(seq)             # <<<<<<<<<<<<<<
 *             if len(seq) != length:
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")
 */
              __pyx_t_13 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __pyx_v_length = __pyx_t_13;
              goto __pyx_L17;
            }
            __pyx_L17:;

            /* "taggd/io/barcode_utils.pyx":35
 *             if length == 0:
 *                 length = len(seq)
 *             if len(seq) != length:             # <<<<<<<<<<<<<<
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")
 *             if seq in res_dict:
 */
            __pyx_t_13 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __pyx_t_12 = ((__pyx_t_13 != __pyx_v_length) != 0);
            if (__pyx_t_12) {

              /* "taggd/io/barcode_utils.pyx":36
 *                 length = len(seq)
 *             if len(seq) != length:
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")             # <<<<<<<<<<<<<<
 *             if seq in res_dict:
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)
 */
              __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_GOTREF(__pyx_t_2);
              __Pyx_Raise(__pyx_t_2, 0, 0, 0);
              __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }

            /* "taggd/io/barcode_utils.pyx":37
 *             if len(seq) != length:
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")
 *             if seq in res_dict:             # <<<<<<<<<<<<<<
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)
 *             res_dict[tmp[0]] = Barcode(tmp[0], tmp[1:])
 */
            __pyx_t_12 = (__Pyx_PyDict_Contains(__pyx_v_seq, __pyx_v_res_dict, Py_EQ)); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __pyx_t_14 = (__pyx_t_12 != 0);
            if (__pyx_t_14) {

              /* "taggd/io/barcode_utils.pyx":38
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")
 *             if seq in res_dict:
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)             # <<<<<<<<<<<<<<
 *             res_dict[tmp[0]] = Barcode(tmp[0], tmp[1:])
 *     return res_dict
 */
              __pyx_t_2 = PyNumber_Add(__pyx_kp_s_Barcode_file_incorrect_duplicate, __pyx_v_seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_GOTREF(__pyx_t_2);
              __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_GOTREF(__pyx_t_5);
              PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
              __Pyx_GIVEREF(__pyx_t_2);
              __pyx_t_2 = 0;
              __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
              __Pyx_GOTREF(__pyx_t_2);
              __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
              __Pyx_Raise(__pyx_t_2, 0, 0, 0);
              __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }

            /* "taggd/io/barcode_utils.pyx":39
 *             if seq in res_dict:
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)
 *             res_dict[tmp[0]] = Barcode(tmp[0], tmp[1:])             # <<<<<<<<<<<<<<
 *     return res_dict
 * 
 */
            if (unlikely(__pyx_v_tmp == Py_None)) {
              PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __pyx_t_2 = __Pyx_GetItemInt_List(__pyx_v_tmp, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
            __Pyx_GOTREF(__pyx_t_2);
            if (unlikely(__pyx_v_tmp == Py_None)) {
              PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __pyx_t_5 = __Pyx_PyList_GetSlice(__pyx_v_tmp, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_5);
            __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_1);
            PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
            __Pyx_GIVEREF(__pyx_t_2);
            PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
            __Pyx_GIVEREF(__pyx_t_5);
            __pyx_t_2 = 0;
            __pyx_t_5 = 0;
            __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5taggd_2io_13barcode_utils_Barcode)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_GOTREF(__pyx_t_5);
            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
            if (unlikely(__pyx_v_tmp == Py_None)) {
              PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            }
            __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_tmp, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
            __Pyx_GOTREF(__pyx_t_1);
            if (unlikely(PyDict_SetItem(__pyx_v_res_dict, __pyx_t_1, __pyx_t_5) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
            __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
            __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;

            /* "taggd/io/barcode_utils.pyx":30
 *     cdef int length = 0
 *     with open(infile_path) as infile:
 *         for line in infile:             # <<<<<<<<<<<<<<
 *             tmp = line.strip().split()
 *             seq = tmp[0]
 */
          }
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
        }
        __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
        __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
        __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
        goto __pyx_L14_try_end;
        __pyx_L7_error:;
        __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
        __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
        __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
        __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
        __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;

        /* "taggd/io/barcode_utils.pyx":29
 *     cdef str seq
 *     cdef int length = 0
 *     with open(infile_path) as infile:             # <<<<<<<<<<<<<<
 *         for line in infile:
 *             tmp = line.strip().split()
 */
        /*except:*/ {
          __Pyx_AddTraceback("taggd.io.barcode_utils.read_barcode_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
          if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_5, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
          __Pyx_GOTREF(__pyx_t_4);
          __Pyx_GOTREF(__pyx_t_5);
          __Pyx_GOTREF(__pyx_t_1);
          __pyx_t_2 = PyTuple_Pack(3, __pyx_t_4, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_15 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, NULL);
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
          if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
          __Pyx_GOTREF(__pyx_t_15);
          __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_15);
          __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
          if (__pyx_t_14 < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
          __pyx_t_12 = ((!(__pyx_t_14 != 0)) != 0);
          if (__pyx_t_12) {
            __Pyx_GIVEREF(__pyx_t_4);
            __Pyx_GIVEREF(__pyx_t_5);
            __Pyx_XGIVEREF(__pyx_t_1);
            __Pyx_ErrRestore(__pyx_t_4, __pyx_t_5, __pyx_t_1);
            __pyx_t_4 = 0; __pyx_t_5 = 0; __pyx_t_1 = 0; 
            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
          }
          __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
          __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
          __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
          goto __pyx_L8_exception_handled;
        }
        __pyx_L9_except_error:;
        __Pyx_XGIVEREF(__pyx_t_6);
        __Pyx_XGIVEREF(__pyx_t_7);
        __Pyx_XGIVEREF(__pyx_t_8);
        __Pyx_ExceptionReset(__pyx_t_6, __pyx_t_7, __pyx_t_8);
        goto __pyx_L1_error;
        __pyx_L8_exception_handled:;
        __Pyx_XGIVEREF(__pyx_t_6);
        __Pyx_XGIVEREF(__pyx_t_7);
        __Pyx_XGIVEREF(__pyx_t_8);
        __Pyx_ExceptionReset(__pyx_t_6, __pyx_t_7, __pyx_t_8);
        __pyx_L14_try_end:;
      }
    }
    /*finally:*/ {
      /*normal exit:*/{
        if (__pyx_t_3) {
          __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__2, NULL);
          __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
          if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
          __Pyx_GOTREF(__pyx_t_8);
          __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
        }
        goto __pyx_L6;
      }
      __pyx_L6:;
    }
    goto __pyx_L23;
    __pyx_L3_error:;
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    goto __pyx_L1_error;
    __pyx_L23:;
  }

  /* "taggd/io/barcode_utils.pyx":40
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)
 *             res_dict[tmp[0]] = Barcode(tmp[0], tmp[1:])
 *     return res_dict             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_res_dict);
  __pyx_r = __pyx_v_res_dict;
  goto __pyx_L0;

  /* "taggd/io/barcode_utils.pyx":18
 * 
 * 
 * cpdef dict read_barcode_file(str infile_path):             # <<<<<<<<<<<<<<
 *     """
 *     Reads a barcode ("chip") file and returns the barcodes.
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_XDECREF(__pyx_t_5);
  __Pyx_XDECREF(__pyx_t_11);
  __Pyx_AddTraceback("taggd.io.barcode_utils.read_barcode_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_res_dict);
  __Pyx_XDECREF(__pyx_v_line);
  __Pyx_XDECREF(__pyx_v_tmp);
  __Pyx_XDECREF(__pyx_v_seq);
  __Pyx_XDECREF(__pyx_v_infile);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_1read_barcode_file(PyObject *__pyx_self, PyObject *__pyx_v_infile_path); /*proto*/
static char __pyx_doc_5taggd_2io_13barcode_utils_read_barcode_file[] = "\n    Reads a barcode (\"chip\") file and returns the barcodes.\n    :param infile_path: chip file.\n    :return: a dictionary with barcode sequences as keys and Barcode instances as values.\n    ";
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_1read_barcode_file(PyObject *__pyx_self, PyObject *__pyx_v_infile_path) {
  CYTHON_UNUSED int __pyx_lineno = 0;
  CYTHON_UNUSED const char *__pyx_filename = NULL;
  CYTHON_UNUSED int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("read_barcode_file (wrapper)", 0);
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_infile_path), (&PyString_Type), 1, "infile_path", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_read_barcode_file(__pyx_self, ((PyObject*)__pyx_v_infile_path));

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

static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_read_barcode_file(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile_path) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("read_barcode_file", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __pyx_f_5taggd_2io_13barcode_utils_read_barcode_file(__pyx_v_infile_path, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("taggd.io.barcode_utils.read_barcode_file", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "taggd/io/barcode_utils.pyx":43
 * 
 * 
 * cpdef int estimate_min_edit_distance(dict true_barcodes, int max_iters):             # <<<<<<<<<<<<<<
 *     """
 *     Reads a barcodes dict and estimates the minimum edit distance
 */

static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_3estimate_min_edit_distance(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_f_5taggd_2io_13barcode_utils_estimate_min_edit_distance(PyObject *__pyx_v_true_barcodes, int __pyx_v_max_iters, CYTHON_UNUSED int __pyx_skip_dispatch) {
  CYTHON_UNUSED int __pyx_v_length;
  int __pyx_v_min_dist;
  PyObject *__pyx_v_seqslist = 0;
  int __pyx_v_i;
  int __pyx_v_j;
  int __pyx_v_dist;
  int __pyx_v_iter;
  int __pyx_r;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  Py_ssize_t __pyx_t_5;
  int __pyx_t_6;
  Py_ssize_t __pyx_t_7;
  long __pyx_t_8;
  int __pyx_t_9;
  int __pyx_t_10;
  struct __pyx_opt_args_5taggd_4misc_16distance_metrics_hamming_distance __pyx_t_11;
  int __pyx_t_12;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("estimate_min_edit_distance", 0);

  /* "taggd/io/barcode_utils.pyx":49
 *     """
 * 
 *     cdef int length = 0             # <<<<<<<<<<<<<<
 *     cdef int min_dist = 1000000000
 *     cdef str ln
 */
  __pyx_v_length = 0;

  /* "taggd/io/barcode_utils.pyx":50
 * 
 *     cdef int length = 0
 *     cdef int min_dist = 1000000000             # <<<<<<<<<<<<<<
 *     cdef str ln
 *     cdef list tmp
 */
  __pyx_v_min_dist = 1000000000;

  /* "taggd/io/barcode_utils.pyx":56
 * 
 *     # Compute minimum edit distance.
 *     cdef list seqslist = true_barcodes.keys()             # <<<<<<<<<<<<<<
 *     random.shuffle(seqslist)
 *     cdef int i
 */
  if (unlikely(__pyx_v_true_barcodes == Py_None)) {
    PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_t_1 = __Pyx_PyDict_Keys(__pyx_v_true_barcodes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_v_seqslist = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "taggd/io/barcode_utils.pyx":57
 *     # Compute minimum edit distance.
 *     cdef list seqslist = true_barcodes.keys()
 *     random.shuffle(seqslist)             # <<<<<<<<<<<<<<
 *     cdef int i
 *     cdef int j
 */
  __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_random); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_shuffle); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = NULL;
  if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_3))) {
    __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
    if (likely(__pyx_t_2)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
      __Pyx_INCREF(__pyx_t_2);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_3, function);
    }
  }
  if (!__pyx_t_2) {
    __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_seqslist); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
  } else {
    __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_4);
    PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
    __Pyx_INCREF(__pyx_v_seqslist);
    PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_seqslist);
    __Pyx_GIVEREF(__pyx_v_seqslist);
    __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  }
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "taggd/io/barcode_utils.pyx":61
 *     cdef int j
 *     cdef int dist
 *     cdef int iter = 0             # <<<<<<<<<<<<<<
 *     for i in xrange(len(seqslist)):
 *         for j in xrange(int(i+1), len(seqslist)):
 */
  __pyx_v_iter = 0;

  /* "taggd/io/barcode_utils.pyx":62
 *     cdef int dist
 *     cdef int iter = 0
 *     for i in xrange(len(seqslist)):             # <<<<<<<<<<<<<<
 *         for j in xrange(int(i+1), len(seqslist)):
 *             dist = hamming_distance(seqslist[i], seqslist[j], min_dist)
 */
  if (unlikely(__pyx_v_seqslist == Py_None)) {
    PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  }
  __pyx_t_5 = PyList_GET_SIZE(__pyx_v_seqslist); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
    __pyx_v_i = __pyx_t_6;

    /* "taggd/io/barcode_utils.pyx":63
 *     cdef int iter = 0
 *     for i in xrange(len(seqslist)):
 *         for j in xrange(int(i+1), len(seqslist)):             # <<<<<<<<<<<<<<
 *             dist = hamming_distance(seqslist[i], seqslist[j], min_dist)
 *             if dist < min_dist:
 */
    if (unlikely(__pyx_v_seqslist == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
    __pyx_t_7 = PyList_GET_SIZE(__pyx_v_seqslist); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __pyx_t_1 = __Pyx_PyInt_From_long((__pyx_v_i + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_3);
    PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
    __Pyx_GIVEREF(__pyx_t_1);
    __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    for (__pyx_t_9 = __pyx_t_8; __pyx_t_9 < __pyx_t_7; __pyx_t_9+=1) {
      __pyx_v_j = __pyx_t_9;

      /* "taggd/io/barcode_utils.pyx":64
 *     for i in xrange(len(seqslist)):
 *         for j in xrange(int(i+1), len(seqslist)):
 *             dist = hamming_distance(seqslist[i], seqslist[j], min_dist)             # <<<<<<<<<<<<<<
 *             if dist < min_dist:
 *                 min_dist = dist
 */
      if (unlikely(__pyx_v_seqslist == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      }
      __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_seqslist, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
      __Pyx_GOTREF(__pyx_t_1);
      if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      if (unlikely(__pyx_v_seqslist == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      }
      __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_seqslist, __pyx_v_j, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
      __Pyx_GOTREF(__pyx_t_3);
      if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
      __pyx_t_11.__pyx_n = 1;
      __pyx_t_11.limit = __pyx_v_min_dist;
      __pyx_t_10 = __pyx_f_5taggd_4misc_16distance_metrics_hamming_distance(((PyObject*)__pyx_t_1), ((PyObject*)__pyx_t_3), &__pyx_t_11); 
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_v_dist = __pyx_t_10;

      /* "taggd/io/barcode_utils.pyx":65
 *         for j in xrange(int(i+1), len(seqslist)):
 *             dist = hamming_distance(seqslist[i], seqslist[j], min_dist)
 *             if dist < min_dist:             # <<<<<<<<<<<<<<
 *                 min_dist = dist
 *             iter += 1
 */
      __pyx_t_12 = ((__pyx_v_dist < __pyx_v_min_dist) != 0);
      if (__pyx_t_12) {

        /* "taggd/io/barcode_utils.pyx":66
 *             dist = hamming_distance(seqslist[i], seqslist[j], min_dist)
 *             if dist < min_dist:
 *                 min_dist = dist             # <<<<<<<<<<<<<<
 *             iter += 1
 *             if iter >= max_iters:
 */
        __pyx_v_min_dist = __pyx_v_dist;
        goto __pyx_L7;
      }
      __pyx_L7:;

      /* "taggd/io/barcode_utils.pyx":67
 *             if dist < min_dist:
 *                 min_dist = dist
 *             iter += 1             # <<<<<<<<<<<<<<
 *             if iter >= max_iters:
 *                 return min_dist
 */
      __pyx_v_iter = (__pyx_v_iter + 1);

      /* "taggd/io/barcode_utils.pyx":68
 *                 min_dist = dist
 *             iter += 1
 *             if iter >= max_iters:             # <<<<<<<<<<<<<<
 *                 return min_dist
 *             #print str(i) + " vs " + str(j) + ": " + str(dist)
 */
      __pyx_t_12 = ((__pyx_v_iter >= __pyx_v_max_iters) != 0);
      if (__pyx_t_12) {

        /* "taggd/io/barcode_utils.pyx":69
 *             iter += 1
 *             if iter >= max_iters:
 *                 return min_dist             # <<<<<<<<<<<<<<
 *             #print str(i) + " vs " + str(j) + ": " + str(dist)
 *     return min_dist
 */
        __pyx_r = __pyx_v_min_dist;
        goto __pyx_L0;
      }
    }
  }

  /* "taggd/io/barcode_utils.pyx":71
 *                 return min_dist
 *             #print str(i) + " vs " + str(j) + ": " + str(dist)
 *     return min_dist             # <<<<<<<<<<<<<<
 */
  __pyx_r = __pyx_v_min_dist;
  goto __pyx_L0;

  /* "taggd/io/barcode_utils.pyx":43
 * 
 * 
 * cpdef int estimate_min_edit_distance(dict true_barcodes, int max_iters):             # <<<<<<<<<<<<<<
 *     """
 *     Reads a barcodes dict and estimates the minimum edit distance
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  __Pyx_WriteUnraisable("taggd.io.barcode_utils.estimate_min_edit_distance", __pyx_clineno, __pyx_lineno, __pyx_filename, 0);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_seqslist);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_3estimate_min_edit_distance(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_5taggd_2io_13barcode_utils_2estimate_min_edit_distance[] = "\n    Reads a barcodes dict and estimates the minimum edit distance\n    by comparing a certain number of pairs.\n    ";
static PyObject *__pyx_pw_5taggd_2io_13barcode_utils_3estimate_min_edit_distance(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_true_barcodes = 0;
  int __pyx_v_max_iters;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("estimate_min_edit_distance (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_true_barcodes,&__pyx_n_s_max_iters,0};
    PyObject* values[2] = {0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        case  0: break;
        default: goto __pyx_L5_argtuple_error;
      }
      kw_args = PyDict_Size(__pyx_kwds);
      switch (pos_args) {
        case  0:
        if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_true_barcodes)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_max_iters)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("estimate_min_edit_distance", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "estimate_min_edit_distance") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
      }
    } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
      goto __pyx_L5_argtuple_error;
    } else {
      values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
      values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
    }
    __pyx_v_true_barcodes = ((PyObject*)values[0]);
    __pyx_v_max_iters = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_max_iters == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("estimate_min_edit_distance", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
  __pyx_L3_error:;
  __Pyx_AddTraceback("taggd.io.barcode_utils.estimate_min_edit_distance", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_true_barcodes), (&PyDict_Type), 1, "true_barcodes", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_r = __pyx_pf_5taggd_2io_13barcode_utils_2estimate_min_edit_distance(__pyx_self, __pyx_v_true_barcodes, __pyx_v_max_iters);

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

static PyObject *__pyx_pf_5taggd_2io_13barcode_utils_2estimate_min_edit_distance(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_true_barcodes, int __pyx_v_max_iters) {
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannySetupContext("estimate_min_edit_distance", 0);
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_f_5taggd_2io_13barcode_utils_estimate_min_edit_distance(__pyx_v_true_barcodes, __pyx_v_max_iters, 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_r = __pyx_t_1;
  __pyx_t_1 = 0;
  goto __pyx_L0;

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_AddTraceback("taggd.io.barcode_utils.estimate_min_edit_distance", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyObject *__pyx_tp_new_5taggd_2io_13barcode_utils_Barcode(PyTypeObject *t, PyObject *a, PyObject *k) {
  struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *p;
  PyObject *o;
  if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
    o = (*t->tp_alloc)(t, 0);
  } else {
    o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
  }
  if (unlikely(!o)) return 0;
  p = ((struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)o);
  p->sequence = ((PyObject*)Py_None); Py_INCREF(Py_None);
  p->attributes = ((PyObject*)Py_None); Py_INCREF(Py_None);
  if (unlikely(__pyx_pw_5taggd_2io_13barcode_utils_7Barcode_1__cinit__(o, a, k) < 0)) {
    Py_DECREF(o); o = 0;
  }
  return o;
}

static void __pyx_tp_dealloc_5taggd_2io_13barcode_utils_Barcode(PyObject *o) {
  struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *p = (struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)o;
  #if PY_VERSION_HEX >= 0x030400a1
  if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
    if (PyObject_CallFinalizerFromDealloc(o)) return;
  }
  #endif
  PyObject_GC_UnTrack(o);
  Py_CLEAR(p->sequence);
  Py_CLEAR(p->attributes);
  (*Py_TYPE(o)->tp_free)(o);
}

static int __pyx_tp_traverse_5taggd_2io_13barcode_utils_Barcode(PyObject *o, visitproc v, void *a) {
  int e;
  struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *p = (struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)o;
  if (p->attributes) {
    e = (*v)(p->attributes, a); if (e) return e;
  }
  return 0;
}

static int __pyx_tp_clear_5taggd_2io_13barcode_utils_Barcode(PyObject *o) {
  PyObject* tmp;
  struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *p = (struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode *)o;
  tmp = ((PyObject*)p->attributes);
  p->attributes = ((PyObject*)Py_None); Py_INCREF(Py_None);
  Py_XDECREF(tmp);
  return 0;
}

static PyObject *__pyx_getprop_5taggd_2io_13barcode_utils_7Barcode_sequence(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_1__get__(o);
}

static int __pyx_setprop_5taggd_2io_13barcode_utils_7Barcode_sequence(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
  if (v) {
    return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_3__set__(o, v);
  }
  else {
    return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_8sequence_5__del__(o);
  }
}

static PyObject *__pyx_getprop_5taggd_2io_13barcode_utils_7Barcode_attributes(PyObject *o, CYTHON_UNUSED void *x) {
  return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_1__get__(o);
}

static int __pyx_setprop_5taggd_2io_13barcode_utils_7Barcode_attributes(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
  if (v) {
    return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_3__set__(o, v);
  }
  else {
    return __pyx_pw_5taggd_2io_13barcode_utils_7Barcode_10attributes_5__del__(o);
  }
}

static PyMethodDef __pyx_methods_5taggd_2io_13barcode_utils_Barcode[] = {
  {0, 0, 0, 0}
};

static struct PyGetSetDef __pyx_getsets_5taggd_2io_13barcode_utils_Barcode[] = {
  {(char *)"sequence", __pyx_getprop_5taggd_2io_13barcode_utils_7Barcode_sequence, __pyx_setprop_5taggd_2io_13barcode_utils_7Barcode_sequence, 0, 0},
  {(char *)"attributes", __pyx_getprop_5taggd_2io_13barcode_utils_7Barcode_attributes, __pyx_setprop_5taggd_2io_13barcode_utils_7Barcode_attributes, 0, 0},
  {0, 0, 0, 0, 0}
};

static PyTypeObject __pyx_type_5taggd_2io_13barcode_utils_Barcode = {
  PyVarObject_HEAD_INIT(0, 0)
  "taggd.io.barcode_utils.Barcode", /*tp_name*/
  sizeof(struct __pyx_obj_5taggd_2io_13barcode_utils_Barcode), /*tp_basicsize*/
  0, /*tp_itemsize*/
  __pyx_tp_dealloc_5taggd_2io_13barcode_utils_Barcode, /*tp_dealloc*/
  0, /*tp_print*/
  0, /*tp_getattr*/
  0, /*tp_setattr*/
  #if PY_MAJOR_VERSION < 3
  0, /*tp_compare*/
  #else
  0, /*reserved*/
  #endif
  0, /*tp_repr*/
  0, /*tp_as_number*/
  0, /*tp_as_sequence*/
  0, /*tp_as_mapping*/
  0, /*tp_hash*/
  0, /*tp_call*/
  0, /*tp_str*/
  0, /*tp_getattro*/
  0, /*tp_setattro*/
  0, /*tp_as_buffer*/
  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
  "\n    Holds a Spatial Transcriptomics barcode sequence and feature coordinates.\n    ", /*tp_doc*/
  __pyx_tp_traverse_5taggd_2io_13barcode_utils_Barcode, /*tp_traverse*/
  __pyx_tp_clear_5taggd_2io_13barcode_utils_Barcode, /*tp_clear*/
  0, /*tp_richcompare*/
  0, /*tp_weaklistoffset*/
  0, /*tp_iter*/
  0, /*tp_iternext*/
  __pyx_methods_5taggd_2io_13barcode_utils_Barcode, /*tp_methods*/
  0, /*tp_members*/
  __pyx_getsets_5taggd_2io_13barcode_utils_Barcode, /*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_5taggd_2io_13barcode_utils_Barcode, /*tp_new*/
  0, /*tp_free*/
  0, /*tp_is_gc*/
  0, /*tp_bases*/
  0, /*tp_mro*/
  0, /*tp_cache*/
  0, /*tp_subclasses*/
  0, /*tp_weaklist*/
  0, /*tp_del*/
  0, /*tp_version_tag*/
  #if PY_VERSION_HEX >= 0x030400a1
  0, /*tp_finalize*/
  #endif
};

static PyMethodDef __pyx_methods[] = {
  {"read_barcode_file", (PyCFunction)__pyx_pw_5taggd_2io_13barcode_utils_1read_barcode_file, METH_O, __pyx_doc_5taggd_2io_13barcode_utils_read_barcode_file},
  {"estimate_min_edit_distance", (PyCFunction)__pyx_pw_5taggd_2io_13barcode_utils_3estimate_min_edit_distance, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5taggd_2io_13barcode_utils_2estimate_min_edit_distance},
  {0, 0, 0, 0}
};

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

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_kp_s_Barcode_file_incorrect_duplicate, __pyx_k_Barcode_file_incorrect_duplicate, sizeof(__pyx_k_Barcode_file_incorrect_duplicate), 0, 0, 1, 0},
  {&__pyx_kp_s_Barcode_file_incorrect_varying_l, __pyx_k_Barcode_file_incorrect_varying_l, sizeof(__pyx_k_Barcode_file_incorrect_varying_l), 0, 0, 1, 0},
  {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
  {&__pyx_n_s_attributes, __pyx_k_attributes, sizeof(__pyx_k_attributes), 0, 0, 1, 1},
  {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1},
  {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1},
  {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
  {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1},
  {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_max_iters, __pyx_k_max_iters, sizeof(__pyx_k_max_iters), 0, 0, 1, 1},
  {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1},
  {&__pyx_n_s_random, __pyx_k_random, sizeof(__pyx_k_random), 0, 0, 1, 1},
  {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
  {&__pyx_n_s_seq, __pyx_k_seq, sizeof(__pyx_k_seq), 0, 0, 1, 1},
  {&__pyx_n_s_shuffle, __pyx_k_shuffle, sizeof(__pyx_k_shuffle), 0, 0, 1, 1},
  {&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1},
  {&__pyx_n_s_strip, __pyx_k_strip, sizeof(__pyx_k_strip), 0, 0, 1, 1},
  {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_true_barcodes, __pyx_k_true_barcodes, sizeof(__pyx_k_true_barcodes), 0, 0, 1, 1},
  {&__pyx_n_s_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #if PY_MAJOR_VERSION >= 3
  __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #else
  __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  return 0;
  __pyx_L1_error:;
  return -1;
}

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

  /* "taggd/io/barcode_utils.pyx":36
 *                 length = len(seq)
 *             if len(seq) != length:
 *                 raise ValueError("Barcode file incorrect, varying lengths among barcodes")             # <<<<<<<<<<<<<<
 *             if seq in res_dict:
 *                 raise ValueError("Barcode file incorrect, duplicate barcode: " + seq)
 */
  __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_s_Barcode_file_incorrect_varying_l); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_tuple_);
  __Pyx_GIVEREF(__pyx_tuple_);

  /* "taggd/io/barcode_utils.pyx":29
 *     cdef str seq
 *     cdef int length = 0
 *     with open(infile_path) as infile:             # <<<<<<<<<<<<<<
 *         for line in infile:
 *             tmp = line.strip().split()
 */
  __pyx_tuple__2 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_tuple__2);
  __Pyx_GIVEREF(__pyx_tuple__2);
  __Pyx_RefNannyFinishContext();
  return 0;
  __pyx_L1_error:;
  __Pyx_RefNannyFinishContext();
  return -1;
}

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

#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC initbarcode_utils(void); /*proto*/
PyMODINIT_FUNC initbarcode_utils(void)
#else
PyMODINIT_FUNC PyInit_barcode_utils(void); /*proto*/
PyMODINIT_FUNC PyInit_barcode_utils(void)
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_lineno = 0;
  const char *__pyx_filename = NULL;
  int __pyx_clineno = 0;
  __Pyx_RefNannyDeclarations
  #if CYTHON_REFNANNY
  __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
  if (!__Pyx_RefNanny) {
      PyErr_Clear();
      __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
      if (!__Pyx_RefNanny)
          Py_FatalError("failed to import 'refnanny' module");
  }
  #endif
  __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_barcode_utils(void)", 0);
  if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #ifdef __Pyx_CyFunction_USED
  if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  #ifdef WITH_THREAD /* Python build with threading support? */
  PyEval_InitThreads();
  #endif
  #endif
  /*--- Module creation code ---*/
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4("barcode_utils", __pyx_methods, __pyx_k_Contains_utilities_for_handling, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  /*--- Initialize various global constants etc. ---*/
  if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
  if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  #endif
  if (__pyx_module_is_main_taggd__io__barcode_utils) {
    if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    if (!PyDict_GetItemString(modules, "taggd.io.barcode_utils")) {
      if (unlikely(PyDict_SetItemString(modules, "taggd.io.barcode_utils", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Constants init code ---*/
  if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Global init code ---*/
  /*--- Variable export code ---*/
  /*--- Function export code ---*/
  if (__Pyx_ExportFunction("read_barcode_file", (void (*)(void))__pyx_f_5taggd_2io_13barcode_utils_read_barcode_file, "PyObject *(PyObject *, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ExportFunction("estimate_min_edit_distance", (void (*)(void))__pyx_f_5taggd_2io_13barcode_utils_estimate_min_edit_distance, "int (PyObject *, int, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Type init code ---*/
  if (PyType_Ready(&__pyx_type_5taggd_2io_13barcode_utils_Barcode) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_type_5taggd_2io_13barcode_utils_Barcode.tp_print = 0;
  if (PyObject_SetAttrString(__pyx_m, "Barcode", (PyObject *)&__pyx_type_5taggd_2io_13barcode_utils_Barcode) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_5taggd_2io_13barcode_utils_Barcode = &__pyx_type_5taggd_2io_13barcode_utils_Barcode;
  /*--- Type import code ---*/
  __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", 
  #if CYTHON_COMPILING_IN_PYPY
  sizeof(PyTypeObject),
  #else
  sizeof(PyHeapTypeObject),
  #endif
  0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  /*--- Variable import code ---*/
  /*--- Function import code ---*/
  __pyx_t_1 = __Pyx_ImportModule("taggd.misc.distance_metrics"); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  if (__Pyx_ImportFunction(__pyx_t_1, "hamming_distance", (void (**)(void))&__pyx_f_5taggd_4misc_16distance_metrics_hamming_distance, "int (PyObject *, PyObject *, struct __pyx_opt_args_5taggd_4misc_16distance_metrics_hamming_distance *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  /*--- Execution code ---*/

  /* "taggd/io/barcode_utils.pyx":6
 * 
 * from taggd.misc.distance_metrics cimport *
 * import random             # <<<<<<<<<<<<<<
 * 
 * cdef class Barcode:
 */
  __pyx_t_2 = __Pyx_Import(__pyx_n_s_random, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_random, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "taggd/io/barcode_utils.pyx":1
 * """             # <<<<<<<<<<<<<<
 * Contains utilities for handling barcodes.
 * """
 */
  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_GOTREF(__pyx_t_2);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

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

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init taggd.io.barcode_utils", __pyx_clineno, __pyx_lineno, __pyx_filename);
      Py_DECREF(__pyx_d); __pyx_d = 0;
    }
    Py_DECREF(__pyx_m); __pyx_m = 0;
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init taggd.io.barcode_utils");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if PY_MAJOR_VERSION < 3
  return;
  #else
  return __pyx_m;
  #endif
}

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

static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
    PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
    if (unlikely(!result)) {
        PyErr_Format(PyExc_NameError,
#if PY_MAJOR_VERSION >= 3
            "name '%U' is not defined", name);
#else
            "name '%.200s' is not defined", PyString_AS_STRING(name));
#endif
    }
    return result;
}

static void __Pyx_RaiseArgtupleInvalid(
    const char* func_name,
    int exact,
    Py_ssize_t num_min,
    Py_ssize_t num_max,
    Py_ssize_t num_found)
{
    Py_ssize_t num_expected;
    const char *more_or_less;
    if (num_found < num_min) {
        num_expected = num_min;
        more_or_less = "at least";
    } else {
        num_expected = num_max;
        more_or_less = "at most";
    }
    if (exact) {
        more_or_less = "exactly";
    }
    PyErr_Format(PyExc_TypeError,
                 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                 func_name, more_or_less, num_expected,
                 (num_expected == 1) ? "" : "s", num_found);
}

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

static int __Pyx_ParseOptionalKeywords(
    PyObject *kwds,
    PyObject **argnames[],
    PyObject *kwds2,
    PyObject *values[],
    Py_ssize_t num_pos_args,
    const char* function_name)
{
    PyObject *key = 0, *value = 0;
    Py_ssize_t pos = 0;
    PyObject*** name;
    PyObject*** first_kw_arg = argnames + num_pos_args;
    while (PyDict_Next(kwds, &pos, &key, &value)) {
        name = first_kw_arg;
        while (*name && (**name != key)) name++;
        if (*name) {
            values[name-argnames] = value;
            continue;
        }
        name = first_kw_arg;
        #if PY_MAJOR_VERSION < 3
        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
            while (*name) {
                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
                        && _PyString_Eq(**name, key)) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    if ((**argname == key) || (
                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
                             && _PyString_Eq(**argname, key))) {
                        goto arg_passed_twice;
                    }
                    argname++;
                }
            }
        } else
        #endif
        if (likely(PyUnicode_Check(key))) {
            while (*name) {
                int cmp = (**name == key) ? 0 :
                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                #endif
                    PyUnicode_Compare(**name, key);
                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                if (cmp == 0) {
                    values[name-argnames] = value;
                    break;
                }
                name++;
            }
            if (*name) continue;
            else {
                PyObject*** argname = argnames;
                while (argname != first_kw_arg) {
                    int cmp = (**argname == key) ? 0 :
                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                    #endif
                        PyUnicode_Compare(**argname, key);
                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
                    if (cmp == 0) goto arg_passed_twice;
                    argname++;
                }
            }
        } else
            goto invalid_keyword_type;
        if (kwds2) {
            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
        } else {
            goto invalid_keyword;
        }
    }
    return 0;
arg_passed_twice:
    __Pyx_RaiseDoubleKeywordsError(function_name, key);
    goto bad;
invalid_keyword_type:
    PyErr_Format(PyExc_TypeError,
        "%.200s() keywords must be strings", function_name);
    goto bad;
invalid_keyword:
    PyErr_Format(PyExc_TypeError,
    #if PY_MAJOR_VERSION < 3
        "%.200s() got an unexpected keyword argument '%.200s'",
        function_name, PyString_AsString(key));
    #else
        "%s() got an unexpected keyword argument '%U'",
        function_name, key);
    #endif
bad:
    return -1;
}

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

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

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

#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_New(1);
    if (unlikely(!args)) return NULL;
    Py_INCREF(arg);
    PyTuple_SET_ITEM(args, 0, arg);
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
#ifdef __Pyx_CyFunction_USED
    if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
    if (likely(PyCFunction_Check(func))) {
#endif
        if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
            return __Pyx_PyObject_CallMethO(func, arg);
        }
    }
    return __Pyx__PyObject_CallOneArg(func, arg);
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject* args = PyTuple_Pack(1, arg);
    return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
}
#endif

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
#ifdef __Pyx_CyFunction_USED
    if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
    if (likely(PyCFunction_Check(func))) {
#endif
        if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) {
            return __Pyx_PyObject_CallMethO(func, NULL);
        }
    }
    return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL);
}
#endif

static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
    PyObject *r;
    if (!j) return NULL;
    r = PyObject_GetItem(o, j);
    Py_DECREF(j);
    return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
    if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
        PyObject *r = PyList_GET_ITEM(o, i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
                                                              int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
    if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
        PyObject *r = PyTuple_GET_ITEM(o, i);
        Py_INCREF(r);
        return r;
    }
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
#else
    return PySequence_GetItem(o, i);
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                     int is_list, int wraparound, int boundscheck) {
#if CYTHON_COMPILING_IN_CPYTHON
    if (is_list || PyList_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
        if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
            PyObject *r = PyList_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    }
    else if (PyTuple_CheckExact(o)) {
        Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
        if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
            PyObject *r = PyTuple_GET_ITEM(o, n);
            Py_INCREF(r);
            return r;
        }
    } else {
        PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
        if (likely(m && m->sq_item)) {
            if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
                Py_ssize_t l = m->sq_length(o);
                if (likely(l >= 0)) {
                    i += l;
                } else {
                    if (PyErr_ExceptionMatches(PyExc_OverflowError))
                        PyErr_Clear();
                    else
                        return NULL;
                }
            }
            return m->sq_item(o, i);
        }
    }
#else
    if (is_list || PySequence_Check(o)) {
        return PySequence_GetItem(o, i);
    }
#endif
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}

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

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

#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE void __Pyx_crop_slice(Py_ssize_t* _start, Py_ssize_t* _stop, Py_ssize_t* _length) {
    Py_ssize_t start = *_start, stop = *_stop, length = *_length;
    if (start < 0) {
        start += length;
        if (start < 0)
            start = 0;
    }
    if (stop < 0)
        stop += length;
    else if (stop > length)
        stop = length;
    *_length = stop - start;
    *_start = start;
    *_stop = stop;
}
static CYTHON_INLINE void __Pyx_copy_object_array(PyObject** CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
    PyObject *v;
    Py_ssize_t i;
    for (i = 0; i < length; i++) {
        v = dest[i] = src[i];
        Py_INCREF(v);
    }
}
static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(
            PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
    PyObject* dest;
    Py_ssize_t length = PyList_GET_SIZE(src);
    __Pyx_crop_slice(&start, &stop, &length);
    if (unlikely(length <= 0))
        return PyList_New(0);
    dest = PyList_New(length);
    if (unlikely(!dest))
        return NULL;
    __Pyx_copy_object_array(
        ((PyListObject*)src)->ob_item + start,
        ((PyListObject*)dest)->ob_item,
        length);
    return dest;
}
static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(
            PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
    PyObject* dest;
    Py_ssize_t length = PyTuple_GET_SIZE(src);
    __Pyx_crop_slice(&start, &stop, &length);
    if (unlikely(length <= 0))
        return PyTuple_New(0);
    dest = PyTuple_New(length);
    if (unlikely(!dest))
        return NULL;
    __Pyx_copy_object_array(
        ((PyTupleObject*)src)->ob_item + start,
        ((PyTupleObject*)dest)->ob_item,
        length);
    return dest;
}
#endif

static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyThreadState *tstate = PyThreadState_GET();
    *type = tstate->exc_type;
    *value = tstate->exc_value;
    *tb = tstate->exc_traceback;
    Py_XINCREF(*type);
    Py_XINCREF(*value);
    Py_XINCREF(*tb);
#else
    PyErr_GetExcInfo(type, value, tb);
#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyThreadState *tstate = PyThreadState_GET();
    tmp_type = tstate->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = type;
    tstate->exc_value = value;
    tstate->exc_traceback = tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
#else
    PyErr_SetExcInfo(type, value, tb);
#endif
}

static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
    PyObject *local_type, *local_value, *local_tb;
#if CYTHON_COMPILING_IN_CPYTHON
    PyObject *tmp_type, *tmp_value, *tmp_tb;
    PyThreadState *tstate = PyThreadState_GET();
    local_type = tstate->curexc_type;
    local_value = tstate->curexc_value;
    local_tb = tstate->curexc_traceback;
    tstate->curexc_type = 0;
    tstate->curexc_value = 0;
    tstate->curexc_traceback = 0;
#else
    PyErr_Fetch(&local_type, &local_value, &local_tb);
#endif
    PyErr_NormalizeException(&local_type, &local_value, &local_tb);
#if CYTHON_COMPILING_IN_CPYTHON
    if (unlikely(tstate->curexc_type))
#else
    if (unlikely(PyErr_Occurred()))
#endif
        goto bad;
    #if PY_MAJOR_VERSION >= 3
    if (local_tb) {
        if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
            goto bad;
    }
    #endif
    Py_XINCREF(local_tb);
    Py_XINCREF(local_type);
    Py_XINCREF(local_value);
    *type = local_type;
    *value = local_value;
    *tb = local_tb;
#if CYTHON_COMPILING_IN_CPYTHON
    tmp_type = tstate->exc_type;
    tmp_value = tstate->exc_value;
    tmp_tb = tstate->exc_traceback;
    tstate->exc_type = local_type;
    tstate->exc_value = local_value;
    tstate->exc_traceback = local_tb;
    Py_XDECREF(tmp_type);
    Py_XDECREF(tmp_value);
    Py_XDECREF(tmp_tb);
#else
    PyErr_SetExcInfo(local_type, local_value, local_tb);
#endif
    return 0;
bad:
    *type = 0;
    *value = 0;
    *tb = 0;
    Py_XDECREF(local_type);
    Py_XDECREF(local_value);
    Py_XDECREF(local_tb);
    return -1;
}

static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
    PyObject *method, *result = NULL;
    method = __Pyx_PyObject_GetAttrStr(obj, method_name);
    if (unlikely(!method)) goto bad;
#if CYTHON_COMPILING_IN_CPYTHON
    if (likely(PyMethod_Check(method))) {
        PyObject *self = PyMethod_GET_SELF(method);
        if (likely(self)) {
            PyObject *args;
            PyObject *function = PyMethod_GET_FUNCTION(method);
            args = PyTuple_New(2);
            if (unlikely(!args)) goto bad;
            Py_INCREF(self);
            PyTuple_SET_ITEM(args, 0, self);
            Py_INCREF(arg);
            PyTuple_SET_ITEM(args, 1, arg);
            Py_INCREF(function);
            Py_DECREF(method); method = NULL;
            result = __Pyx_PyObject_Call(function, args, NULL);
            Py_DECREF(args);
            Py_DECREF(function);
            return result;
        }
    }
#endif
    result = __Pyx_PyObject_CallOneArg(method, arg);
bad:
    Py_XDECREF(method);
    return result;
}

static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) {
    if (PY_MAJOR_VERSION >= 3)
        return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d);
    else
        return PyDict_Keys(d);
}

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

static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
                                  int full_traceback) {
    PyObject *old_exc, *old_val, *old_tb;
    PyObject *ctx;
    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
    if (full_traceback) {
        Py_XINCREF(old_exc);
        Py_XINCREF(old_val);
        Py_XINCREF(old_tb);
        __Pyx_ErrRestore(old_exc, old_val, old_tb);
        PyErr_PrintEx(1);
    }
    #if PY_MAJOR_VERSION < 3
    ctx = PyString_FromString(name);
    #else
    ctx = PyUnicode_FromString(name);
    #endif
    __Pyx_ErrRestore(old_exc, old_val, old_tb);
    if (!ctx) {
        PyErr_WriteUnraisable(Py_None);
    } else {
        PyErr_WriteUnraisable(ctx);
        Py_DECREF(ctx);
    }
}

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

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

static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
    PyObject *empty_list = 0;
    PyObject *module = 0;
    PyObject *global_dict = 0;
    PyObject *empty_dict = 0;
    PyObject *list;
    #if PY_VERSION_HEX < 0x03030000
    PyObject *py_import;
    py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
    if (!py_import)
        goto bad;
    #endif
    if (from_list)
        list = from_list;
    else {
        empty_list = PyList_New(0);
        if (!empty_list)
            goto bad;
        list = empty_list;
    }
    global_dict = PyModule_GetDict(__pyx_m);
    if (!global_dict)
        goto bad;
    empty_dict = PyDict_New();
    if (!empty_dict)
        goto bad;
    {
        #if PY_MAJOR_VERSION >= 3
        if (level == -1) {
            if (strchr(__Pyx_MODULE_NAME, '.')) {
                #if PY_VERSION_HEX < 0x03030000
                PyObject *py_level = PyInt_FromLong(1);
                if (!py_level)
                    goto bad;
                module = PyObject_CallFunctionObjArgs(py_import,
                    name, global_dict, empty_dict, list, py_level, NULL);
                Py_DECREF(py_level);
                #else
                module = PyImport_ImportModuleLevelObject(
                    name, global_dict, empty_dict, list, 1);
                #endif
                if (!module) {
                    if (!PyErr_ExceptionMatches(PyExc_ImportError))
                        goto bad;
                    PyErr_Clear();
                }
            }
            level = 0;
        }
        #endif
        if (!module) {
            #if PY_VERSION_HEX < 0x03030000
            PyObject *py_level = PyInt_FromLong(level);
            if (!py_level)
                goto bad;
            module = PyObject_CallFunctionObjArgs(py_import,
                name, global_dict, empty_dict, list, py_level, NULL);
            Py_DECREF(py_level);
            #else
            module = PyImport_ImportModuleLevelObject(
                name, global_dict, empty_dict, list, level);
            #endif
        }
    }
bad:
    #if PY_VERSION_HEX < 0x03030000
    Py_XDECREF(py_import);
    #endif
    Py_XDECREF(empty_list);
    Py_XDECREF(empty_dict);
    return module;
}

#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)       \
    {                                                                     \
        func_type value = func_value;                                     \
        if (sizeof(target_type) < sizeof(func_type)) {                    \
            if (unlikely(value != (func_type) (target_type) value)) {     \
                func_type zero = 0;                                       \
                if (is_unsigned && unlikely(value < zero))                \
                    goto raise_neg_overflow;                              \
                else                                                      \
                    goto raise_overflow;                                  \
            }                                                             \
        }                                                                 \
        return (target_type) value;                                       \
    }

#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
 #if CYTHON_USE_PYLONG_INTERNALS
  #include "longintrepr.h"
 #endif
#endif

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

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

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

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

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

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

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

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

#ifndef __PYX_HAVE_RT_ImportFunction
#define __PYX_HAVE_RT_ImportFunction
static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
    PyObject *d = 0;
    PyObject *cobj = 0;
    union {
        void (*fp)(void);
        void *p;
    } tmp;
    d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
    if (!d)
        goto bad;
    cobj = PyDict_GetItemString(d, funcname);
    if (!cobj) {
        PyErr_Format(PyExc_ImportError,
            "%.200s does not export expected C function %.200s",
                PyModule_GetName(module), funcname);
        goto bad;
    }
#if PY_VERSION_HEX >= 0x02070000
    if (!PyCapsule_IsValid(cobj, sig)) {
        PyErr_Format(PyExc_TypeError,
            "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
        goto bad;
    }
    tmp.p = PyCapsule_GetPointer(cobj, sig);
#else
    {const char *desc, *s1, *s2;
    desc = (const char *)PyCObject_GetDesc(cobj);
    if (!desc)
        goto bad;
    s1 = desc; s2 = sig;
    while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
    if (*s1 != *s2) {
        PyErr_Format(PyExc_TypeError,
            "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
             PyModule_GetName(module), funcname, sig, desc);
        goto bad;
    }
    tmp.p = PyCObject_AsVoidPtr(cobj);}
#endif
    *f = tmp.fp;
    if (!(*f))
        goto bad;
    Py_DECREF(d);
    return 0;
bad:
    Py_XDECREF(d);
    return -1;
}
#endif

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

static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
}
static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
    Py_ssize_t ignore;
    return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
    if (
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
            __Pyx_sys_getdefaultencoding_not_ascii &&
#endif
            PyUnicode_Check(o)) {
#if PY_VERSION_HEX < 0x03030000
        char* defenc_c;
        PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
        if (!defenc) return NULL;
        defenc_c = PyBytes_AS_STRING(defenc);
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
        {
            char* end = defenc_c + PyBytes_GET_SIZE(defenc);
            char* c;
            for (c = defenc_c; c < end; c++) {
                if ((unsigned char) (*c) >= 128) {
                    PyUnicode_AsASCIIString(o);
                    return NULL;
                }
            }
        }
#endif
        *length = PyBytes_GET_SIZE(defenc);
        return defenc_c;
#else
        if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
        if (PyUnicode_IS_ASCII(o)) {
            *length = PyUnicode_GET_LENGTH(o);
            return PyUnicode_AsUTF8(o);
        } else {
            PyUnicode_AsASCIIString(o);
            return NULL;
        }
#else
        return PyUnicode_AsUTF8AndSize(o, length);
#endif
#endif
    } else
#endif
#if !CYTHON_COMPILING_IN_PYPY
    if (PyByteArray_Check(o)) {
        *length = PyByteArray_GET_SIZE(o);
        return PyByteArray_AS_STRING(o);
    } else
#endif
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (unlikely(r < 0)) {
            return NULL;
        } else {
            return result;
        }
    }
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
  PyNumberMethods *m;
  const char *name = NULL;
  PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
  if (PyInt_Check(x) || PyLong_Check(x))
#else
  if (PyLong_Check(x))
#endif
    return Py_INCREF(x), x;
  m = Py_TYPE(x)->tp_as_number;
#if PY_MAJOR_VERSION < 3
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Int(x);
  }
  else if (m && m->nb_long) {
    name = "long";
    res = PyNumber_Long(x);
  }
#else
  if (m && m->nb_int) {
    name = "int";
    res = PyNumber_Long(x);
  }
#endif
  if (res) {
#if PY_MAJOR_VERSION < 3
    if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
    if (!PyLong_Check(res)) {
#endif
      PyErr_Format(PyExc_TypeError,
                   "__%.4s__ returned non-%.4s (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;
#if PY_MAJOR_VERSION < 3
  if (likely(PyInt_CheckExact(b)))
      return PyInt_AS_LONG(b);
#endif
  if (likely(PyLong_CheckExact(b))) {
    #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
     #if CYTHON_USE_PYLONG_INTERNALS
       switch (Py_SIZE(b)) {
       case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
       case  0: return 0;
       case  1: return ((PyLongObject*)b)->ob_digit[0];
       }
     #endif
    #endif
    return PyLong_AsSsize_t(b);
  }
  x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
    return PyInt_FromSize_t(ival);
}


#endif /* Py_PYTHON_H */
