/* Generated by Cython 0.24 */

/* BEGIN: Cython Metadata
{
    "distutils": {}
}
END: Cython Metadata */

#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
    #error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
    #error Cython requires Python 2.6+ or Python 3.2+.
#else
#define CYTHON_ABI "0_24"
#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 !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000
  #define CYTHON_USE_PYLONG_INTERNALS 1
#endif
#if CYTHON_USE_PYLONG_INTERNALS
  #include "longintrepr.h"
  #undef SHIFT
  #undef BASE
  #undef MASK
#endif
#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
  #define Py_OptimizeFlag 0
#endif
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
#if PY_MAJOR_VERSION < 3
  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyClass_Type
#else
  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
  #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
          PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
  #define __Pyx_DefaultClassType PyType_Type
#endif
#ifndef Py_TPFLAGS_CHECKTYPES
  #define Py_TPFLAGS_CHECKTYPES 0
#endif
#ifndef Py_TPFLAGS_HAVE_INDEX
  #define Py_TPFLAGS_HAVE_INDEX 0
#endif
#ifndef Py_TPFLAGS_HAVE_NEWBUFFER
  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
#ifndef Py_TPFLAGS_HAVE_FINALIZE
  #define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
#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)
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#else
  #define CYTHON_PEP393_ENABLED 0
  #define __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]))
  #define __Pyx_PyUnicode_IS_TRUE(u)      (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
  #define __Pyx_PyUnicode_Concat(a, b)      PyNumber_Add(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  PyNumber_Add(a, b)
#else
  #define __Pyx_PyUnicode_Concat(a, b)      PyUnicode_Concat(a, b)
  #define __Pyx_PyUnicode_ConcatSafe(a, b)  ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
      PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
  #define PyUnicode_Contains(u, s)  PySequence_Contains(u, s)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
  #define PyObject_Format(obj, fmt)  PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
  #define PyObject_Malloc(s)   PyMem_Malloc(s)
  #define PyObject_Free(p)     PyMem_Free(p)
  #define PyObject_Realloc(p)  PyMem_Realloc(p)
#endif
#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 && !defined(PyObject_ASCII)
  #define PyObject_ASCII(o)            PyObject_Repr(o)
#endif
#if PY_MAJOR_VERSION >= 3
  #define PyBaseString_Type            PyUnicode_Type
  #define PyStringObject               PyUnicodeObject
  #define PyString_Type                PyUnicode_Type
  #define PyString_Check               PyUnicode_Check
  #define PyString_CheckExact          PyUnicode_CheckExact
#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_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
  #ifndef PyUnicode_InternFromString
    #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
  #endif
#endif
#if PY_VERSION_HEX < 0x030200A4
  typedef long Py_hash_t;
  #define __Pyx_PyInt_FromHash_t PyInt_FromLong
  #define __Pyx_PyInt_AsHash_t   PyInt_AsLong
#else
  #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
  #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
  #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#else
  #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
#if PY_VERSION_HEX >= 0x030500B1
#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
typedef struct {
    unaryfunc am_await;
    unaryfunc am_aiter;
    unaryfunc am_anext;
} __Pyx_PyAsyncMethodsStruct;
#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
#else
#define __Pyx_PyType_AsAsync(obj) NULL
#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
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)

#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

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


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

#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

#define __PYX_HAVE__Mikado__scales__contrast
#define __PYX_HAVE_API__Mikado__scales__contrast
#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
#ifndef CYTHON_NCP_UNUSED
# if CYTHON_COMPILING_IN_CPYTHON
#  define CYTHON_NCP_UNUSED
# else
#  define CYTHON_NCP_UNUSED CYTHON_UNUSED
# endif
#endif
typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
                const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;

#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
#define __Pyx_uchar_cast(c) ((unsigned char)c)
#define __Pyx_long_cast(x) ((long)x)
#define __Pyx_fits_Py_ssize_t(v, type, is_signed)  (\
    (sizeof(type) < sizeof(Py_ssize_t))  ||\
    (sizeof(type) > sizeof(Py_ssize_t) &&\
          likely(v < (type)PY_SSIZE_T_MAX ||\
                 v == (type)PY_SSIZE_T_MAX)  &&\
          (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
                                v == (type)PY_SSIZE_T_MIN)))  ||\
    (sizeof(type) == sizeof(Py_ssize_t) &&\
          (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
                               v == (type)PY_SSIZE_T_MAX)))  )
#if defined (__cplusplus) && __cplusplus >= 201103L
    #include <cstdlib>
    #define __Pyx_sst_abs(value) std::abs(value)
#elif SIZEOF_INT >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) abs(value)
#elif SIZEOF_LONG >= SIZEOF_SIZE_T
    #define __Pyx_sst_abs(value) labs(value)
#elif defined (_MSC_VER) && defined (_M_X64)
    #define __Pyx_sst_abs(value) _abs64(value)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
    #define __Pyx_sst_abs(value) llabs(value)
#elif defined (__GNUC__)
    #define __Pyx_sst_abs(value) __builtin_llabs(value)
#else
    #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
#endif
static CYTHON_INLINE 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_FromCString(s)  __Pyx_PyObject_FromString((const char*)s)
#define __Pyx_PyBytes_FromCString(s)   __Pyx_PyBytes_FromString((const char*)s)
#define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
#define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
#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_NewRef(obj) (Py_INCREF(obj), obj)
#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(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
#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
#else
#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
#endif
#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
static int __Pyx_sys_getdefaultencoding_not_ascii;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    PyObject* ascii_chars_u = NULL;
    PyObject* ascii_chars_b = NULL;
    const char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    if (strcmp(default_encoding_c, "ascii") == 0) {
        __Pyx_sys_getdefaultencoding_not_ascii = 0;
    } else {
        char ascii_chars[128];
        int c;
        for (c = 0; c < 128; c++) {
            ascii_chars[c] = c;
        }
        __Pyx_sys_getdefaultencoding_not_ascii = 1;
        ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
        if (!ascii_chars_u) goto bad;
        ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
        if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
            PyErr_Format(
                PyExc_ValueError,
                "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
                default_encoding_c);
            goto bad;
        }
        Py_DECREF(ascii_chars_u);
        Py_DECREF(ascii_chars_b);
    }
    Py_DECREF(default_encoding);
    return 0;
bad:
    Py_XDECREF(default_encoding);
    Py_XDECREF(ascii_chars_u);
    Py_XDECREF(ascii_chars_b);
    return -1;
}
#endif
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
#else
#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
static char* __PYX_DEFAULT_STRING_ENCODING;
static int __Pyx_init_sys_getdefaultencoding_params(void) {
    PyObject* sys;
    PyObject* default_encoding = NULL;
    char* default_encoding_c;
    sys = PyImport_ImportModule("sys");
    if (!sys) goto bad;
    default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
    Py_DECREF(sys);
    if (!default_encoding) goto bad;
    default_encoding_c = PyBytes_AsString(default_encoding);
    if (!default_encoding_c) goto bad;
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
    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 PyObject *__pyx_empty_unicode;
static int __pyx_lineno;
static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;


static const char *__pyx_f[] = {
  "Mikado/scales/contrast.pyx",
};

/*--- Type declarations ---*/
struct __pyx_opt_args_6Mikado_9utilities_7overlap_overlap;

/* "utilities/overlap.pxd":1
 * cpdef long overlap(first, second, long flank=?, bint positive=?)             # <<<<<<<<<<<<<<
 * cdef long c_overlap(long start, long end, long ostart, long oend, long flank, bint positive)
 */
struct __pyx_opt_args_6Mikado_9utilities_7overlap_overlap {
  int __pyx_n;
  long flank;
  int positive;
};
struct __pyx_opt_args_6Mikado_6scales_8contrast_compare;

/* "Mikado/scales/contrast.pxd":1
 * cpdef tuple compare(prediction, reference, bint lenient=?)             # <<<<<<<<<<<<<<
 * cdef str __assign_multiexonic_ccode(prediction, reference, long nucl_overlap, double stats[9])
 * cdef str __assign_monoexonic_ccode(prediction, reference, long nucl_overlap, double stats[9])
 */
struct __pyx_opt_args_6Mikado_6scales_8contrast_compare {
  int __pyx_n;
  int lenient;
};

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

/* PyObjectGetAttrStr.proto */
#if CYTHON_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

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

/* Profile.proto */
#ifndef CYTHON_PROFILE
#if CYTHON_COMPILING_IN_PYPY
  #define CYTHON_PROFILE 0
#else
  #define CYTHON_PROFILE 1
#endif
#endif
#ifndef CYTHON_TRACE_NOGIL
  #define CYTHON_TRACE_NOGIL 0
#else
  #if CYTHON_TRACE_NOGIL && !defined(CYTHON_TRACE)
    #define CYTHON_TRACE 1
  #endif
#endif
#ifndef CYTHON_TRACE
  #define CYTHON_TRACE 0
#endif
#if CYTHON_TRACE
  #undef CYTHON_PROFILE_REUSE_FRAME
#endif
#ifndef CYTHON_PROFILE_REUSE_FRAME
  #define CYTHON_PROFILE_REUSE_FRAME 0
#endif
#if CYTHON_PROFILE || CYTHON_TRACE
  #include "compile.h"
  #include "frameobject.h"
  #include "traceback.h"
  #if CYTHON_PROFILE_REUSE_FRAME
    #define CYTHON_FRAME_MODIFIER static
    #define CYTHON_FRAME_DEL(frame)
  #else
    #define CYTHON_FRAME_MODIFIER
    #define CYTHON_FRAME_DEL(frame) Py_CLEAR(frame)
  #endif
  #define __Pyx_TraceDeclarations\
  static PyCodeObject *__pyx_frame_code = NULL;\
  CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL;\
  int __Pyx_use_tracing = 0;
  #define __Pyx_TraceFrameInit(codeobj)\
  if (codeobj) __pyx_frame_code = (PyCodeObject*) codeobj;
  #ifdef WITH_THREAD
  #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\
  if (nogil) {\
      if (CYTHON_TRACE_NOGIL) {\
          PyThreadState *tstate;\
          PyGILState_STATE state = PyGILState_Ensure();\
          tstate = PyThreadState_GET();\
          if (unlikely(tstate->use_tracing) && !tstate->tracing &&\
                  (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {\
              __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno);\
          }\
          PyGILState_Release(state);\
          if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
      }\
  } else {\
      PyThreadState* tstate = PyThreadState_GET();\
      if (unlikely(tstate->use_tracing) && !tstate->tracing &&\
              (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {\
          __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno);\
          if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
      }\
  }
  #else
  #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\
  {   PyThreadState* tstate = PyThreadState_GET();\
      if (unlikely(tstate->use_tracing) && !tstate->tracing &&\
              (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {\
          __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno);\
          if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
      }\
  }
  #endif
  #define __Pyx_TraceException()\
  if (likely(!__Pyx_use_tracing)); else {\
      PyThreadState* tstate = PyThreadState_GET();\
      if (tstate->use_tracing &&\
              (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {\
          tstate->tracing++;\
          tstate->use_tracing = 0;\
          PyObject *exc_info = __Pyx_GetExceptionTuple(tstate);\
          if (exc_info) {\
              if (CYTHON_TRACE && tstate->c_tracefunc)\
                  tstate->c_tracefunc(\
                      tstate->c_traceobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\
              tstate->c_profilefunc(\
                  tstate->c_profileobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\
              Py_DECREF(exc_info);\
          }\
          tstate->use_tracing = 1;\
          tstate->tracing--;\
      }\
  }
  static void __Pyx_call_return_trace_func(PyThreadState *tstate, PyFrameObject *frame, PyObject *result) {
      PyObject *type, *value, *traceback;
      PyErr_Fetch(&type, &value, &traceback);
      tstate->tracing++;
      tstate->use_tracing = 0;
      if (CYTHON_TRACE && tstate->c_tracefunc)
          tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_RETURN, result);
      if (tstate->c_profilefunc)
          tstate->c_profilefunc(tstate->c_profileobj, frame, PyTrace_RETURN, result);
      CYTHON_FRAME_DEL(frame);
      tstate->use_tracing = 1;
      tstate->tracing--;
      PyErr_Restore(type, value, traceback);
  }
  #ifdef WITH_THREAD
  #define __Pyx_TraceReturn(result, nogil)\
  if (likely(!__Pyx_use_tracing)); else {\
      if (nogil) {\
          if (CYTHON_TRACE_NOGIL) {\
              PyThreadState *tstate;\
              PyGILState_STATE state = PyGILState_Ensure();\
              tstate = PyThreadState_GET();\
              if (tstate->use_tracing) {\
                  __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
              }\
              PyGILState_Release(state);\
          }\
      } else {\
          PyThreadState* tstate = PyThreadState_GET();\
          if (tstate->use_tracing) {\
              __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
          }\
      }\
  }
  #else
  #define __Pyx_TraceReturn(result, nogil)\
  if (likely(!__Pyx_use_tracing)); else {\
      PyThreadState* tstate = PyThreadState_GET();\
      if (tstate->use_tracing) {\
          __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
      }\
  }
  #endif
  static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno);
  static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno);
#else
  #define __Pyx_TraceDeclarations
  #define __Pyx_TraceFrameInit(codeobj)
  #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)   if (1); else goto_error;
  #define __Pyx_TraceException()
  #define __Pyx_TraceReturn(result, nogil)
#endif
#if CYTHON_TRACE
  static int __Pyx_call_line_trace_func(PyThreadState *tstate, PyFrameObject *frame, int lineno) {
      int ret;
      PyObject *type, *value, *traceback;
      PyErr_Fetch(&type, &value, &traceback);
      frame->f_lineno = lineno;
      tstate->tracing++;
      tstate->use_tracing = 0;
      ret = tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_LINE, NULL);
      tstate->use_tracing = 1;
      tstate->tracing--;
      if (likely(!ret)) {
          PyErr_Restore(type, value, traceback);
      } else {
          Py_XDECREF(type);
          Py_XDECREF(value);
          Py_XDECREF(traceback);
      }
      return ret;
  }
  #ifdef WITH_THREAD
  #define __Pyx_TraceLine(lineno, nogil, goto_error)\
  if (likely(!__Pyx_use_tracing)); else {\
      if (nogil) {\
          if (CYTHON_TRACE_NOGIL) {\
              int ret = 0;\
              PyThreadState *tstate;\
              PyGILState_STATE state = PyGILState_Ensure();\
              tstate = PyThreadState_GET();\
              if (unlikely(tstate->use_tracing && tstate->c_tracefunc)) {\
                  ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
              }\
              PyGILState_Release(state);\
              if (unlikely(ret)) goto_error;\
          }\
      } else {\
          PyThreadState* tstate = PyThreadState_GET();\
          if (unlikely(tstate->use_tracing && tstate->c_tracefunc)) {\
              int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
              if (unlikely(ret)) goto_error;\
          }\
      }\
  }
  #else
  #define __Pyx_TraceLine(lineno, nogil, goto_error)\
  if (likely(!__Pyx_use_tracing)); else {\
      PyThreadState* tstate = PyThreadState_GET();\
      if (unlikely(tstate->use_tracing && tstate->c_tracefunc)) {\
          int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
          if (unlikely(ret)) goto_error;\
      }\
  }
  #endif
#else
  #define __Pyx_TraceLine(lineno, nogil, goto_error)   if (1); else goto_error;
#endif

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/* PyIntBinop.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\
    (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2))
#endif

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

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

/* PyThreadStateGet.proto */
#if CYTHON_COMPILING_IN_CPYTHON
#define __Pyx_PyThreadState_declare  PyThreadState *__pyx_tstate;
#define __Pyx_PyThreadState_assign  __pyx_tstate = PyThreadState_GET();
#else
#define __Pyx_PyThreadState_declare
#define __Pyx_PyThreadState_assign
#endif

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

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

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

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

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

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

/* ImportFrom.proto */
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);

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

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

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

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

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

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

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

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

/* PyIdentifierFromString.proto */
#if !defined(__Pyx_PyIdentifier_FromString)
#if PY_MAJOR_VERSION < 3
  #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
#else
  #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
#endif
#endif

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

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

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


/* Module declarations from 'Mikado.utilities.overlap' */
static long (*__pyx_f_6Mikado_9utilities_7overlap_c_overlap)(long, long, long, long, long, int); /*proto*/

/* Module declarations from 'Mikado.scales.f1' */
static double (*__pyx_f_6Mikado_6scales_2f1_calc_f1)(double, double, int __pyx_skip_dispatch); /*proto*/

/* Module declarations from 'cython' */

/* Module declarations from 'Mikado.scales.contrast' */
static PyObject *__pyx_f_6Mikado_6scales_8contrast_compare(PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_6Mikado_6scales_8contrast_compare *__pyx_optional_args); /*proto*/
static PyObject *__pyx_f_6Mikado_6scales_8contrast___assign_multiexonic_ccode(PyObject *, PyObject *, long, double *); /*proto*/
static PyObject *__pyx_f_6Mikado_6scales_8contrast___assign_monoexonic_ccode(PyObject *, PyObject *, long, double *); /*proto*/
static CYTHON_INLINE long __pyx_f_6Mikado_6scales_8contrast_long_max(long, long); /*proto*/
static CYTHON_INLINE double __pyx_f_6Mikado_6scales_8contrast_double_min(double, double); /*proto*/
#define __Pyx_MODULE_NAME "Mikado.scales.contrast"
int __pyx_module_is_main_Mikado__scales__contrast = 0;

/* Implementation of 'Mikado.scales.contrast' */
static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_min;
static PyObject *__pyx_builtin_round;
static PyObject *__pyx_builtin_ValueError;
static const char __pyx_k_[] = "";
static const char __pyx_k_C[] = "C";
static const char __pyx_k_G[] = "G";
static const char __pyx_k_I[] = "I";
static const char __pyx_k_J[] = "J";
static const char __pyx_k_P[] = "P";
static const char __pyx_k_X[] = "X";
static const char __pyx_k_c[] = "c";
static const char __pyx_k_e[] = "e";
static const char __pyx_k_g[] = "g";
static const char __pyx_k_h[] = "h";
static const char __pyx_k_i[] = "i";
static const char __pyx_k_j[] = "j";
static const char __pyx_k_m[] = "m";
static const char __pyx_k_n[] = "n";
static const char __pyx_k_o[] = "o";
static const char __pyx_k_p[] = "p";
static const char __pyx_k_u[] = "u";
static const char __pyx_k_x[] = "x";
static const char __pyx_k__2[] = "_";
static const char __pyx_k__3[] = "=";
static const char __pyx_k__4[] = ",";
static const char __pyx_k_id[] = "id";
static const char __pyx_k_rI[] = "rI";
static const char __pyx_k_ri[] = "ri";
static const char __pyx_k_end[] = "end";
static const char __pyx_k_max[] = "max";
static const char __pyx_k_min[] = "min";
static const char __pyx_k_copy[] = "copy";
static const char __pyx_k_join[] = "join";
static const char __pyx_k_loci[] = "loci";
static const char __pyx_k_main[] = "__main__";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_exons[] = "exons";
static const char __pyx_k_round[] = "round";
static const char __pyx_k_start[] = "start";
static const char __pyx_k_author[] = "__author__";
static const char __pyx_k_format[] = "format";
static const char __pyx_k_import[] = "__import__";
static const char __pyx_k_parent[] = "parent";
static const char __pyx_k_remove[] = "remove";
static const char __pyx_k_strand[] = "strand";
static const char __pyx_k_introns[] = "introns";
static const char __pyx_k_lenient[] = "lenient";
static const char __pyx_k_splices[] = "splices";
static const char __pyx_k_exon_num[] = "exon_num";
static const char __pyx_k_finalize[] = "finalize";
static const char __pyx_k_reference[] = "reference";
static const char __pyx_k_Transcript[] = "Transcript";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_prediction[] = "prediction";
static const char __pyx_k_cdna_length[] = "cdna_length";
static const char __pyx_k_ResultStorer[] = "ResultStorer";
static const char __pyx_k_intersection[] = "intersection";
static const char __pyx_k_resultstorer[] = "resultstorer";
static const char __pyx_k_Luca_Venturini[] = "Luca Venturini";
static const char __pyx_k_Ccode_is_null_0[] = "Ccode is null;\n{0}";
static PyObject *__pyx_kp_s_;
static PyObject *__pyx_n_s_C;
static PyObject *__pyx_kp_s_Ccode_is_null_0;
static PyObject *__pyx_n_s_G;
static PyObject *__pyx_n_s_I;
static PyObject *__pyx_n_s_J;
static PyObject *__pyx_kp_s_Luca_Venturini;
static PyObject *__pyx_n_s_P;
static PyObject *__pyx_n_s_ResultStorer;
static PyObject *__pyx_n_s_Transcript;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_n_s_X;
static PyObject *__pyx_n_s__2;
static PyObject *__pyx_kp_s__3;
static PyObject *__pyx_kp_s__4;
static PyObject *__pyx_n_s_author;
static PyObject *__pyx_n_s_c;
static PyObject *__pyx_n_s_cdna_length;
static PyObject *__pyx_n_s_copy;
static PyObject *__pyx_n_s_e;
static PyObject *__pyx_n_s_end;
static PyObject *__pyx_n_s_exon_num;
static PyObject *__pyx_n_s_exons;
static PyObject *__pyx_n_s_finalize;
static PyObject *__pyx_n_s_format;
static PyObject *__pyx_n_s_g;
static PyObject *__pyx_n_s_h;
static PyObject *__pyx_n_s_i;
static PyObject *__pyx_n_s_id;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_intersection;
static PyObject *__pyx_n_s_introns;
static PyObject *__pyx_n_s_j;
static PyObject *__pyx_n_s_join;
static PyObject *__pyx_n_s_lenient;
static PyObject *__pyx_n_s_loci;
static PyObject *__pyx_n_s_m;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_max;
static PyObject *__pyx_n_s_min;
static PyObject *__pyx_n_s_n;
static PyObject *__pyx_n_s_o;
static PyObject *__pyx_n_s_p;
static PyObject *__pyx_n_s_parent;
static PyObject *__pyx_n_s_prediction;
static PyObject *__pyx_n_s_rI;
static PyObject *__pyx_n_s_reference;
static PyObject *__pyx_n_s_remove;
static PyObject *__pyx_n_s_resultstorer;
static PyObject *__pyx_n_s_ri;
static PyObject *__pyx_n_s_round;
static PyObject *__pyx_n_s_splices;
static PyObject *__pyx_n_s_start;
static PyObject *__pyx_n_s_strand;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_u;
static PyObject *__pyx_n_s_x;
static PyObject *__pyx_pf_6Mikado_6scales_8contrast_compare(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_prediction, PyObject *__pyx_v_reference, int __pyx_v_lenient); /* proto */
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_2;

/* "Mikado/scales/contrast.pyx":10
 * __author__ = 'Luca Venturini'
 * 
 * cdef inline long long_max(long a, long b): return a if a >= b else b             # <<<<<<<<<<<<<<
 * cdef inline double double_min(double a, double b): return a if a <= b else b
 * 
 */

static CYTHON_INLINE long __pyx_f_6Mikado_6scales_8contrast_long_max(long __pyx_v_a, long __pyx_v_b) {
  long __pyx_r;
  __Pyx_RefNannyDeclarations
  long __pyx_t_1;
  __Pyx_RefNannySetupContext("long_max", 0);
  if (((__pyx_v_a >= __pyx_v_b) != 0)) {
    __pyx_t_1 = __pyx_v_a;
  } else {
    __pyx_t_1 = __pyx_v_b;
  }
  __pyx_r = __pyx_t_1;
  goto __pyx_L0;

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

/* "Mikado/scales/contrast.pyx":11
 * 
 * cdef inline long long_max(long a, long b): return a if a >= b else b
 * cdef inline double double_min(double a, double b): return a if a <= b else b             # <<<<<<<<<<<<<<
 * 
 * @cython.profile(True)
 */

static CYTHON_INLINE double __pyx_f_6Mikado_6scales_8contrast_double_min(double __pyx_v_a, double __pyx_v_b) {
  double __pyx_r;
  __Pyx_RefNannyDeclarations
  double __pyx_t_1;
  __Pyx_RefNannySetupContext("double_min", 0);
  if (((__pyx_v_a <= __pyx_v_b) != 0)) {
    __pyx_t_1 = __pyx_v_a;
  } else {
    __pyx_t_1 = __pyx_v_b;
  }
  __pyx_r = __pyx_t_1;
  goto __pyx_L0;

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

/* "Mikado/scales/contrast.pyx":15
 * @cython.profile(True)
 * @cython.boundscheck(False)
 * cdef str __assign_monoexonic_ccode(prediction, reference, long nucl_overlap, double stats[9]):             # <<<<<<<<<<<<<<
 * 
 *     cdef:
 */

static PyObject *__pyx_f_6Mikado_6scales_8contrast___assign_monoexonic_ccode(PyObject *__pyx_v_prediction, PyObject *__pyx_v_reference, long __pyx_v_nucl_overlap, double *__pyx_v_stats) {
  PyObject *__pyx_v_ccode = 0;
  double __pyx_v_nucl_recall;
  double __pyx_v_nucl_precision;
  double __pyx_v_nucl_f1;
  CYTHON_UNUSED double __pyx_v_exon_recall;
  CYTHON_UNUSED double __pyx_v_exon_precision;
  CYTHON_UNUSED double __pyx_v_exon_f1;
  CYTHON_UNUSED double __pyx_v_junction_recall;
  CYTHON_UNUSED double __pyx_v_junction_precision;
  CYTHON_UNUSED double __pyx_v_junction_f1;
  short __pyx_v_p_exon_num;
  short __pyx_v_r_exon_num;
  long __pyx_v_p_start;
  long __pyx_v_p_end;
  long __pyx_v_r_start;
  long __pyx_v_r_end;
  long __pyx_v_over;
  long __pyx_v_over_left;
  long __pyx_v_over_right;
  CYTHON_UNUSED long __pyx_v_p_cdna_length;
  long __pyx_v_i_length;
  long __pyx_v_i_start;
  long __pyx_v_i_end;
  long __pyx_v_introns[2];
  long __pyx_v_overlaps[3];
  unsigned short __pyx_v_index;
  PyObject *__pyx_v_r_strand = 0;
  PyObject *__pyx_v_p_strand = 0;
  PyObject *__pyx_v_intron = NULL;
  CYTHON_UNUSED PyObject *__pyx_v_reference_exon = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_TraceDeclarations
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  short __pyx_t_2;
  long __pyx_t_3;
  long __pyx_t_4;
  int __pyx_t_5;
  int __pyx_t_6;
  PyObject *__pyx_t_7 = NULL;
  PyObject *__pyx_t_8 = NULL;
  int __pyx_t_9;
  Py_ssize_t __pyx_t_10;
  int __pyx_t_11;
  __Pyx_RefNannySetupContext("__assign_monoexonic_ccode", 0);
  __Pyx_TraceCall("__assign_monoexonic_ccode", __pyx_f[0], 15, 0, __PYX_ERR(0, 15, __pyx_L1_error));

  /* "Mikado/scales/contrast.pyx":34
 *         # double stats[9]
 * 
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end             # <<<<<<<<<<<<<<
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 *     if reference.strand is None:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_short(__pyx_t_1); if (unlikely((__pyx_t_2 == (short)-1) && PyErr_Occurred())) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_3 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 34, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_p_exon_num = __pyx_t_2;
  __pyx_v_p_start = __pyx_t_3;
  __pyx_v_p_end = __pyx_t_4;

  /* "Mikado/scales/contrast.pyx":35
 * 
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end             # <<<<<<<<<<<<<<
 *     if reference.strand is None:
 *         r_strand = ""
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_2 = __Pyx_PyInt_As_short(__pyx_t_1); if (unlikely((__pyx_t_2 == (short)-1) && PyErr_Occurred())) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_3 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 35, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_r_exon_num = __pyx_t_2;
  __pyx_v_r_start = __pyx_t_4;
  __pyx_v_r_end = __pyx_t_3;

  /* "Mikado/scales/contrast.pyx":36
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 *     if reference.strand is None:             # <<<<<<<<<<<<<<
 *         r_strand = ""
 *     else:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_5 = (__pyx_t_1 == Py_None);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_6 = (__pyx_t_5 != 0);
  if (__pyx_t_6) {

    /* "Mikado/scales/contrast.pyx":37
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 *     if reference.strand is None:
 *         r_strand = ""             # <<<<<<<<<<<<<<
 *     else:
 *         r_strand = reference.strand
 */
    __Pyx_INCREF(__pyx_kp_s_);
    __pyx_v_r_strand = __pyx_kp_s_;

    /* "Mikado/scales/contrast.pyx":36
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 *     if reference.strand is None:             # <<<<<<<<<<<<<<
 *         r_strand = ""
 *     else:
 */
    goto __pyx_L3;
  }

  /* "Mikado/scales/contrast.pyx":39
 *         r_strand = ""
 *     else:
 *         r_strand = reference.strand             # <<<<<<<<<<<<<<
 * 
 *     if prediction.strand is None:
 */
  /*else*/ {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 39, __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_ERR(0, 39, __pyx_L1_error)
    __pyx_v_r_strand = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
  }
  __pyx_L3:;

  /* "Mikado/scales/contrast.pyx":41
 *         r_strand = reference.strand
 * 
 *     if prediction.strand is None:             # <<<<<<<<<<<<<<
 *         p_strand = ""
 *     else:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 41, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_6 = (__pyx_t_1 == Py_None);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_5 = (__pyx_t_6 != 0);
  if (__pyx_t_5) {

    /* "Mikado/scales/contrast.pyx":42
 * 
 *     if prediction.strand is None:
 *         p_strand = ""             # <<<<<<<<<<<<<<
 *     else:
 *         p_strand = prediction.strand
 */
    __Pyx_INCREF(__pyx_kp_s_);
    __pyx_v_p_strand = __pyx_kp_s_;

    /* "Mikado/scales/contrast.pyx":41
 *         r_strand = reference.strand
 * 
 *     if prediction.strand is None:             # <<<<<<<<<<<<<<
 *         p_strand = ""
 *     else:
 */
    goto __pyx_L4;
  }

  /* "Mikado/scales/contrast.pyx":44
 *         p_strand = ""
 *     else:
 *         p_strand = prediction.strand             # <<<<<<<<<<<<<<
 * 
 *     ccode = ""
 */
  /*else*/ {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 44, __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_ERR(0, 44, __pyx_L1_error)
    __pyx_v_p_strand = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
  }
  __pyx_L4:;

  /* "Mikado/scales/contrast.pyx":46
 *         p_strand = prediction.strand
 * 
 *     ccode = ""             # <<<<<<<<<<<<<<
 *     nucl_recall = stats[0]
 *     nucl_precision = stats[1]
 */
  __Pyx_INCREF(__pyx_kp_s_);
  __pyx_v_ccode = __pyx_kp_s_;

  /* "Mikado/scales/contrast.pyx":47
 * 
 *     ccode = ""
 *     nucl_recall = stats[0]             # <<<<<<<<<<<<<<
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]
 */
  __pyx_v_nucl_recall = (__pyx_v_stats[0]);

  /* "Mikado/scales/contrast.pyx":48
 *     ccode = ""
 *     nucl_recall = stats[0]
 *     nucl_precision = stats[1]             # <<<<<<<<<<<<<<
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]
 */
  __pyx_v_nucl_precision = (__pyx_v_stats[1]);

  /* "Mikado/scales/contrast.pyx":49
 *     nucl_recall = stats[0]
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]             # <<<<<<<<<<<<<<
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]
 */
  __pyx_v_nucl_f1 = (__pyx_v_stats[2]);

  /* "Mikado/scales/contrast.pyx":50
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]             # <<<<<<<<<<<<<<
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]
 */
  __pyx_v_exon_recall = (__pyx_v_stats[3]);

  /* "Mikado/scales/contrast.pyx":51
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]             # <<<<<<<<<<<<<<
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]
 */
  __pyx_v_exon_precision = (__pyx_v_stats[4]);

  /* "Mikado/scales/contrast.pyx":52
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]             # <<<<<<<<<<<<<<
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]
 */
  __pyx_v_exon_f1 = (__pyx_v_stats[5]);

  /* "Mikado/scales/contrast.pyx":53
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]             # <<<<<<<<<<<<<<
 *     junction_precision = stats[7]
 *     junction_f1 = stats[8]
 */
  __pyx_v_junction_recall = (__pyx_v_stats[6]);

  /* "Mikado/scales/contrast.pyx":54
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]             # <<<<<<<<<<<<<<
 *     junction_f1 = stats[8]
 * 
 */
  __pyx_v_junction_precision = (__pyx_v_stats[7]);

  /* "Mikado/scales/contrast.pyx":55
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]
 *     junction_f1 = stats[8]             # <<<<<<<<<<<<<<
 * 
 *     if p_exon_num == 1 and r_exon_num > 1:
 */
  __pyx_v_junction_f1 = (__pyx_v_stats[8]);

  /* "Mikado/scales/contrast.pyx":57
 *     junction_f1 = stats[8]
 * 
 *     if p_exon_num == 1 and r_exon_num > 1:             # <<<<<<<<<<<<<<
 *         if nucl_precision < 1 and nucl_overlap > 0:
 *             index = -1
 */
  __pyx_t_6 = ((__pyx_v_p_exon_num == 1) != 0);
  if (__pyx_t_6) {
  } else {
    __pyx_t_5 = __pyx_t_6;
    goto __pyx_L6_bool_binop_done;
  }
  __pyx_t_6 = ((__pyx_v_r_exon_num > 1) != 0);
  __pyx_t_5 = __pyx_t_6;
  __pyx_L6_bool_binop_done:;
  if (__pyx_t_5) {

    /* "Mikado/scales/contrast.pyx":58
 * 
 *     if p_exon_num == 1 and r_exon_num > 1:
 *         if nucl_precision < 1 and nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             index = -1
 *             for intron in sorted(reference.introns):
 */
    __pyx_t_6 = ((__pyx_v_nucl_precision < 1.0) != 0);
    if (__pyx_t_6) {
    } else {
      __pyx_t_5 = __pyx_t_6;
      goto __pyx_L9_bool_binop_done;
    }
    __pyx_t_6 = ((__pyx_v_nucl_overlap > 0) != 0);
    __pyx_t_5 = __pyx_t_6;
    __pyx_L9_bool_binop_done:;
    if (__pyx_t_5) {

      /* "Mikado/scales/contrast.pyx":59
 *     if p_exon_num == 1 and r_exon_num > 1:
 *         if nucl_precision < 1 and nucl_overlap > 0:
 *             index = -1             # <<<<<<<<<<<<<<
 *             for intron in sorted(reference.introns):
 *                 i_start, i_end = intron[0], intron[1]
 */
      __pyx_v_index = -1;

      /* "Mikado/scales/contrast.pyx":60
 *         if nucl_precision < 1 and nucl_overlap > 0:
 *             index = -1
 *             for intron in sorted(reference.introns):             # <<<<<<<<<<<<<<
 *                 i_start, i_end = intron[0], intron[1]
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 */
      __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_introns); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 60, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
      __pyx_t_8 = PySequence_List(__pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 60, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_8);
      __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
      __pyx_t_1 = ((PyObject*)__pyx_t_8);
      __pyx_t_8 = 0;
      __pyx_t_9 = PyList_Sort(__pyx_t_1); if (unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 60, __pyx_L1_error)
      if (unlikely(__pyx_t_1 == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
        __PYX_ERR(0, 60, __pyx_L1_error)
      }
      __pyx_t_8 = __pyx_t_1; __Pyx_INCREF(__pyx_t_8); __pyx_t_10 = 0;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      for (;;) {
        if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
        #if CYTHON_COMPILING_IN_CPYTHON
        __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_1); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 60, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 60, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
        __Pyx_XDECREF_SET(__pyx_v_intron, __pyx_t_1);
        __pyx_t_1 = 0;

        /* "Mikado/scales/contrast.pyx":61
 *             index = -1
 *             for intron in sorted(reference.introns):
 *                 i_start, i_end = intron[0], intron[1]             # <<<<<<<<<<<<<<
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 *                 if over > 0:
 */
        __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_intron, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_3 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_3 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 61, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_intron, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 61, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 61, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
        __pyx_v_i_start = __pyx_t_3;
        __pyx_v_i_end = __pyx_t_4;

        /* "Mikado/scales/contrast.pyx":62
 *             for intron in sorted(reference.introns):
 *                 i_start, i_end = intron[0], intron[1]
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)             # <<<<<<<<<<<<<<
 *                 if over > 0:
 *                     index += 1
 */
        __pyx_v_over = __pyx_f_6Mikado_9utilities_7overlap_c_overlap(__pyx_v_i_start, __pyx_v_i_end, __pyx_v_p_start, __pyx_v_p_end, 0, 1);

        /* "Mikado/scales/contrast.pyx":63
 *                 i_start, i_end = intron[0], intron[1]
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 *                 if over > 0:             # <<<<<<<<<<<<<<
 *                     index += 1
 *                     if index > 1:
 */
        __pyx_t_5 = ((__pyx_v_over > 0) != 0);
        if (__pyx_t_5) {

          /* "Mikado/scales/contrast.pyx":64
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 *                 if over > 0:
 *                     index += 1             # <<<<<<<<<<<<<<
 *                     if index > 1:
 *                         break
 */
          __pyx_v_index = (__pyx_v_index + 1);

          /* "Mikado/scales/contrast.pyx":65
 *                 if over > 0:
 *                     index += 1
 *                     if index > 1:             # <<<<<<<<<<<<<<
 *                         break
 *                     i_length = i_end - i_start + 1
 */
          __pyx_t_5 = ((__pyx_v_index > 1) != 0);
          if (__pyx_t_5) {

            /* "Mikado/scales/contrast.pyx":66
 *                     index += 1
 *                     if index > 1:
 *                         break             # <<<<<<<<<<<<<<
 *                     i_length = i_end - i_start + 1
 *                     overlaps[index] = over
 */
            goto __pyx_L12_break;

            /* "Mikado/scales/contrast.pyx":65
 *                 if over > 0:
 *                     index += 1
 *                     if index > 1:             # <<<<<<<<<<<<<<
 *                         break
 *                     i_length = i_end - i_start + 1
 */
          }

          /* "Mikado/scales/contrast.pyx":67
 *                     if index > 1:
 *                         break
 *                     i_length = i_end - i_start + 1             # <<<<<<<<<<<<<<
 *                     overlaps[index] = over
 *                     introns[index] = i_length
 */
          __pyx_v_i_length = ((__pyx_v_i_end - __pyx_v_i_start) + 1);

          /* "Mikado/scales/contrast.pyx":68
 *                         break
 *                     i_length = i_end - i_start + 1
 *                     overlaps[index] = over             # <<<<<<<<<<<<<<
 *                     introns[index] = i_length
 * 
 */
          (__pyx_v_overlaps[__pyx_v_index]) = __pyx_v_over;

          /* "Mikado/scales/contrast.pyx":69
 *                     i_length = i_end - i_start + 1
 *                     overlaps[index] = over
 *                     introns[index] = i_length             # <<<<<<<<<<<<<<
 * 
 *             if index == -1:
 */
          (__pyx_v_introns[__pyx_v_index]) = __pyx_v_i_length;

          /* "Mikado/scales/contrast.pyx":63
 *                 i_start, i_end = intron[0], intron[1]
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 *                 if over > 0:             # <<<<<<<<<<<<<<
 *                     index += 1
 *                     if index > 1:
 */
        }

        /* "Mikado/scales/contrast.pyx":60
 *         if nucl_precision < 1 and nucl_overlap > 0:
 *             index = -1
 *             for intron in sorted(reference.introns):             # <<<<<<<<<<<<<<
 *                 i_start, i_end = intron[0], intron[1]
 *                 over = c_overlap(i_start, i_end, p_start, p_end, flank=0, positive=True)
 */
      }
      __pyx_L12_break:;
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;

      /* "Mikado/scales/contrast.pyx":71
 *                     introns[index] = i_length
 * 
 *             if index == -1:             # <<<<<<<<<<<<<<
 *                 # Completely contained inside
 *                 ccode = "g"
 */
      __pyx_t_5 = ((__pyx_v_index == -1L) != 0);
      if (__pyx_t_5) {

        /* "Mikado/scales/contrast.pyx":73
 *             if index == -1:
 *                 # Completely contained inside
 *                 ccode = "g"             # <<<<<<<<<<<<<<
 *             elif index == 0:
 *                 over = overlaps[0]
 */
        __Pyx_INCREF(__pyx_n_s_g);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_g);

        /* "Mikado/scales/contrast.pyx":71
 *                     introns[index] = i_length
 * 
 *             if index == -1:             # <<<<<<<<<<<<<<
 *                 # Completely contained inside
 *                 ccode = "g"
 */
        goto __pyx_L15;
      }

      /* "Mikado/scales/contrast.pyx":74
 *                 # Completely contained inside
 *                 ccode = "g"
 *             elif index == 0:             # <<<<<<<<<<<<<<
 *                 over = overlaps[0]
 *                 i_length = introns[0]
 */
      __pyx_t_5 = ((__pyx_v_index == 0) != 0);
      if (__pyx_t_5) {

        /* "Mikado/scales/contrast.pyx":75
 *                 ccode = "g"
 *             elif index == 0:
 *                 over = overlaps[0]             # <<<<<<<<<<<<<<
 *                 i_length = introns[0]
 *                 # over, i_length = overlaps[0][0], overlaps[0][1]
 */
        __pyx_v_over = (__pyx_v_overlaps[0]);

        /* "Mikado/scales/contrast.pyx":76
 *             elif index == 0:
 *                 over = overlaps[0]
 *                 i_length = introns[0]             # <<<<<<<<<<<<<<
 *                 # over, i_length = overlaps[0][0], overlaps[0][1]
 *                 p_cdna_length = prediction.cdna_length
 */
        __pyx_v_i_length = (__pyx_v_introns[0]);

        /* "Mikado/scales/contrast.pyx":78
 *                 i_length = introns[0]
 *                 # over, i_length = overlaps[0][0], overlaps[0][1]
 *                 p_cdna_length = prediction.cdna_length             # <<<<<<<<<<<<<<
 *                 if (10 < over < i_length) and (r_start < p_start < p_end < r_end):
 *                     ccode = "e"
 */
        __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_cdna_length); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 78, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_8);
        __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_8); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 78, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
        __pyx_v_p_cdna_length = __pyx_t_4;

        /* "Mikado/scales/contrast.pyx":79
 *                 # over, i_length = overlaps[0][0], overlaps[0][1]
 *                 p_cdna_length = prediction.cdna_length
 *                 if (10 < over < i_length) and (r_start < p_start < p_end < r_end):             # <<<<<<<<<<<<<<
 *                     ccode = "e"
 *                 else:
 */
        __pyx_t_6 = (10 < __pyx_v_over);
        if (__pyx_t_6) {
          __pyx_t_6 = (__pyx_v_over < __pyx_v_i_length);
        }
        __pyx_t_11 = (__pyx_t_6 != 0);
        if (__pyx_t_11) {
        } else {
          __pyx_t_5 = __pyx_t_11;
          goto __pyx_L17_bool_binop_done;
        }
        __pyx_t_11 = (__pyx_v_r_start < __pyx_v_p_start);
        if (__pyx_t_11) {
          __pyx_t_11 = (__pyx_v_p_start < __pyx_v_p_end);
          if (__pyx_t_11) {
            __pyx_t_11 = (__pyx_v_p_end < __pyx_v_r_end);
          }
        }
        __pyx_t_6 = (__pyx_t_11 != 0);
        __pyx_t_5 = __pyx_t_6;
        __pyx_L17_bool_binop_done:;
        if (__pyx_t_5) {

          /* "Mikado/scales/contrast.pyx":80
 *                 p_cdna_length = prediction.cdna_length
 *                 if (10 < over < i_length) and (r_start < p_start < p_end < r_end):
 *                     ccode = "e"             # <<<<<<<<<<<<<<
 *                 else:
 *                     ccode = "g"
 */
          __Pyx_INCREF(__pyx_n_s_e);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_e);

          /* "Mikado/scales/contrast.pyx":79
 *                 # over, i_length = overlaps[0][0], overlaps[0][1]
 *                 p_cdna_length = prediction.cdna_length
 *                 if (10 < over < i_length) and (r_start < p_start < p_end < r_end):             # <<<<<<<<<<<<<<
 *                     ccode = "e"
 *                 else:
 */
          goto __pyx_L16;
        }

        /* "Mikado/scales/contrast.pyx":82
 *                     ccode = "e"
 *                 else:
 *                     ccode = "g"             # <<<<<<<<<<<<<<
 *             elif index > 1:
 *                 ccode = "g"
 */
        /*else*/ {
          __Pyx_INCREF(__pyx_n_s_g);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_g);
        }
        __pyx_L16:;

        /* "Mikado/scales/contrast.pyx":74
 *                 # Completely contained inside
 *                 ccode = "g"
 *             elif index == 0:             # <<<<<<<<<<<<<<
 *                 over = overlaps[0]
 *                 i_length = introns[0]
 */
        goto __pyx_L15;
      }

      /* "Mikado/scales/contrast.pyx":83
 *                 else:
 *                     ccode = "g"
 *             elif index > 1:             # <<<<<<<<<<<<<<
 *                 ccode = "g"
 *             elif index == 1:
 */
      __pyx_t_5 = ((__pyx_v_index > 1) != 0);
      if (__pyx_t_5) {

        /* "Mikado/scales/contrast.pyx":84
 *                     ccode = "g"
 *             elif index > 1:
 *                 ccode = "g"             # <<<<<<<<<<<<<<
 *             elif index == 1:
 *                 over_left, over_right = overlaps[0], overlaps[1]
 */
        __Pyx_INCREF(__pyx_n_s_g);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_g);

        /* "Mikado/scales/contrast.pyx":83
 *                 else:
 *                     ccode = "g"
 *             elif index > 1:             # <<<<<<<<<<<<<<
 *                 ccode = "g"
 *             elif index == 1:
 */
        goto __pyx_L15;
      }

      /* "Mikado/scales/contrast.pyx":85
 *             elif index > 1:
 *                 ccode = "g"
 *             elif index == 1:             # <<<<<<<<<<<<<<
 *                 over_left, over_right = overlaps[0], overlaps[1]
 *                 if over_left < 10 and over_right < 10:
 */
      __pyx_t_5 = ((__pyx_v_index == 1) != 0);
      if (__pyx_t_5) {

        /* "Mikado/scales/contrast.pyx":86
 *                 ccode = "g"
 *             elif index == 1:
 *                 over_left, over_right = overlaps[0], overlaps[1]             # <<<<<<<<<<<<<<
 *                 if over_left < 10 and over_right < 10:
 *                     ccode = "g"
 */
        __pyx_t_4 = (__pyx_v_overlaps[0]);
        __pyx_t_3 = (__pyx_v_overlaps[1]);
        __pyx_v_over_left = __pyx_t_4;
        __pyx_v_over_right = __pyx_t_3;

        /* "Mikado/scales/contrast.pyx":87
 *             elif index == 1:
 *                 over_left, over_right = overlaps[0], overlaps[1]
 *                 if over_left < 10 and over_right < 10:             # <<<<<<<<<<<<<<
 *                     ccode = "g"
 *                 else:
 */
        __pyx_t_6 = ((__pyx_v_over_left < 10) != 0);
        if (__pyx_t_6) {
        } else {
          __pyx_t_5 = __pyx_t_6;
          goto __pyx_L20_bool_binop_done;
        }
        __pyx_t_6 = ((__pyx_v_over_right < 10) != 0);
        __pyx_t_5 = __pyx_t_6;
        __pyx_L20_bool_binop_done:;
        if (__pyx_t_5) {

          /* "Mikado/scales/contrast.pyx":88
 *                 over_left, over_right = overlaps[0], overlaps[1]
 *                 if over_left < 10 and over_right < 10:
 *                     ccode = "g"             # <<<<<<<<<<<<<<
 *                 else:
 *                     ccode = "e"
 */
          __Pyx_INCREF(__pyx_n_s_g);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_g);

          /* "Mikado/scales/contrast.pyx":87
 *             elif index == 1:
 *                 over_left, over_right = overlaps[0], overlaps[1]
 *                 if over_left < 10 and over_right < 10:             # <<<<<<<<<<<<<<
 *                     ccode = "g"
 *                 else:
 */
          goto __pyx_L19;
        }

        /* "Mikado/scales/contrast.pyx":90
 *                     ccode = "g"
 *                 else:
 *                     ccode = "e"             # <<<<<<<<<<<<<<
 *         elif nucl_overlap > 0:
 *             ccode = "g"
 */
        /*else*/ {
          __Pyx_INCREF(__pyx_n_s_e);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_e);
        }
        __pyx_L19:;

        /* "Mikado/scales/contrast.pyx":85
 *             elif index > 1:
 *                 ccode = "g"
 *             elif index == 1:             # <<<<<<<<<<<<<<
 *                 over_left, over_right = overlaps[0], overlaps[1]
 *                 if over_left < 10 and over_right < 10:
 */
      }
      __pyx_L15:;

      /* "Mikado/scales/contrast.pyx":58
 * 
 *     if p_exon_num == 1 and r_exon_num > 1:
 *         if nucl_precision < 1 and nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             index = -1
 *             for intron in sorted(reference.introns):
 */
      goto __pyx_L8;
    }

    /* "Mikado/scales/contrast.pyx":91
 *                 else:
 *                     ccode = "e"
 *         elif nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             ccode = "g"
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 */
    __pyx_t_5 = ((__pyx_v_nucl_overlap > 0) != 0);
    if (__pyx_t_5) {

      /* "Mikado/scales/contrast.pyx":92
 *                     ccode = "e"
 *         elif nucl_overlap > 0:
 *             ccode = "g"             # <<<<<<<<<<<<<<
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 *             ccode = "i"  # Monoexonic fragment inside an intron
 */
      __Pyx_INCREF(__pyx_n_s_g);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_g);

      /* "Mikado/scales/contrast.pyx":91
 *                 else:
 *                     ccode = "e"
 *         elif nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             ccode = "g"
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 */
      goto __pyx_L8;
    }

    /* "Mikado/scales/contrast.pyx":93
 *         elif nucl_overlap > 0:
 *             ccode = "g"
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):             # <<<<<<<<<<<<<<
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:
 */
    __pyx_t_6 = ((__pyx_v_nucl_recall == 0.0) != 0);
    if (__pyx_t_6) {
    } else {
      __pyx_t_5 = __pyx_t_6;
      goto __pyx_L22_bool_binop_done;
    }
    __pyx_t_6 = (__pyx_v_r_start < __pyx_v_p_start);
    if (__pyx_t_6) {
      __pyx_t_6 = (__pyx_v_p_start < __pyx_v_r_end);
    }
    __pyx_t_11 = (__pyx_t_6 != 0);
    __pyx_t_5 = __pyx_t_11;
    __pyx_L22_bool_binop_done:;
    if (__pyx_t_5) {

      /* "Mikado/scales/contrast.pyx":94
 *             ccode = "g"
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 *             ccode = "i"  # Monoexonic fragment inside an intron             # <<<<<<<<<<<<<<
 *     elif p_exon_num > 1 and r_exon_num == 1:
 *         if nucl_overlap > 0:
 */
      __Pyx_INCREF(__pyx_n_s_i);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_i);

      /* "Mikado/scales/contrast.pyx":93
 *         elif nucl_overlap > 0:
 *             ccode = "g"
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):             # <<<<<<<<<<<<<<
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:
 */
    }
    __pyx_L8:;

    /* "Mikado/scales/contrast.pyx":57
 *     junction_f1 = stats[8]
 * 
 *     if p_exon_num == 1 and r_exon_num > 1:             # <<<<<<<<<<<<<<
 *         if nucl_precision < 1 and nucl_overlap > 0:
 *             index = -1
 */
    goto __pyx_L5;
  }

  /* "Mikado/scales/contrast.pyx":95
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:             # <<<<<<<<<<<<<<
 *         if nucl_overlap > 0:
 *             ccode = "G"  # Reverse generic overlap
 */
  __pyx_t_11 = ((__pyx_v_p_exon_num > 1) != 0);
  if (__pyx_t_11) {
  } else {
    __pyx_t_5 = __pyx_t_11;
    goto __pyx_L24_bool_binop_done;
  }
  __pyx_t_11 = ((__pyx_v_r_exon_num == 1) != 0);
  __pyx_t_5 = __pyx_t_11;
  __pyx_L24_bool_binop_done:;
  if (__pyx_t_5) {

    /* "Mikado/scales/contrast.pyx":96
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:
 *         if nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             ccode = "G"  # Reverse generic overlap
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:
 */
    __pyx_t_5 = ((__pyx_v_nucl_overlap > 0) != 0);
    if (__pyx_t_5) {

      /* "Mikado/scales/contrast.pyx":97
 *     elif p_exon_num > 1 and r_exon_num == 1:
 *         if nucl_overlap > 0:
 *             ccode = "G"  # Reverse generic overlap             # <<<<<<<<<<<<<<
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:
 *             ccode = "ri"
 */
      __Pyx_INCREF(__pyx_n_s_G);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_G);

      /* "Mikado/scales/contrast.pyx":96
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:
 *         if nucl_overlap > 0:             # <<<<<<<<<<<<<<
 *             ccode = "G"  # Reverse generic overlap
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:
 */
      goto __pyx_L26;
    }

    /* "Mikado/scales/contrast.pyx":98
 *         if nucl_overlap > 0:
 *             ccode = "G"  # Reverse generic overlap
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:             # <<<<<<<<<<<<<<
 *             ccode = "ri"
 *         else:
 */
    __pyx_t_5 = ((__pyx_f_6Mikado_9utilities_7overlap_c_overlap(__pyx_v_p_start, __pyx_v_p_end, __pyx_v_r_start, __pyx_v_r_end, 0, 1) > 0) != 0);
    if (__pyx_t_5) {

      /* "Mikado/scales/contrast.pyx":99
 *             ccode = "G"  # Reverse generic overlap
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:
 *             ccode = "ri"             # <<<<<<<<<<<<<<
 *         else:
 *             ccode = "p"
 */
      __Pyx_INCREF(__pyx_n_s_ri);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_ri);

      /* "Mikado/scales/contrast.pyx":98
 *         if nucl_overlap > 0:
 *             ccode = "G"  # Reverse generic overlap
 *         elif c_overlap(p_start, p_end, r_start, r_end, 0, 1) > 0:             # <<<<<<<<<<<<<<
 *             ccode = "ri"
 *         else:
 */
      goto __pyx_L26;
    }

    /* "Mikado/scales/contrast.pyx":101
 *             ccode = "ri"
 *         else:
 *             ccode = "p"             # <<<<<<<<<<<<<<
 *     elif p_exon_num == r_exon_num == 1:
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:
 */
    /*else*/ {
      __Pyx_INCREF(__pyx_n_s_p);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_p);
    }
    __pyx_L26:;

    /* "Mikado/scales/contrast.pyx":95
 *         elif (nucl_recall == 0 and r_start < p_start < r_end):
 *             ccode = "i"  # Monoexonic fragment inside an intron
 *     elif p_exon_num > 1 and r_exon_num == 1:             # <<<<<<<<<<<<<<
 *         if nucl_overlap > 0:
 *             ccode = "G"  # Reverse generic overlap
 */
    goto __pyx_L5;
  }

  /* "Mikado/scales/contrast.pyx":102
 *         else:
 *             ccode = "p"
 *     elif p_exon_num == r_exon_num == 1:             # <<<<<<<<<<<<<<
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:
 *             reference_exon = reference.exons[0]
 */
  __pyx_t_5 = (__pyx_v_p_exon_num == __pyx_v_r_exon_num);
  if (__pyx_t_5) {
    __pyx_t_5 = (__pyx_v_r_exon_num == 1);
  }
  __pyx_t_11 = (__pyx_t_5 != 0);
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":103
 *             ccode = "p"
 *     elif p_exon_num == r_exon_num == 1:
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:             # <<<<<<<<<<<<<<
 *             reference_exon = reference.exons[0]
 *             ccode = "_"
 */
    __pyx_t_5 = ((__pyx_v_nucl_f1 >= 0.95) != 0);
    if (__pyx_t_5) {
    } else {
      __pyx_t_11 = __pyx_t_5;
      goto __pyx_L28_bool_binop_done;
    }
    __pyx_t_5 = (__Pyx_PyString_Equals(__pyx_v_r_strand, __pyx_v_p_strand, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 103, __pyx_L1_error)
    __pyx_t_6 = (__pyx_t_5 != 0);
    __pyx_t_11 = __pyx_t_6;
    __pyx_L28_bool_binop_done:;
    if (__pyx_t_11) {

      /* "Mikado/scales/contrast.pyx":104
 *     elif p_exon_num == r_exon_num == 1:
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:
 *             reference_exon = reference.exons[0]             # <<<<<<<<<<<<<<
 *             ccode = "_"
 *         elif nucl_precision == 1:
 */
      __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 104, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_8);
      __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_8, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 104, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
      __pyx_v_reference_exon = __pyx_t_1;
      __pyx_t_1 = 0;

      /* "Mikado/scales/contrast.pyx":105
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:
 *             reference_exon = reference.exons[0]
 *             ccode = "_"             # <<<<<<<<<<<<<<
 *         elif nucl_precision == 1:
 *             ccode = "c"  # contained
 */
      __Pyx_INCREF(__pyx_n_s__2);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s__2);

      /* "Mikado/scales/contrast.pyx":103
 *             ccode = "p"
 *     elif p_exon_num == r_exon_num == 1:
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:             # <<<<<<<<<<<<<<
 *             reference_exon = reference.exons[0]
 *             ccode = "_"
 */
      goto __pyx_L27;
    }

    /* "Mikado/scales/contrast.pyx":106
 *             reference_exon = reference.exons[0]
 *             ccode = "_"
 *         elif nucl_precision == 1:             # <<<<<<<<<<<<<<
 *             ccode = "c"  # contained
 *         else:
 */
    __pyx_t_11 = ((__pyx_v_nucl_precision == 1.0) != 0);
    if (__pyx_t_11) {

      /* "Mikado/scales/contrast.pyx":107
 *             ccode = "_"
 *         elif nucl_precision == 1:
 *             ccode = "c"  # contained             # <<<<<<<<<<<<<<
 *         else:
 *             ccode = "m"  # just a generic exon overlap b/w two monoexonic transcripts
 */
      __Pyx_INCREF(__pyx_n_s_c);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_c);

      /* "Mikado/scales/contrast.pyx":106
 *             reference_exon = reference.exons[0]
 *             ccode = "_"
 *         elif nucl_precision == 1:             # <<<<<<<<<<<<<<
 *             ccode = "c"  # contained
 *         else:
 */
      goto __pyx_L27;
    }

    /* "Mikado/scales/contrast.pyx":109
 *             ccode = "c"  # contained
 *         else:
 *             ccode = "m"  # just a generic exon overlap b/w two monoexonic transcripts             # <<<<<<<<<<<<<<
 * 
 *     return ccode
 */
    /*else*/ {
      __Pyx_INCREF(__pyx_n_s_m);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_m);
    }
    __pyx_L27:;

    /* "Mikado/scales/contrast.pyx":102
 *         else:
 *             ccode = "p"
 *     elif p_exon_num == r_exon_num == 1:             # <<<<<<<<<<<<<<
 *         if nucl_f1 >= 0.95 and r_strand == p_strand:
 *             reference_exon = reference.exons[0]
 */
  }
  __pyx_L5:;

  /* "Mikado/scales/contrast.pyx":111
 *             ccode = "m"  # just a generic exon overlap b/w two monoexonic transcripts
 * 
 *     return ccode             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_ccode);
  __pyx_r = __pyx_v_ccode;
  goto __pyx_L0;

  /* "Mikado/scales/contrast.pyx":15
 * @cython.profile(True)
 * @cython.boundscheck(False)
 * cdef str __assign_monoexonic_ccode(prediction, reference, long nucl_overlap, double stats[9]):             # <<<<<<<<<<<<<<
 * 
 *     cdef:
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_7);
  __Pyx_XDECREF(__pyx_t_8);
  __Pyx_AddTraceback("Mikado.scales.contrast.__assign_monoexonic_ccode", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_ccode);
  __Pyx_XDECREF(__pyx_v_r_strand);
  __Pyx_XDECREF(__pyx_v_p_strand);
  __Pyx_XDECREF(__pyx_v_intron);
  __Pyx_XDECREF(__pyx_v_reference_exon);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_TraceReturn(__pyx_r, 0);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "Mikado/scales/contrast.pyx":114
 * 
 * 
 * cdef str __assign_multiexonic_ccode(prediction, reference, long nucl_overlap, double stats[9]):             # <<<<<<<<<<<<<<
 * 
 *     """
 */

static PyObject *__pyx_f_6Mikado_6scales_8contrast___assign_multiexonic_ccode(PyObject *__pyx_v_prediction, PyObject *__pyx_v_reference, long __pyx_v_nucl_overlap, double *__pyx_v_stats) {
  PyObject *__pyx_v_ccode = 0;
  CYTHON_UNUSED double __pyx_v_nucl_recall;
  double __pyx_v_nucl_precision;
  double __pyx_v_nucl_f1;
  CYTHON_UNUSED double __pyx_v_exon_recall;
  CYTHON_UNUSED double __pyx_v_exon_precision;
  CYTHON_UNUSED double __pyx_v_exon_f1;
  double __pyx_v_junction_recall;
  double __pyx_v_junction_precision;
  CYTHON_UNUSED double __pyx_v_junction_f1;
  CYTHON_UNUSED int __pyx_v_p_exon_num;
  CYTHON_UNUSED int __pyx_v_r_exon_num;
  long __pyx_v_p_start;
  long __pyx_v_p_end;
  long __pyx_v_r_start;
  long __pyx_v_r_end;
  PyObject *__pyx_v_r_splices = 0;
  PyObject *__pyx_v_p_splices = 0;
  PyObject *__pyx_v_r_introns = 0;
  PyObject *__pyx_v_p_introns = 0;
  long __pyx_v_intron_start;
  long __pyx_v_intron_end;
  int __pyx_v_start_in;
  long __pyx_v_min_splice;
  long __pyx_v_max_splice;
  long __pyx_v_splice;
  unsigned short __pyx_v_overlapping_introns;
  PyObject *__pyx_v_missed_introns = NULL;
  long __pyx_v_end_in;
  PyObject *__pyx_v_intron = NULL;
  PyObject *__pyx_v_ref_intron = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  int __pyx_t_3;
  long __pyx_t_4;
  long __pyx_t_5;
  int __pyx_t_6;
  int __pyx_t_7;
  PyObject *(*__pyx_t_8)(PyObject *);
  int __pyx_t_9;
  Py_ssize_t __pyx_t_10;
  PyObject *__pyx_t_11 = NULL;
  PyObject *__pyx_t_12 = NULL;
  PyObject *(*__pyx_t_13)(PyObject *);
  PyObject *(*__pyx_t_14)(PyObject *);
  long __pyx_t_15;
  long __pyx_t_16;
  __Pyx_RefNannySetupContext("__assign_multiexonic_ccode", 0);

  /* "Mikado/scales/contrast.pyx":146
 *         short unsigned int index
 * 
 *     r_splices, p_splices = reference.splices, prediction.splices             # <<<<<<<<<<<<<<
 *     r_introns, p_introns = reference.introns, prediction.introns
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 146, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (!(likely(PySet_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_1)->tp_name), 0))) __PYX_ERR(0, 146, __pyx_L1_error)
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_splices); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 146, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (!(likely(PySet_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_2)->tp_name), 0))) __PYX_ERR(0, 146, __pyx_L1_error)
  __pyx_v_r_splices = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;
  __pyx_v_p_splices = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;

  /* "Mikado/scales/contrast.pyx":147
 * 
 *     r_splices, p_splices = reference.splices, prediction.splices
 *     r_introns, p_introns = reference.introns, prediction.introns             # <<<<<<<<<<<<<<
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_introns); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 147, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  if (!(likely(PySet_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_2)->tp_name), 0))) __PYX_ERR(0, 147, __pyx_L1_error)
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_introns); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 147, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (!(likely(PySet_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_1)->tp_name), 0))) __PYX_ERR(0, 147, __pyx_L1_error)
  __pyx_v_r_introns = ((PyObject*)__pyx_t_2);
  __pyx_t_2 = 0;
  __pyx_v_p_introns = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":148
 *     r_splices, p_splices = reference.splices, prediction.splices
 *     r_introns, p_introns = reference.introns, prediction.introns
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end             # <<<<<<<<<<<<<<
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 * 
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 148, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_p_exon_num = __pyx_t_3;
  __pyx_v_p_start = __pyx_t_4;
  __pyx_v_p_end = __pyx_t_5;

  /* "Mikado/scales/contrast.pyx":149
 *     r_introns, p_introns = reference.introns, prediction.introns
 *     p_exon_num, p_start, p_end = prediction.exon_num, prediction.start, prediction.end
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end             # <<<<<<<<<<<<<<
 * 
 *     nucl_recall = stats[0]
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 149, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_r_exon_num = __pyx_t_3;
  __pyx_v_r_start = __pyx_t_5;
  __pyx_v_r_end = __pyx_t_4;

  /* "Mikado/scales/contrast.pyx":151
 *     r_exon_num, r_start, r_end = reference.exon_num, reference.start, reference.end
 * 
 *     nucl_recall = stats[0]             # <<<<<<<<<<<<<<
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]
 */
  __pyx_v_nucl_recall = (__pyx_v_stats[0]);

  /* "Mikado/scales/contrast.pyx":152
 * 
 *     nucl_recall = stats[0]
 *     nucl_precision = stats[1]             # <<<<<<<<<<<<<<
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]
 */
  __pyx_v_nucl_precision = (__pyx_v_stats[1]);

  /* "Mikado/scales/contrast.pyx":153
 *     nucl_recall = stats[0]
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]             # <<<<<<<<<<<<<<
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]
 */
  __pyx_v_nucl_f1 = (__pyx_v_stats[2]);

  /* "Mikado/scales/contrast.pyx":154
 *     nucl_precision = stats[1]
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]             # <<<<<<<<<<<<<<
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]
 */
  __pyx_v_exon_recall = (__pyx_v_stats[3]);

  /* "Mikado/scales/contrast.pyx":155
 *     nucl_f1 = stats[2]
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]             # <<<<<<<<<<<<<<
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]
 */
  __pyx_v_exon_precision = (__pyx_v_stats[4]);

  /* "Mikado/scales/contrast.pyx":156
 *     exon_recall = stats[3]
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]             # <<<<<<<<<<<<<<
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]
 */
  __pyx_v_exon_f1 = (__pyx_v_stats[5]);

  /* "Mikado/scales/contrast.pyx":157
 *     exon_precision = stats[4]
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]             # <<<<<<<<<<<<<<
 *     junction_precision = stats[7]
 *     junction_f1 = stats[8]
 */
  __pyx_v_junction_recall = (__pyx_v_stats[6]);

  /* "Mikado/scales/contrast.pyx":158
 *     exon_f1 = stats[5]
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]             # <<<<<<<<<<<<<<
 *     junction_f1 = stats[8]
 * 
 */
  __pyx_v_junction_precision = (__pyx_v_stats[7]);

  /* "Mikado/scales/contrast.pyx":159
 *     junction_recall = stats[6]
 *     junction_precision = stats[7]
 *     junction_f1 = stats[8]             # <<<<<<<<<<<<<<
 * 
 *     ccode = ""
 */
  __pyx_v_junction_f1 = (__pyx_v_stats[8]);

  /* "Mikado/scales/contrast.pyx":161
 *     junction_f1 = stats[8]
 * 
 *     ccode = ""             # <<<<<<<<<<<<<<
 *     if junction_recall == 1 and junction_precision < 1:
 *         # Check if this is an extension
 */
  __Pyx_INCREF(__pyx_kp_s_);
  __pyx_v_ccode = __pyx_kp_s_;

  /* "Mikado/scales/contrast.pyx":162
 * 
 *     ccode = ""
 *     if junction_recall == 1 and junction_precision < 1:             # <<<<<<<<<<<<<<
 *         # Check if this is an extension
 *         # If one of the new splices is internal to the intron chain, it's a j
 */
  __pyx_t_7 = ((__pyx_v_junction_recall == 1.0) != 0);
  if (__pyx_t_7) {
  } else {
    __pyx_t_6 = __pyx_t_7;
    goto __pyx_L4_bool_binop_done;
  }
  __pyx_t_7 = ((__pyx_v_junction_precision < 1.0) != 0);
  __pyx_t_6 = __pyx_t_7;
  __pyx_L4_bool_binop_done:;
  if (__pyx_t_6) {

    /* "Mikado/scales/contrast.pyx":166
 *         # If one of the new splices is internal to the intron chain, it's a j
 * 
 *         ccode = "n"             # <<<<<<<<<<<<<<
 *         max_splice = max(reference.splices)
 *         min_splice = min(reference.splices)
 */
    __Pyx_INCREF(__pyx_n_s_n);
    __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_n);

    /* "Mikado/scales/contrast.pyx":167
 * 
 *         ccode = "n"
 *         max_splice = max(reference.splices)             # <<<<<<<<<<<<<<
 *         min_splice = min(reference.splices)
 *         for splice in p_splices:
 */
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 167, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 167, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_GIVEREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
    __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 167, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 167, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_v_max_splice = __pyx_t_4;

    /* "Mikado/scales/contrast.pyx":168
 *         ccode = "n"
 *         max_splice = max(reference.splices)
 *         min_splice = min(reference.splices)             # <<<<<<<<<<<<<<
 *         for splice in p_splices:
 *             if splice in r_splices:
 */
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 168, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 168, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __Pyx_GIVEREF(__pyx_t_1);
    PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
    __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_min, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 168, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
    __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 168, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_v_min_splice = __pyx_t_4;

    /* "Mikado/scales/contrast.pyx":169
 *         max_splice = max(reference.splices)
 *         min_splice = min(reference.splices)
 *         for splice in p_splices:             # <<<<<<<<<<<<<<
 *             if splice in r_splices:
 *                 continue
 */
    __pyx_t_1 = PyObject_GetIter(__pyx_v_p_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 169, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 169, __pyx_L1_error)
    for (;;) {
      {
        __pyx_t_2 = __pyx_t_8(__pyx_t_1);
        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_ERR(0, 169, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_2);
      }
      __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 169, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_v_splice = __pyx_t_4;

      /* "Mikado/scales/contrast.pyx":170
 *         min_splice = min(reference.splices)
 *         for splice in p_splices:
 *             if splice in r_splices:             # <<<<<<<<<<<<<<
 *                 continue
 *             if min_splice < splice < max_splice:
 */
      __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_splice); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 170, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_t_2, __pyx_v_r_splices, Py_EQ)); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 170, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_t_7 = (__pyx_t_6 != 0);
      if (__pyx_t_7) {

        /* "Mikado/scales/contrast.pyx":171
 *         for splice in p_splices:
 *             if splice in r_splices:
 *                 continue             # <<<<<<<<<<<<<<
 *             if min_splice < splice < max_splice:
 *                 ccode = "j"
 */
        goto __pyx_L6_continue;

        /* "Mikado/scales/contrast.pyx":170
 *         min_splice = min(reference.splices)
 *         for splice in p_splices:
 *             if splice in r_splices:             # <<<<<<<<<<<<<<
 *                 continue
 *             if min_splice < splice < max_splice:
 */
      }

      /* "Mikado/scales/contrast.pyx":172
 *             if splice in r_splices:
 *                 continue
 *             if min_splice < splice < max_splice:             # <<<<<<<<<<<<<<
 *                 ccode = "j"
 *                 break
 */
      __pyx_t_7 = (__pyx_v_min_splice < __pyx_v_splice);
      if (__pyx_t_7) {
        __pyx_t_7 = (__pyx_v_splice < __pyx_v_max_splice);
      }
      __pyx_t_6 = (__pyx_t_7 != 0);
      if (__pyx_t_6) {

        /* "Mikado/scales/contrast.pyx":173
 *                 continue
 *             if min_splice < splice < max_splice:
 *                 ccode = "j"             # <<<<<<<<<<<<<<
 *                 break
 *             elif r_start < splice < r_end:
 */
        __Pyx_INCREF(__pyx_n_s_j);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_j);

        /* "Mikado/scales/contrast.pyx":174
 *             if min_splice < splice < max_splice:
 *                 ccode = "j"
 *                 break             # <<<<<<<<<<<<<<
 *             elif r_start < splice < r_end:
 *                 ccode = "J"
 */
        goto __pyx_L7_break;

        /* "Mikado/scales/contrast.pyx":172
 *             if splice in r_splices:
 *                 continue
 *             if min_splice < splice < max_splice:             # <<<<<<<<<<<<<<
 *                 ccode = "j"
 *                 break
 */
      }

      /* "Mikado/scales/contrast.pyx":175
 *                 ccode = "j"
 *                 break
 *             elif r_start < splice < r_end:             # <<<<<<<<<<<<<<
 *                 ccode = "J"
 * 
 */
      __pyx_t_6 = (__pyx_v_r_start < __pyx_v_splice);
      if (__pyx_t_6) {
        __pyx_t_6 = (__pyx_v_splice < __pyx_v_r_end);
      }
      __pyx_t_7 = (__pyx_t_6 != 0);
      if (__pyx_t_7) {

        /* "Mikado/scales/contrast.pyx":176
 *                 break
 *             elif r_start < splice < r_end:
 *                 ccode = "J"             # <<<<<<<<<<<<<<
 * 
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:
 */
        __Pyx_INCREF(__pyx_n_s_J);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_J);

        /* "Mikado/scales/contrast.pyx":175
 *                 ccode = "j"
 *                 break
 *             elif r_start < splice < r_end:             # <<<<<<<<<<<<<<
 *                 ccode = "J"
 * 
 */
      }

      /* "Mikado/scales/contrast.pyx":169
 *         max_splice = max(reference.splices)
 *         min_splice = min(reference.splices)
 *         for splice in p_splices:             # <<<<<<<<<<<<<<
 *             if splice in r_splices:
 *                 continue
 */
      __pyx_L6_continue:;
    }
    __pyx_L7_break:;
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

    /* "Mikado/scales/contrast.pyx":162
 * 
 *     ccode = ""
 *     if junction_recall == 1 and junction_precision < 1:             # <<<<<<<<<<<<<<
 *         # Check if this is an extension
 *         # If one of the new splices is internal to the intron chain, it's a j
 */
    goto __pyx_L3;
  }

  /* "Mikado/scales/contrast.pyx":178
 *                 ccode = "J"
 * 
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:             # <<<<<<<<<<<<<<
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:
 */
  __pyx_t_6 = (0.0 < __pyx_v_junction_recall);
  if (__pyx_t_6) {
    __pyx_t_6 = (__pyx_v_junction_recall < 1.0);
  }
  __pyx_t_9 = (__pyx_t_6 != 0);
  if (__pyx_t_9) {
  } else {
    __pyx_t_7 = __pyx_t_9;
    goto __pyx_L10_bool_binop_done;
  }
  __pyx_t_9 = (0.0 < __pyx_v_junction_precision);
  if (__pyx_t_9) {
    __pyx_t_9 = (__pyx_v_junction_precision < 1.0);
  }
  __pyx_t_6 = (__pyx_t_9 != 0);
  __pyx_t_7 = __pyx_t_6;
  __pyx_L10_bool_binop_done:;
  if (__pyx_t_7) {

    /* "Mikado/scales/contrast.pyx":179
 * 
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:
 *         ccode = "j"             # <<<<<<<<<<<<<<
 *     elif junction_precision == 1 and junction_recall < 1:
 *         if nucl_precision == 1:
 */
    __Pyx_INCREF(__pyx_n_s_j);
    __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_j);

    /* "Mikado/scales/contrast.pyx":178
 *                 ccode = "J"
 * 
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:             # <<<<<<<<<<<<<<
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:
 */
    goto __pyx_L3;
  }

  /* "Mikado/scales/contrast.pyx":180
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:             # <<<<<<<<<<<<<<
 *         if nucl_precision == 1:
 *             # assert nucl_recall < 1
 */
  __pyx_t_6 = ((__pyx_v_junction_precision == 1.0) != 0);
  if (__pyx_t_6) {
  } else {
    __pyx_t_7 = __pyx_t_6;
    goto __pyx_L12_bool_binop_done;
  }
  __pyx_t_6 = ((__pyx_v_junction_recall < 1.0) != 0);
  __pyx_t_7 = __pyx_t_6;
  __pyx_L12_bool_binop_done:;
  if (__pyx_t_7) {

    /* "Mikado/scales/contrast.pyx":181
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:
 *         if nucl_precision == 1:             # <<<<<<<<<<<<<<
 *             # assert nucl_recall < 1
 *             ccode = "c"
 */
    __pyx_t_7 = ((__pyx_v_nucl_precision == 1.0) != 0);
    if (__pyx_t_7) {

      /* "Mikado/scales/contrast.pyx":183
 *         if nucl_precision == 1:
 *             # assert nucl_recall < 1
 *             ccode = "c"             # <<<<<<<<<<<<<<
 *         else:
 *             missed_introns = r_introns - p_introns
 */
      __Pyx_INCREF(__pyx_n_s_c);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_c);

      /* "Mikado/scales/contrast.pyx":181
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:
 *         if nucl_precision == 1:             # <<<<<<<<<<<<<<
 *             # assert nucl_recall < 1
 *             ccode = "c"
 */
      goto __pyx_L14;
    }

    /* "Mikado/scales/contrast.pyx":185
 *             ccode = "c"
 *         else:
 *             missed_introns = r_introns - p_introns             # <<<<<<<<<<<<<<
 *             min_splice, max_splice = min(prediction.splices), max(prediction.splices)
 *             start_in = 0
 */
    /*else*/ {
      __pyx_t_1 = PyNumber_Subtract(__pyx_v_r_introns, __pyx_v_p_introns); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 185, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_v_missed_introns = __pyx_t_1;
      __pyx_t_1 = 0;

      /* "Mikado/scales/contrast.pyx":186
 *         else:
 *             missed_introns = r_introns - p_introns
 *             min_splice, max_splice = min(prediction.splices), max(prediction.splices)             # <<<<<<<<<<<<<<
 *             start_in = 0
 *             end_in = 0
 */
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __Pyx_GIVEREF(__pyx_t_1);
      PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
      __pyx_t_1 = 0;
      __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_min, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_splices); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __Pyx_GIVEREF(__pyx_t_1);
      PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
      __pyx_t_1 = 0;
      __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
      __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 186, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_v_min_splice = __pyx_t_4;
      __pyx_v_max_splice = __pyx_t_5;

      /* "Mikado/scales/contrast.pyx":187
 *             missed_introns = r_introns - p_introns
 *             min_splice, max_splice = min(prediction.splices), max(prediction.splices)
 *             start_in = 0             # <<<<<<<<<<<<<<
 *             end_in = 0
 *             for intron in missed_introns:
 */
      __pyx_v_start_in = 0;

      /* "Mikado/scales/contrast.pyx":188
 *             min_splice, max_splice = min(prediction.splices), max(prediction.splices)
 *             start_in = 0
 *             end_in = 0             # <<<<<<<<<<<<<<
 *             for intron in missed_introns:
 *                 intron_start, intron_end = intron
 */
      __pyx_v_end_in = 0;

      /* "Mikado/scales/contrast.pyx":189
 *             start_in = 0
 *             end_in = 0
 *             for intron in missed_introns:             # <<<<<<<<<<<<<<
 *                 intron_start, intron_end = intron
 *                 if p_start < intron_start and intron_end < min_splice:
 */
      if (likely(PyList_CheckExact(__pyx_v_missed_introns)) || PyTuple_CheckExact(__pyx_v_missed_introns)) {
        __pyx_t_1 = __pyx_v_missed_introns; __Pyx_INCREF(__pyx_t_1); __pyx_t_10 = 0;
        __pyx_t_8 = NULL;
      } else {
        __pyx_t_10 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_missed_introns); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 189, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 189, __pyx_L1_error)
      }
      for (;;) {
        if (likely(!__pyx_t_8)) {
          if (likely(PyList_CheckExact(__pyx_t_1))) {
            if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_1)) break;
            #if CYTHON_COMPILING_IN_CPYTHON
            __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 189, __pyx_L1_error)
            #else
            __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 189, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_2);
            #endif
          } else {
            if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
            #if CYTHON_COMPILING_IN_CPYTHON
            __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 189, __pyx_L1_error)
            #else
            __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 189, __pyx_L1_error)
            __Pyx_GOTREF(__pyx_t_2);
            #endif
          }
        } else {
          __pyx_t_2 = __pyx_t_8(__pyx_t_1);
          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_ERR(0, 189, __pyx_L1_error)
            }
            break;
          }
          __Pyx_GOTREF(__pyx_t_2);
        }
        __Pyx_XDECREF_SET(__pyx_v_intron, __pyx_t_2);
        __pyx_t_2 = 0;

        /* "Mikado/scales/contrast.pyx":190
 *             end_in = 0
 *             for intron in missed_introns:
 *                 intron_start, intron_end = intron             # <<<<<<<<<<<<<<
 *                 if p_start < intron_start and intron_end < min_splice:
 *                     start_in = 1
 */
        if ((likely(PyTuple_CheckExact(__pyx_v_intron))) || (PyList_CheckExact(__pyx_v_intron))) {
          PyObject* sequence = __pyx_v_intron;
          #if CYTHON_COMPILING_IN_CPYTHON
          Py_ssize_t size = Py_SIZE(sequence);
          #else
          Py_ssize_t size = PySequence_Size(sequence);
          #endif
          if (unlikely(size != 2)) {
            if (size > 2) __Pyx_RaiseTooManyValuesError(2);
            else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
            __PYX_ERR(0, 190, __pyx_L1_error)
          }
          #if CYTHON_COMPILING_IN_CPYTHON
          if (likely(PyTuple_CheckExact(sequence))) {
            __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0); 
            __pyx_t_11 = PyTuple_GET_ITEM(sequence, 1); 
          } else {
            __pyx_t_2 = PyList_GET_ITEM(sequence, 0); 
            __pyx_t_11 = PyList_GET_ITEM(sequence, 1); 
          }
          __Pyx_INCREF(__pyx_t_2);
          __Pyx_INCREF(__pyx_t_11);
          #else
          __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 190, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_11 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 190, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_11);
          #endif
        } else {
          Py_ssize_t index = -1;
          __pyx_t_12 = PyObject_GetIter(__pyx_v_intron); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 190, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_12);
          __pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
          index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_2)) goto __pyx_L17_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_2);
          index = 1; __pyx_t_11 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_11)) goto __pyx_L17_unpacking_failed;
          __Pyx_GOTREF(__pyx_t_11);
          if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) __PYX_ERR(0, 190, __pyx_L1_error)
          __pyx_t_13 = NULL;
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          goto __pyx_L18_unpacking_done;
          __pyx_L17_unpacking_failed:;
          __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
          __pyx_t_13 = NULL;
          if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
          __PYX_ERR(0, 190, __pyx_L1_error)
          __pyx_L18_unpacking_done:;
        }
        __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 190, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
        __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_11); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 190, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
        __pyx_v_intron_start = __pyx_t_5;
        __pyx_v_intron_end = __pyx_t_4;

        /* "Mikado/scales/contrast.pyx":191
 *             for intron in missed_introns:
 *                 intron_start, intron_end = intron
 *                 if p_start < intron_start and intron_end < min_splice:             # <<<<<<<<<<<<<<
 *                     start_in = 1
 *                     break
 */
        __pyx_t_6 = ((__pyx_v_p_start < __pyx_v_intron_start) != 0);
        if (__pyx_t_6) {
        } else {
          __pyx_t_7 = __pyx_t_6;
          goto __pyx_L20_bool_binop_done;
        }
        __pyx_t_6 = ((__pyx_v_intron_end < __pyx_v_min_splice) != 0);
        __pyx_t_7 = __pyx_t_6;
        __pyx_L20_bool_binop_done:;
        if (__pyx_t_7) {

          /* "Mikado/scales/contrast.pyx":192
 *                 intron_start, intron_end = intron
 *                 if p_start < intron_start and intron_end < min_splice:
 *                     start_in = 1             # <<<<<<<<<<<<<<
 *                     break
 *                 if p_end > intron_end and intron_start > max_splice:
 */
          __pyx_v_start_in = 1;

          /* "Mikado/scales/contrast.pyx":193
 *                 if p_start < intron_start and intron_end < min_splice:
 *                     start_in = 1
 *                     break             # <<<<<<<<<<<<<<
 *                 if p_end > intron_end and intron_start > max_splice:
 *                     end_in = 1
 */
          goto __pyx_L16_break;

          /* "Mikado/scales/contrast.pyx":191
 *             for intron in missed_introns:
 *                 intron_start, intron_end = intron
 *                 if p_start < intron_start and intron_end < min_splice:             # <<<<<<<<<<<<<<
 *                     start_in = 1
 *                     break
 */
        }

        /* "Mikado/scales/contrast.pyx":194
 *                     start_in = 1
 *                     break
 *                 if p_end > intron_end and intron_start > max_splice:             # <<<<<<<<<<<<<<
 *                     end_in = 1
 *                     break
 */
        __pyx_t_6 = ((__pyx_v_p_end > __pyx_v_intron_end) != 0);
        if (__pyx_t_6) {
        } else {
          __pyx_t_7 = __pyx_t_6;
          goto __pyx_L23_bool_binop_done;
        }
        __pyx_t_6 = ((__pyx_v_intron_start > __pyx_v_max_splice) != 0);
        __pyx_t_7 = __pyx_t_6;
        __pyx_L23_bool_binop_done:;
        if (__pyx_t_7) {

          /* "Mikado/scales/contrast.pyx":195
 *                     break
 *                 if p_end > intron_end and intron_start > max_splice:
 *                     end_in = 1             # <<<<<<<<<<<<<<
 *                     break
 * 
 */
          __pyx_v_end_in = 1;

          /* "Mikado/scales/contrast.pyx":196
 *                 if p_end > intron_end and intron_start > max_splice:
 *                     end_in = 1
 *                     break             # <<<<<<<<<<<<<<
 * 
 *             if start_in or end_in:
 */
          goto __pyx_L16_break;

          /* "Mikado/scales/contrast.pyx":194
 *                     start_in = 1
 *                     break
 *                 if p_end > intron_end and intron_start > max_splice:             # <<<<<<<<<<<<<<
 *                     end_in = 1
 *                     break
 */
        }

        /* "Mikado/scales/contrast.pyx":189
 *             start_in = 0
 *             end_in = 0
 *             for intron in missed_introns:             # <<<<<<<<<<<<<<
 *                 intron_start, intron_end = intron
 *                 if p_start < intron_start and intron_end < min_splice:
 */
      }
      __pyx_L16_break:;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

      /* "Mikado/scales/contrast.pyx":198
 *                     break
 * 
 *             if start_in or end_in:             # <<<<<<<<<<<<<<
 *                 ccode = "j"
 *             else:
 */
      __pyx_t_6 = (__pyx_v_start_in != 0);
      if (!__pyx_t_6) {
      } else {
        __pyx_t_7 = __pyx_t_6;
        goto __pyx_L26_bool_binop_done;
      }
      __pyx_t_6 = (__pyx_v_end_in != 0);
      __pyx_t_7 = __pyx_t_6;
      __pyx_L26_bool_binop_done:;
      if (__pyx_t_7) {

        /* "Mikado/scales/contrast.pyx":199
 * 
 *             if start_in or end_in:
 *                 ccode = "j"             # <<<<<<<<<<<<<<
 *             else:
 *                 ccode = "C"
 */
        __Pyx_INCREF(__pyx_n_s_j);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_j);

        /* "Mikado/scales/contrast.pyx":198
 *                     break
 * 
 *             if start_in or end_in:             # <<<<<<<<<<<<<<
 *                 ccode = "j"
 *             else:
 */
        goto __pyx_L25;
      }

      /* "Mikado/scales/contrast.pyx":201
 *                 ccode = "j"
 *             else:
 *                 ccode = "C"             # <<<<<<<<<<<<<<
 * 
 *     elif junction_recall == 0 and junction_precision == 0:
 */
      /*else*/ {
        __Pyx_INCREF(__pyx_n_s_C);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_C);
      }
      __pyx_L25:;
    }
    __pyx_L14:;

    /* "Mikado/scales/contrast.pyx":180
 *     elif 0 < junction_recall < 1 and 0 < junction_precision < 1:
 *         ccode = "j"
 *     elif junction_precision == 1 and junction_recall < 1:             # <<<<<<<<<<<<<<
 *         if nucl_precision == 1:
 *             # assert nucl_recall < 1
 */
    goto __pyx_L3;
  }

  /* "Mikado/scales/contrast.pyx":203
 *                 ccode = "C"
 * 
 *     elif junction_recall == 0 and junction_precision == 0:             # <<<<<<<<<<<<<<
 *         if nucl_f1 > 0:
 *             overlapping_introns = 0
 */
  __pyx_t_6 = ((__pyx_v_junction_recall == 0.0) != 0);
  if (__pyx_t_6) {
  } else {
    __pyx_t_7 = __pyx_t_6;
    goto __pyx_L28_bool_binop_done;
  }
  __pyx_t_6 = ((__pyx_v_junction_precision == 0.0) != 0);
  __pyx_t_7 = __pyx_t_6;
  __pyx_L28_bool_binop_done:;
  if (__pyx_t_7) {

    /* "Mikado/scales/contrast.pyx":204
 * 
 *     elif junction_recall == 0 and junction_precision == 0:
 *         if nucl_f1 > 0:             # <<<<<<<<<<<<<<
 *             overlapping_introns = 0
 *             ccode = "o"
 */
    __pyx_t_7 = ((__pyx_v_nucl_f1 > 0.0) != 0);
    if (__pyx_t_7) {

      /* "Mikado/scales/contrast.pyx":205
 *     elif junction_recall == 0 and junction_precision == 0:
 *         if nucl_f1 > 0:
 *             overlapping_introns = 0             # <<<<<<<<<<<<<<
 *             ccode = "o"
 *             for intron in p_introns:
 */
      __pyx_v_overlapping_introns = 0;

      /* "Mikado/scales/contrast.pyx":206
 *         if nucl_f1 > 0:
 *             overlapping_introns = 0
 *             ccode = "o"             # <<<<<<<<<<<<<<
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:
 */
      __Pyx_INCREF(__pyx_n_s_o);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_o);

      /* "Mikado/scales/contrast.pyx":207
 *             overlapping_introns = 0
 *             ccode = "o"
 *             for intron in p_introns:             # <<<<<<<<<<<<<<
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 */
      __pyx_t_1 = PyObject_GetIter(__pyx_v_p_introns); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 207, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 207, __pyx_L1_error)
      for (;;) {
        {
          __pyx_t_11 = __pyx_t_8(__pyx_t_1);
          if (unlikely(!__pyx_t_11)) {
            PyObject* exc_type = PyErr_Occurred();
            if (exc_type) {
              if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
              else __PYX_ERR(0, 207, __pyx_L1_error)
            }
            break;
          }
          __Pyx_GOTREF(__pyx_t_11);
        }
        __Pyx_XDECREF_SET(__pyx_v_intron, __pyx_t_11);
        __pyx_t_11 = 0;

        /* "Mikado/scales/contrast.pyx":208
 *             ccode = "o"
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:             # <<<<<<<<<<<<<<
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 *                                  intron[0], intron[1],
 */
        __pyx_t_11 = PyObject_GetIter(__pyx_v_r_introns); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 208, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_11);
        __pyx_t_14 = Py_TYPE(__pyx_t_11)->tp_iternext; if (unlikely(!__pyx_t_14)) __PYX_ERR(0, 208, __pyx_L1_error)
        for (;;) {
          {
            __pyx_t_2 = __pyx_t_14(__pyx_t_11);
            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_ERR(0, 208, __pyx_L1_error)
              }
              break;
            }
            __Pyx_GOTREF(__pyx_t_2);
          }
          __Pyx_XDECREF_SET(__pyx_v_ref_intron, __pyx_t_2);
          __pyx_t_2 = 0;

          /* "Mikado/scales/contrast.pyx":209
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],             # <<<<<<<<<<<<<<
 *                                  intron[0], intron[1],
 *                                  0, 1) > 0:
 */
          __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_ref_intron, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 209, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 209, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
          __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_ref_intron, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 209, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 209, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

          /* "Mikado/scales/contrast.pyx":210
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 *                                  intron[0], intron[1],             # <<<<<<<<<<<<<<
 *                                  0, 1) > 0:
 *                         # corr_exons.append((ref_index, pred_index))
 */
          __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_intron, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 210, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_15 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_15 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 210, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
          __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_intron, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 210, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_2);
          __pyx_t_16 = __Pyx_PyInt_As_long(__pyx_t_2); if (unlikely((__pyx_t_16 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 210, __pyx_L1_error)
          __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

          /* "Mikado/scales/contrast.pyx":211
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 *                                  intron[0], intron[1],
 *                                  0, 1) > 0:             # <<<<<<<<<<<<<<
 *                         # corr_exons.append((ref_index, pred_index))
 *                         overlapping_introns += 1
 */
          __pyx_t_7 = ((__pyx_f_6Mikado_9utilities_7overlap_c_overlap(__pyx_t_4, __pyx_t_5, __pyx_t_15, __pyx_t_16, 0, 1) > 0) != 0);

          /* "Mikado/scales/contrast.pyx":209
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],             # <<<<<<<<<<<<<<
 *                                  intron[0], intron[1],
 *                                  0, 1) > 0:
 */
          if (__pyx_t_7) {

            /* "Mikado/scales/contrast.pyx":213
 *                                  0, 1) > 0:
 *                         # corr_exons.append((ref_index, pred_index))
 *                         overlapping_introns += 1             # <<<<<<<<<<<<<<
 *                 if overlapping_introns >= 1:
 *                     ccode = "h"
 */
            __pyx_v_overlapping_introns = (__pyx_v_overlapping_introns + 1);

            /* "Mikado/scales/contrast.pyx":209
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],             # <<<<<<<<<<<<<<
 *                                  intron[0], intron[1],
 *                                  0, 1) > 0:
 */
          }

          /* "Mikado/scales/contrast.pyx":208
 *             ccode = "o"
 *             for intron in p_introns:
 *                 for ref_intron in r_introns:             # <<<<<<<<<<<<<<
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 *                                  intron[0], intron[1],
 */
        }
        __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;

        /* "Mikado/scales/contrast.pyx":214
 *                         # corr_exons.append((ref_index, pred_index))
 *                         overlapping_introns += 1
 *                 if overlapping_introns >= 1:             # <<<<<<<<<<<<<<
 *                     ccode = "h"
 *                     break
 */
        __pyx_t_7 = ((__pyx_v_overlapping_introns >= 1) != 0);
        if (__pyx_t_7) {

          /* "Mikado/scales/contrast.pyx":215
 *                         overlapping_introns += 1
 *                 if overlapping_introns >= 1:
 *                     ccode = "h"             # <<<<<<<<<<<<<<
 *                     break
 *         else:
 */
          __Pyx_INCREF(__pyx_n_s_h);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_h);

          /* "Mikado/scales/contrast.pyx":216
 *                 if overlapping_introns >= 1:
 *                     ccode = "h"
 *                     break             # <<<<<<<<<<<<<<
 *         else:
 *             if nucl_overlap == 0:
 */
          goto __pyx_L32_break;

          /* "Mikado/scales/contrast.pyx":214
 *                         # corr_exons.append((ref_index, pred_index))
 *                         overlapping_introns += 1
 *                 if overlapping_introns >= 1:             # <<<<<<<<<<<<<<
 *                     ccode = "h"
 *                     break
 */
        }

        /* "Mikado/scales/contrast.pyx":207
 *             overlapping_introns = 0
 *             ccode = "o"
 *             for intron in p_introns:             # <<<<<<<<<<<<<<
 *                 for ref_intron in r_introns:
 *                     if c_overlap(ref_intron[0], ref_intron[1],
 */
      }
      __pyx_L32_break:;
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

      /* "Mikado/scales/contrast.pyx":204
 * 
 *     elif junction_recall == 0 and junction_precision == 0:
 *         if nucl_f1 > 0:             # <<<<<<<<<<<<<<
 *             overlapping_introns = 0
 *             ccode = "o"
 */
      goto __pyx_L30;
    }

    /* "Mikado/scales/contrast.pyx":218
 *                     break
 *         else:
 *             if nucl_overlap == 0:             # <<<<<<<<<<<<<<
 *                 # The only explanation for no nucleotide overlap
 *                 # and no junction overlap is that it is inside an intron
 */
    /*else*/ {
      __pyx_t_7 = ((__pyx_v_nucl_overlap == 0) != 0);
      if (__pyx_t_7) {

        /* "Mikado/scales/contrast.pyx":221
 *                 # The only explanation for no nucleotide overlap
 *                 # and no junction overlap is that it is inside an intron
 *                 if r_start < p_start < r_end:             # <<<<<<<<<<<<<<
 *                     ccode = "I"
 *                 elif p_start < r_start < p_end:
 */
        __pyx_t_7 = (__pyx_v_r_start < __pyx_v_p_start);
        if (__pyx_t_7) {
          __pyx_t_7 = (__pyx_v_p_start < __pyx_v_r_end);
        }
        __pyx_t_6 = (__pyx_t_7 != 0);
        if (__pyx_t_6) {

          /* "Mikado/scales/contrast.pyx":222
 *                 # and no junction overlap is that it is inside an intron
 *                 if r_start < p_start < r_end:
 *                     ccode = "I"             # <<<<<<<<<<<<<<
 *                 elif p_start < r_start < p_end:
 *                     ccode = "rI"  # reverse intron retention
 */
          __Pyx_INCREF(__pyx_n_s_I);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_I);

          /* "Mikado/scales/contrast.pyx":221
 *                 # The only explanation for no nucleotide overlap
 *                 # and no junction overlap is that it is inside an intron
 *                 if r_start < p_start < r_end:             # <<<<<<<<<<<<<<
 *                     ccode = "I"
 *                 elif p_start < r_start < p_end:
 */
          goto __pyx_L38;
        }

        /* "Mikado/scales/contrast.pyx":223
 *                 if r_start < p_start < r_end:
 *                     ccode = "I"
 *                 elif p_start < r_start < p_end:             # <<<<<<<<<<<<<<
 *                     ccode = "rI"  # reverse intron retention
 * 
 */
        __pyx_t_6 = (__pyx_v_p_start < __pyx_v_r_start);
        if (__pyx_t_6) {
          __pyx_t_6 = (__pyx_v_r_start < __pyx_v_p_end);
        }
        __pyx_t_7 = (__pyx_t_6 != 0);
        if (__pyx_t_7) {

          /* "Mikado/scales/contrast.pyx":224
 *                     ccode = "I"
 *                 elif p_start < r_start < p_end:
 *                     ccode = "rI"  # reverse intron retention             # <<<<<<<<<<<<<<
 * 
 *     return ccode
 */
          __Pyx_INCREF(__pyx_n_s_rI);
          __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_rI);

          /* "Mikado/scales/contrast.pyx":223
 *                 if r_start < p_start < r_end:
 *                     ccode = "I"
 *                 elif p_start < r_start < p_end:             # <<<<<<<<<<<<<<
 *                     ccode = "rI"  # reverse intron retention
 * 
 */
        }
        __pyx_L38:;

        /* "Mikado/scales/contrast.pyx":218
 *                     break
 *         else:
 *             if nucl_overlap == 0:             # <<<<<<<<<<<<<<
 *                 # The only explanation for no nucleotide overlap
 *                 # and no junction overlap is that it is inside an intron
 */
      }
    }
    __pyx_L30:;

    /* "Mikado/scales/contrast.pyx":203
 *                 ccode = "C"
 * 
 *     elif junction_recall == 0 and junction_precision == 0:             # <<<<<<<<<<<<<<
 *         if nucl_f1 > 0:
 *             overlapping_introns = 0
 */
  }
  __pyx_L3:;

  /* "Mikado/scales/contrast.pyx":226
 *                     ccode = "rI"  # reverse intron retention
 * 
 *     return ccode             # <<<<<<<<<<<<<<
 * 
 * 
 */
  __Pyx_XDECREF(__pyx_r);
  __Pyx_INCREF(__pyx_v_ccode);
  __pyx_r = __pyx_v_ccode;
  goto __pyx_L0;

  /* "Mikado/scales/contrast.pyx":114
 * 
 * 
 * cdef str __assign_multiexonic_ccode(prediction, reference, long nucl_overlap, double stats[9]):             # <<<<<<<<<<<<<<
 * 
 *     """
 */

  /* function exit code */
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_11);
  __Pyx_XDECREF(__pyx_t_12);
  __Pyx_AddTraceback("Mikado.scales.contrast.__assign_multiexonic_ccode", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v_ccode);
  __Pyx_XDECREF(__pyx_v_r_splices);
  __Pyx_XDECREF(__pyx_v_p_splices);
  __Pyx_XDECREF(__pyx_v_r_introns);
  __Pyx_XDECREF(__pyx_v_p_introns);
  __Pyx_XDECREF(__pyx_v_missed_introns);
  __Pyx_XDECREF(__pyx_v_intron);
  __Pyx_XDECREF(__pyx_v_ref_intron);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* "Mikado/scales/contrast.pyx":231
 * @cython.profile(True)
 * @cython.cdivision(True)
 * cpdef tuple compare(prediction, reference, bint lenient=False):             # <<<<<<<<<<<<<<
 * 
 *     """Cython function to compare two transcripts and determine a ccode.
 */

static PyObject *__pyx_pw_6Mikado_6scales_8contrast_1compare(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_f_6Mikado_6scales_8contrast_compare(PyObject *__pyx_v_prediction, PyObject *__pyx_v_reference, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_6Mikado_6scales_8contrast_compare *__pyx_optional_args) {
  int __pyx_v_lenient = ((int)0);
  long __pyx_v_nucl_overlap;
  long __pyx_v_distance;
  PyObject *__pyx_v___pred_exons = 0;
  PyObject *__pyx_v___ref_exons = 0;
  long __pyx_v_exon_a;
  long __pyx_v_exon_b;
  long __pyx_v_other_exon_a;
  long __pyx_v_other_exon_b;
  double __pyx_v_p_cdna_length;
  double __pyx_v_r_cdna_length;
  double __pyx_v_nucl_recall;
  double __pyx_v_nucl_precision;
  double __pyx_v_nucl_f1;
  double __pyx_v_exon_recall;
  double __pyx_v_exon_precision;
  double __pyx_v_exon_f1;
  double __pyx_v_junction_recall;
  double __pyx_v_junction_precision;
  double __pyx_v_junction_f1;
  long __pyx_v_r_exon_num;
  long __pyx_v_p_exon_num;
  long __pyx_v_p_start;
  long __pyx_v_p_end;
  long __pyx_v_r_start;
  long __pyx_v_r_end;
  double __pyx_v_recalled_exons;
  PyObject *__pyx_v_r_splices = 0;
  PyObject *__pyx_v_p_splices = 0;
  long __pyx_v_junction_overlap;
  double __pyx_v_stats[9];
  PyObject *__pyx_v_r_strand = 0;
  PyObject *__pyx_v_p_strand = 0;
  PyObject *__pyx_v_exon = NULL;
  PyObject *__pyx_v_other_exon = NULL;
  PyObject *__pyx_v_reference_exon = NULL;
  PyObject *__pyx_v_len_rsplices = NULL;
  PyObject *__pyx_v_len_psplices = NULL;
  PyObject *__pyx_v_ccode = NULL;
  PyObject *__pyx_v_result = NULL;
  PyObject *__pyx_r = NULL;
  __Pyx_TraceDeclarations
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  double __pyx_t_4;
  double __pyx_t_5;
  long __pyx_t_6;
  long __pyx_t_7;
  long __pyx_t_8;
  long __pyx_t_9;
  int __pyx_t_10;
  int __pyx_t_11;
  Py_ssize_t __pyx_t_12;
  PyObject *(*__pyx_t_13)(PyObject *);
  int __pyx_t_14;
  Py_ssize_t __pyx_t_15;
  PyObject *(*__pyx_t_16)(PyObject *);
  PyObject *__pyx_t_17 = NULL;
  PyObject *__pyx_t_18 = NULL;
  PyObject *__pyx_t_19 = NULL;
  int __pyx_t_20;
  PyObject *__pyx_t_21 = NULL;
  PyObject *__pyx_t_22 = NULL;
  PyObject *__pyx_t_23 = NULL;
  PyObject *__pyx_t_24 = NULL;
  PyObject *__pyx_t_25 = NULL;
  PyObject *__pyx_t_26 = NULL;
  PyObject *__pyx_t_27 = NULL;
  PyObject *__pyx_t_28 = NULL;
  PyObject *__pyx_t_29 = NULL;
  PyObject *__pyx_t_30 = NULL;
  PyObject *__pyx_t_31 = NULL;
  PyObject *__pyx_t_32 = NULL;
  PyObject *__pyx_t_33 = NULL;
  PyObject *__pyx_t_34 = NULL;
  __Pyx_RefNannySetupContext("compare", 0);
  __Pyx_TraceCall("compare", __pyx_f[0], 231, 0, __PYX_ERR(0, 231, __pyx_L1_error));
  if (__pyx_optional_args) {
    if (__pyx_optional_args->__pyx_n > 0) {
      __pyx_v_lenient = __pyx_optional_args->lenient;
    }
  }

  /* "Mikado/scales/contrast.pyx":285
 *     """
 * 
 *     prediction.finalize()             # <<<<<<<<<<<<<<
 *     reference.finalize()
 * 
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_finalize); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 285, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = NULL;
  if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  if (__pyx_t_3) {
    __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 285, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  } else {
    __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 285, __pyx_L1_error)
  }
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":286
 * 
 *     prediction.finalize()
 *     reference.finalize()             # <<<<<<<<<<<<<<
 * 
 *     cdef:
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_finalize); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 286, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_3 = NULL;
  if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_2, function);
    }
  }
  if (__pyx_t_3) {
    __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 286, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  } else {
    __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 286, __pyx_L1_error)
  }
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":305
 *         str r_strand, p_strand
 * 
 *     p_cdna_length, r_cdna_length = prediction.cdna_length, reference.cdna_length             # <<<<<<<<<<<<<<
 *     p_exon_num, r_exon_num = prediction.exon_num, reference.exon_num
 *     p_start, p_end, r_start, r_end = (prediction.start, prediction.end,
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_cdna_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 305, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_4 = __pyx_PyFloat_AsDouble(__pyx_t_1); if (unlikely((__pyx_t_4 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 305, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_cdna_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 305, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_1); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 305, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_p_cdna_length = __pyx_t_4;
  __pyx_v_r_cdna_length = __pyx_t_5;

  /* "Mikado/scales/contrast.pyx":306
 * 
 *     p_cdna_length, r_cdna_length = prediction.cdna_length, reference.cdna_length
 *     p_exon_num, r_exon_num = prediction.exon_num, reference.exon_num             # <<<<<<<<<<<<<<
 *     p_start, p_end, r_start, r_end = (prediction.start, prediction.end,
 *                                       reference.start, reference.end)
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 306, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_6 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_6 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 306, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exon_num); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 306, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_7 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_7 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 306, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_p_exon_num = __pyx_t_6;
  __pyx_v_r_exon_num = __pyx_t_7;

  /* "Mikado/scales/contrast.pyx":307
 *     p_cdna_length, r_cdna_length = prediction.cdna_length, reference.cdna_length
 *     p_exon_num, r_exon_num = prediction.exon_num, reference.exon_num
 *     p_start, p_end, r_start, r_end = (prediction.start, prediction.end,             # <<<<<<<<<<<<<<
 *                                       reference.start, reference.end)
 * 
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 307, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_7 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_7 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 307, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 307, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_6 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_6 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 307, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":308
 *     p_exon_num, r_exon_num = prediction.exon_num, reference.exon_num
 *     p_start, p_end, r_start, r_end = (prediction.start, prediction.end,
 *                                       reference.start, reference.end)             # <<<<<<<<<<<<<<
 * 
 *     if reference.strand is None:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 308, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 308, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 308, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_9 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_9 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 308, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_v_p_start = __pyx_t_7;
  __pyx_v_p_end = __pyx_t_6;
  __pyx_v_r_start = __pyx_t_8;
  __pyx_v_r_end = __pyx_t_9;

  /* "Mikado/scales/contrast.pyx":310
 *                                       reference.start, reference.end)
 * 
 *     if reference.strand is None:             # <<<<<<<<<<<<<<
 *         r_strand = ""
 *     else:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 310, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_10 = (__pyx_t_1 == Py_None);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_11 = (__pyx_t_10 != 0);
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":311
 * 
 *     if reference.strand is None:
 *         r_strand = ""             # <<<<<<<<<<<<<<
 *     else:
 *         r_strand = reference.strand
 */
    __Pyx_INCREF(__pyx_kp_s_);
    __pyx_v_r_strand = __pyx_kp_s_;

    /* "Mikado/scales/contrast.pyx":310
 *                                       reference.start, reference.end)
 * 
 *     if reference.strand is None:             # <<<<<<<<<<<<<<
 *         r_strand = ""
 *     else:
 */
    goto __pyx_L3;
  }

  /* "Mikado/scales/contrast.pyx":313
 *         r_strand = ""
 *     else:
 *         r_strand = reference.strand             # <<<<<<<<<<<<<<
 * 
 *     if prediction.strand is None:
 */
  /*else*/ {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 313, __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_ERR(0, 313, __pyx_L1_error)
    __pyx_v_r_strand = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
  }
  __pyx_L3:;

  /* "Mikado/scales/contrast.pyx":315
 *         r_strand = reference.strand
 * 
 *     if prediction.strand is None:             # <<<<<<<<<<<<<<
 *         p_strand = ""
 *     else:
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 315, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_t_11 = (__pyx_t_1 == Py_None);
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_10 = (__pyx_t_11 != 0);
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":316
 * 
 *     if prediction.strand is None:
 *         p_strand = ""             # <<<<<<<<<<<<<<
 *     else:
 *         p_strand = prediction.strand
 */
    __Pyx_INCREF(__pyx_kp_s_);
    __pyx_v_p_strand = __pyx_kp_s_;

    /* "Mikado/scales/contrast.pyx":315
 *         r_strand = reference.strand
 * 
 *     if prediction.strand is None:             # <<<<<<<<<<<<<<
 *         p_strand = ""
 *     else:
 */
    goto __pyx_L4;
  }

  /* "Mikado/scales/contrast.pyx":318
 *         p_strand = ""
 *     else:
 *         p_strand = prediction.strand             # <<<<<<<<<<<<<<
 * 
 *     nucl_overlap = 0
 */
  /*else*/ {
    __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 318, __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_ERR(0, 318, __pyx_L1_error)
    __pyx_v_p_strand = ((PyObject*)__pyx_t_1);
    __pyx_t_1 = 0;
  }
  __pyx_L4:;

  /* "Mikado/scales/contrast.pyx":320
 *         p_strand = prediction.strand
 * 
 *     nucl_overlap = 0             # <<<<<<<<<<<<<<
 * 
 *     __pred_exons = set()
 */
  __pyx_v_nucl_overlap = 0;

  /* "Mikado/scales/contrast.pyx":322
 *     nucl_overlap = 0
 * 
 *     __pred_exons = set()             # <<<<<<<<<<<<<<
 *     __ref_exons = set()
 * 
 */
  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 322, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v___pred_exons = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":323
 * 
 *     __pred_exons = set()
 *     __ref_exons = set()             # <<<<<<<<<<<<<<
 * 
 *     for exon in prediction.exons:
 */
  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 323, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __pyx_v___ref_exons = ((PyObject*)__pyx_t_1);
  __pyx_t_1 = 0;

  /* "Mikado/scales/contrast.pyx":325
 *     __ref_exons = set()
 * 
 *     for exon in prediction.exons:             # <<<<<<<<<<<<<<
 *         exon_a, exon_b = exon[0], exon[1] + 1
 *         __pred_exons.add(exon)
 */
  __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 325, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
    __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0;
    __pyx_t_13 = NULL;
  } else {
    __pyx_t_12 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 325, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_2);
    __pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 325, __pyx_L1_error)
  }
  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  for (;;) {
    if (likely(!__pyx_t_13)) {
      if (likely(PyList_CheckExact(__pyx_t_2))) {
        if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_COMPILING_IN_CPYTHON
        __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) __PYX_ERR(0, 325, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 325, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      } else {
        if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
        #if CYTHON_COMPILING_IN_CPYTHON
        __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) __PYX_ERR(0, 325, __pyx_L1_error)
        #else
        __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 325, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        #endif
      }
    } else {
      __pyx_t_1 = __pyx_t_13(__pyx_t_2);
      if (unlikely(!__pyx_t_1)) {
        PyObject* exc_type = PyErr_Occurred();
        if (exc_type) {
          if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
          else __PYX_ERR(0, 325, __pyx_L1_error)
        }
        break;
      }
      __Pyx_GOTREF(__pyx_t_1);
    }
    __Pyx_XDECREF_SET(__pyx_v_exon, __pyx_t_1);
    __pyx_t_1 = 0;

    /* "Mikado/scales/contrast.pyx":326
 * 
 *     for exon in prediction.exons:
 *         exon_a, exon_b = exon[0], exon[1] + 1             # <<<<<<<<<<<<<<
 *         __pred_exons.add(exon)
 *         for other_exon in reference.exons:
 */
    __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_exon, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 326, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_9 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_9 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 326, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_exon, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 326, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_1);
    __pyx_t_3 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 326, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
    __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 326, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __pyx_v_exon_a = __pyx_t_9;
    __pyx_v_exon_b = __pyx_t_8;

    /* "Mikado/scales/contrast.pyx":327
 *     for exon in prediction.exons:
 *         exon_a, exon_b = exon[0], exon[1] + 1
 *         __pred_exons.add(exon)             # <<<<<<<<<<<<<<
 *         for other_exon in reference.exons:
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1
 */
    __pyx_t_14 = PySet_Add(__pyx_v___pred_exons, __pyx_v_exon); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 327, __pyx_L1_error)

    /* "Mikado/scales/contrast.pyx":328
 *         exon_a, exon_b = exon[0], exon[1] + 1
 *         __pred_exons.add(exon)
 *         for other_exon in reference.exons:             # <<<<<<<<<<<<<<
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1
 *             __ref_exons.add(other_exon)
 */
    __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 328, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    if (likely(PyList_CheckExact(__pyx_t_3)) || PyTuple_CheckExact(__pyx_t_3)) {
      __pyx_t_1 = __pyx_t_3; __Pyx_INCREF(__pyx_t_1); __pyx_t_15 = 0;
      __pyx_t_16 = NULL;
    } else {
      __pyx_t_15 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 328, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_16 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 328, __pyx_L1_error)
    }
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    for (;;) {
      if (likely(!__pyx_t_16)) {
        if (likely(PyList_CheckExact(__pyx_t_1))) {
          if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_COMPILING_IN_CPYTHON
          __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(0, 328, __pyx_L1_error)
          #else
          __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 328, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_3);
          #endif
        } else {
          if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
          #if CYTHON_COMPILING_IN_CPYTHON
          __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) __PYX_ERR(0, 328, __pyx_L1_error)
          #else
          __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 328, __pyx_L1_error)
          __Pyx_GOTREF(__pyx_t_3);
          #endif
        }
      } else {
        __pyx_t_3 = __pyx_t_16(__pyx_t_1);
        if (unlikely(!__pyx_t_3)) {
          PyObject* exc_type = PyErr_Occurred();
          if (exc_type) {
            if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
            else __PYX_ERR(0, 328, __pyx_L1_error)
          }
          break;
        }
        __Pyx_GOTREF(__pyx_t_3);
      }
      __Pyx_XDECREF_SET(__pyx_v_other_exon, __pyx_t_3);
      __pyx_t_3 = 0;

      /* "Mikado/scales/contrast.pyx":329
 *         __pred_exons.add(exon)
 *         for other_exon in reference.exons:
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1             # <<<<<<<<<<<<<<
 *             __ref_exons.add(other_exon)
 *             nucl_overlap += c_overlap(exon_a, exon_b,
 */
      __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_other_exon, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 329, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 329, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_other_exon, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 329, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_17 = __Pyx_PyInt_AddObjC(__pyx_t_3, __pyx_int_1, 1, 0); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 329, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_9 = __Pyx_PyInt_As_long(__pyx_t_17); if (unlikely((__pyx_t_9 == (long)-1) && PyErr_Occurred())) __PYX_ERR(0, 329, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
      __pyx_v_other_exon_a = __pyx_t_8;
      __pyx_v_other_exon_b = __pyx_t_9;

      /* "Mikado/scales/contrast.pyx":330
 *         for other_exon in reference.exons:
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1
 *             __ref_exons.add(other_exon)             # <<<<<<<<<<<<<<
 *             nucl_overlap += c_overlap(exon_a, exon_b,
 *                                       other_exon_a, other_exon_b,
 */
      __pyx_t_14 = PySet_Add(__pyx_v___ref_exons, __pyx_v_other_exon); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 330, __pyx_L1_error)

      /* "Mikado/scales/contrast.pyx":331
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1
 *             __ref_exons.add(other_exon)
 *             nucl_overlap += c_overlap(exon_a, exon_b,             # <<<<<<<<<<<<<<
 *                                       other_exon_a, other_exon_b,
 *                                       flank=0,
 */
      __pyx_v_nucl_overlap = (__pyx_v_nucl_overlap + __pyx_f_6Mikado_9utilities_7overlap_c_overlap(__pyx_v_exon_a, __pyx_v_exon_b, __pyx_v_other_exon_a, __pyx_v_other_exon_b, 0, 1));

      /* "Mikado/scales/contrast.pyx":328
 *         exon_a, exon_b = exon[0], exon[1] + 1
 *         __pred_exons.add(exon)
 *         for other_exon in reference.exons:             # <<<<<<<<<<<<<<
 *             other_exon_a, other_exon_b = other_exon[0], other_exon[1] + 1
 *             __ref_exons.add(other_exon)
 */
    }
    __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;

    /* "Mikado/scales/contrast.pyx":325
 *     __ref_exons = set()
 * 
 *     for exon in prediction.exons:             # <<<<<<<<<<<<<<
 *         exon_a, exon_b = exon[0], exon[1] + 1
 *         __pred_exons.add(exon)
 */
  }
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "Mikado/scales/contrast.pyx":337
 * 
 *     # Quick verification that the overlap is not too big
 *     assert nucl_overlap <= double_min(r_cdna_length, p_cdna_length), \             # <<<<<<<<<<<<<<
 *         (prediction.id, prediction.cdna_length,
 *          reference.id, reference.cdna_length, nucl_overlap)
 */
  #ifndef CYTHON_WITHOUT_ASSERTIONS
  if (unlikely(!Py_OptimizeFlag)) {
    if (unlikely(!((__pyx_v_nucl_overlap <= __pyx_f_6Mikado_6scales_8contrast_double_min(__pyx_v_r_cdna_length, __pyx_v_p_cdna_length)) != 0))) {

      /* "Mikado/scales/contrast.pyx":338
 *     # Quick verification that the overlap is not too big
 *     assert nucl_overlap <= double_min(r_cdna_length, p_cdna_length), \
 *         (prediction.id, prediction.cdna_length,             # <<<<<<<<<<<<<<
 *          reference.id, reference.cdna_length, nucl_overlap)
 * 
 */
      __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_id); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 338, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_2);
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_cdna_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 338, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);

      /* "Mikado/scales/contrast.pyx":339
 *     assert nucl_overlap <= double_min(r_cdna_length, p_cdna_length), \
 *         (prediction.id, prediction.cdna_length,
 *          reference.id, reference.cdna_length, nucl_overlap)             # <<<<<<<<<<<<<<
 * 
 *     nucl_recall = nucl_overlap / r_cdna_length  # Sensitivity
 */
      __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_id); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 339, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_cdna_length); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 339, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_18 = __Pyx_PyInt_From_long(__pyx_v_nucl_overlap); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 339, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);

      /* "Mikado/scales/contrast.pyx":338
 *     # Quick verification that the overlap is not too big
 *     assert nucl_overlap <= double_min(r_cdna_length, p_cdna_length), \
 *         (prediction.id, prediction.cdna_length,             # <<<<<<<<<<<<<<
 *          reference.id, reference.cdna_length, nucl_overlap)
 * 
 */
      __pyx_t_19 = PyTuple_New(5); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 338, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_GIVEREF(__pyx_t_2);
      PyTuple_SET_ITEM(__pyx_t_19, 0, __pyx_t_2);
      __Pyx_GIVEREF(__pyx_t_1);
      PyTuple_SET_ITEM(__pyx_t_19, 1, __pyx_t_1);
      __Pyx_GIVEREF(__pyx_t_17);
      PyTuple_SET_ITEM(__pyx_t_19, 2, __pyx_t_17);
      __Pyx_GIVEREF(__pyx_t_3);
      PyTuple_SET_ITEM(__pyx_t_19, 3, __pyx_t_3);
      __Pyx_GIVEREF(__pyx_t_18);
      PyTuple_SET_ITEM(__pyx_t_19, 4, __pyx_t_18);
      __pyx_t_2 = 0;
      __pyx_t_1 = 0;
      __pyx_t_17 = 0;
      __pyx_t_3 = 0;
      __pyx_t_18 = 0;
      __pyx_t_18 = PyTuple_Pack(1, __pyx_t_19); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 338, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      PyErr_SetObject(PyExc_AssertionError, __pyx_t_18);
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
      __PYX_ERR(0, 337, __pyx_L1_error)
    }
  }
  #endif

  /* "Mikado/scales/contrast.pyx":341
 *          reference.id, reference.cdna_length, nucl_overlap)
 * 
 *     nucl_recall = nucl_overlap / r_cdna_length  # Sensitivity             # <<<<<<<<<<<<<<
 *     nucl_precision = nucl_overlap / p_cdna_length
 *     nucl_f1 = calc_f1(nucl_recall, nucl_precision)
 */
  __pyx_v_nucl_recall = (__pyx_v_nucl_overlap / __pyx_v_r_cdna_length);

  /* "Mikado/scales/contrast.pyx":342
 * 
 *     nucl_recall = nucl_overlap / r_cdna_length  # Sensitivity
 *     nucl_precision = nucl_overlap / p_cdna_length             # <<<<<<<<<<<<<<
 *     nucl_f1 = calc_f1(nucl_recall, nucl_precision)
 * 
 */
  __pyx_v_nucl_precision = (__pyx_v_nucl_overlap / __pyx_v_p_cdna_length);

  /* "Mikado/scales/contrast.pyx":343
 *     nucl_recall = nucl_overlap / r_cdna_length  # Sensitivity
 *     nucl_precision = nucl_overlap / p_cdna_length
 *     nucl_f1 = calc_f1(nucl_recall, nucl_precision)             # <<<<<<<<<<<<<<
 * 
 *     # Exon statistics
 */
  __pyx_v_nucl_f1 = __pyx_f_6Mikado_6scales_2f1_calc_f1(__pyx_v_nucl_recall, __pyx_v_nucl_precision, 0);

  /* "Mikado/scales/contrast.pyx":346
 * 
 *     # Exon statistics
 *     if lenient is True:             # <<<<<<<<<<<<<<
 *         if len(__pred_exons) > 1 and len(__ref_exons) > 1:
 *             # If both are multiexonic, consider only the internal boundary
 */
  __pyx_t_10 = ((__pyx_v_lenient == 1) != 0);
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":347
 *     # Exon statistics
 *     if lenient is True:
 *         if len(__pred_exons) > 1 and len(__ref_exons) > 1:             # <<<<<<<<<<<<<<
 *             # If both are multiexonic, consider only the internal boundary
 *             __pred_exons.remove(prediction.exons[0])
 */
    __pyx_t_12 = PySet_GET_SIZE(__pyx_v___pred_exons); if (unlikely(__pyx_t_12 == -1)) __PYX_ERR(0, 347, __pyx_L1_error)
    __pyx_t_11 = ((__pyx_t_12 > 1) != 0);
    if (__pyx_t_11) {
    } else {
      __pyx_t_10 = __pyx_t_11;
      goto __pyx_L11_bool_binop_done;
    }
    __pyx_t_12 = PySet_GET_SIZE(__pyx_v___ref_exons); if (unlikely(__pyx_t_12 == -1)) __PYX_ERR(0, 347, __pyx_L1_error)
    __pyx_t_11 = ((__pyx_t_12 > 1) != 0);
    __pyx_t_10 = __pyx_t_11;
    __pyx_L11_bool_binop_done:;
    if (__pyx_t_10) {

      /* "Mikado/scales/contrast.pyx":349
 *         if len(__pred_exons) > 1 and len(__ref_exons) > 1:
 *             # If both are multiexonic, consider only the internal boundary
 *             __pred_exons.remove(prediction.exons[0])             # <<<<<<<<<<<<<<
 *             __pred_exons.add(prediction.exons[0][1])
 *             __pred_exons.remove(prediction.exons[-1])
 */
      __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v___pred_exons, __pyx_n_s_remove); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 349, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 349, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_17 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 349, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_3 = NULL;
      if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
        __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_19);
        if (likely(__pyx_t_3)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
          __Pyx_INCREF(__pyx_t_3);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_19, function);
        }
      }
      if (!__pyx_t_3) {
        __pyx_t_18 = __Pyx_PyObject_CallOneArg(__pyx_t_19, __pyx_t_17); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 349, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
        __Pyx_GOTREF(__pyx_t_18);
      } else {
        __pyx_t_1 = PyTuple_New(1+1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 349, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); __pyx_t_3 = NULL;
        __Pyx_GIVEREF(__pyx_t_17);
        PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_17);
        __pyx_t_17 = 0;
        __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_1, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 349, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_18);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      }
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":350
 *             # If both are multiexonic, consider only the internal boundary
 *             __pred_exons.remove(prediction.exons[0])
 *             __pred_exons.add(prediction.exons[0][1])             # <<<<<<<<<<<<<<
 *             __pred_exons.remove(prediction.exons[-1])
 *             __pred_exons.add(prediction.exons[-1][0])
 */
      __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 350, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __pyx_t_19 = __Pyx_GetItemInt(__pyx_t_18, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 350, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
      __pyx_t_18 = __Pyx_GetItemInt(__pyx_t_19, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 350, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_14 = PySet_Add(__pyx_v___pred_exons, __pyx_t_18); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 350, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":351
 *             __pred_exons.remove(prediction.exons[0])
 *             __pred_exons.add(prediction.exons[0][1])
 *             __pred_exons.remove(prediction.exons[-1])             # <<<<<<<<<<<<<<
 *             __pred_exons.add(prediction.exons[-1][0])
 *             __ref_exons.remove(reference.exons[0])
 */
      __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v___pred_exons, __pyx_n_s_remove); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 351, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 351, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_17 = __Pyx_GetItemInt(__pyx_t_1, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 351, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_1 = NULL;
      if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
        __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_19);
        if (likely(__pyx_t_1)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
          __Pyx_INCREF(__pyx_t_1);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_19, function);
        }
      }
      if (!__pyx_t_1) {
        __pyx_t_18 = __Pyx_PyObject_CallOneArg(__pyx_t_19, __pyx_t_17); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 351, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
        __Pyx_GOTREF(__pyx_t_18);
      } else {
        __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 351, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); __pyx_t_1 = NULL;
        __Pyx_GIVEREF(__pyx_t_17);
        PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_17);
        __pyx_t_17 = 0;
        __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_3, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 351, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_18);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      }
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":352
 *             __pred_exons.add(prediction.exons[0][1])
 *             __pred_exons.remove(prediction.exons[-1])
 *             __pred_exons.add(prediction.exons[-1][0])             # <<<<<<<<<<<<<<
 *             __ref_exons.remove(reference.exons[0])
 *             __ref_exons.add(reference.exons[0][1])
 */
      __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 352, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __pyx_t_19 = __Pyx_GetItemInt(__pyx_t_18, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 352, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
      __pyx_t_18 = __Pyx_GetItemInt(__pyx_t_19, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 352, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_14 = PySet_Add(__pyx_v___pred_exons, __pyx_t_18); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 352, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":353
 *             __pred_exons.remove(prediction.exons[-1])
 *             __pred_exons.add(prediction.exons[-1][0])
 *             __ref_exons.remove(reference.exons[0])             # <<<<<<<<<<<<<<
 *             __ref_exons.add(reference.exons[0][1])
 *             __ref_exons.remove(reference.exons[-1])
 */
      __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v___ref_exons, __pyx_n_s_remove); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 353, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 353, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_3);
      __pyx_t_17 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 353, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      __pyx_t_3 = NULL;
      if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
        __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_19);
        if (likely(__pyx_t_3)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
          __Pyx_INCREF(__pyx_t_3);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_19, function);
        }
      }
      if (!__pyx_t_3) {
        __pyx_t_18 = __Pyx_PyObject_CallOneArg(__pyx_t_19, __pyx_t_17); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 353, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
        __Pyx_GOTREF(__pyx_t_18);
      } else {
        __pyx_t_1 = PyTuple_New(1+1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 353, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_1);
        __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); __pyx_t_3 = NULL;
        __Pyx_GIVEREF(__pyx_t_17);
        PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_17);
        __pyx_t_17 = 0;
        __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_1, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 353, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_18);
        __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      }
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":354
 *             __pred_exons.add(prediction.exons[-1][0])
 *             __ref_exons.remove(reference.exons[0])
 *             __ref_exons.add(reference.exons[0][1])             # <<<<<<<<<<<<<<
 *             __ref_exons.remove(reference.exons[-1])
 *             __ref_exons.add(reference.exons[-1][0])
 */
      __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 354, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __pyx_t_19 = __Pyx_GetItemInt(__pyx_t_18, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 354, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
      __pyx_t_18 = __Pyx_GetItemInt(__pyx_t_19, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 354, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_14 = PySet_Add(__pyx_v___ref_exons, __pyx_t_18); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 354, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":355
 *             __ref_exons.remove(reference.exons[0])
 *             __ref_exons.add(reference.exons[0][1])
 *             __ref_exons.remove(reference.exons[-1])             # <<<<<<<<<<<<<<
 *             __ref_exons.add(reference.exons[-1][0])
 *         elif len(__pred_exons) == len(__ref_exons) == 1 and nucl_f1 > 0.8:
 */
      __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v___ref_exons, __pyx_n_s_remove); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 355, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 355, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_1);
      __pyx_t_17 = __Pyx_GetItemInt(__pyx_t_1, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 355, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_17);
      __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
      __pyx_t_1 = NULL;
      if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
        __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_19);
        if (likely(__pyx_t_1)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
          __Pyx_INCREF(__pyx_t_1);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_19, function);
        }
      }
      if (!__pyx_t_1) {
        __pyx_t_18 = __Pyx_PyObject_CallOneArg(__pyx_t_19, __pyx_t_17); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 355, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
        __Pyx_GOTREF(__pyx_t_18);
      } else {
        __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 355, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_3);
        __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); __pyx_t_1 = NULL;
        __Pyx_GIVEREF(__pyx_t_17);
        PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_17);
        __pyx_t_17 = 0;
        __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_3, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 355, __pyx_L1_error)
        __Pyx_GOTREF(__pyx_t_18);
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      }
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":356
 *             __ref_exons.add(reference.exons[0][1])
 *             __ref_exons.remove(reference.exons[-1])
 *             __ref_exons.add(reference.exons[-1][0])             # <<<<<<<<<<<<<<
 *         elif len(__pred_exons) == len(__ref_exons) == 1 and nucl_f1 > 0.8:
 *             # If both are monoexonic and nucleotide F1 is >= 0.8
 */
      __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 356, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __pyx_t_19 = __Pyx_GetItemInt(__pyx_t_18, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 356, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
      __pyx_t_18 = __Pyx_GetItemInt(__pyx_t_19, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 356, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_14 = PySet_Add(__pyx_v___ref_exons, __pyx_t_18); if (unlikely(__pyx_t_14 == -1)) __PYX_ERR(0, 356, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":347
 *     # Exon statistics
 *     if lenient is True:
 *         if len(__pred_exons) > 1 and len(__ref_exons) > 1:             # <<<<<<<<<<<<<<
 *             # If both are multiexonic, consider only the internal boundary
 *             __pred_exons.remove(prediction.exons[0])
 */
      goto __pyx_L10;
    }

    /* "Mikado/scales/contrast.pyx":357
 *             __ref_exons.remove(reference.exons[-1])
 *             __ref_exons.add(reference.exons[-1][0])
 *         elif len(__pred_exons) == len(__ref_exons) == 1 and nucl_f1 > 0.8:             # <<<<<<<<<<<<<<
 *             # If both are monoexonic and nucleotide F1 is >= 0.8
 *             __ref_exons = __pred_exons.copy()
 */
    __pyx_t_12 = PySet_GET_SIZE(__pyx_v___pred_exons); if (unlikely(__pyx_t_12 == -1)) __PYX_ERR(0, 357, __pyx_L1_error)
    __pyx_t_15 = PySet_GET_SIZE(__pyx_v___ref_exons); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 357, __pyx_L1_error)
    __pyx_t_11 = (__pyx_t_12 == __pyx_t_15);
    if (__pyx_t_11) {
      __pyx_t_11 = (__pyx_t_15 == 1);
    }
    __pyx_t_20 = (__pyx_t_11 != 0);
    if (__pyx_t_20) {
    } else {
      __pyx_t_10 = __pyx_t_20;
      goto __pyx_L13_bool_binop_done;
    }
    __pyx_t_20 = ((__pyx_v_nucl_f1 > 0.8) != 0);
    __pyx_t_10 = __pyx_t_20;
    __pyx_L13_bool_binop_done:;
    if (__pyx_t_10) {

      /* "Mikado/scales/contrast.pyx":359
 *         elif len(__pred_exons) == len(__ref_exons) == 1 and nucl_f1 > 0.8:
 *             # If both are monoexonic and nucleotide F1 is >= 0.8
 *             __ref_exons = __pred_exons.copy()             # <<<<<<<<<<<<<<
 * 
 *     recalled_exons = len(set.intersection(__pred_exons, __ref_exons))
 */
      __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v___pred_exons, __pyx_n_s_copy); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 359, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __pyx_t_3 = NULL;
      if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
        __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_19);
        if (likely(__pyx_t_3)) {
          PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
          __Pyx_INCREF(__pyx_t_3);
          __Pyx_INCREF(function);
          __Pyx_DECREF_SET(__pyx_t_19, function);
        }
      }
      if (__pyx_t_3) {
        __pyx_t_18 = __Pyx_PyObject_CallOneArg(__pyx_t_19, __pyx_t_3); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 359, __pyx_L1_error)
        __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
      } else {
        __pyx_t_18 = __Pyx_PyObject_CallNoArg(__pyx_t_19); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 359, __pyx_L1_error)
      }
      __Pyx_GOTREF(__pyx_t_18);
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      if (!(likely(PySet_CheckExact(__pyx_t_18))||((__pyx_t_18) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_18)->tp_name), 0))) __PYX_ERR(0, 359, __pyx_L1_error)
      __Pyx_DECREF_SET(__pyx_v___ref_exons, ((PyObject*)__pyx_t_18));
      __pyx_t_18 = 0;

      /* "Mikado/scales/contrast.pyx":357
 *             __ref_exons.remove(reference.exons[-1])
 *             __ref_exons.add(reference.exons[-1][0])
 *         elif len(__pred_exons) == len(__ref_exons) == 1 and nucl_f1 > 0.8:             # <<<<<<<<<<<<<<
 *             # If both are monoexonic and nucleotide F1 is >= 0.8
 *             __ref_exons = __pred_exons.copy()
 */
    }
    __pyx_L10:;

    /* "Mikado/scales/contrast.pyx":346
 * 
 *     # Exon statistics
 *     if lenient is True:             # <<<<<<<<<<<<<<
 *         if len(__pred_exons) > 1 and len(__ref_exons) > 1:
 *             # If both are multiexonic, consider only the internal boundary
 */
  }

  /* "Mikado/scales/contrast.pyx":361
 *             __ref_exons = __pred_exons.copy()
 * 
 *     recalled_exons = len(set.intersection(__pred_exons, __ref_exons))             # <<<<<<<<<<<<<<
 *     exon_recall = recalled_exons / r_exon_num
 *     exon_precision = recalled_exons / p_exon_num
 */
  __pyx_t_19 = __Pyx_PyObject_GetAttrStr(((PyObject *)(&PySet_Type)), __pyx_n_s_intersection); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 361, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_19);
  __pyx_t_3 = NULL;
  __pyx_t_15 = 0;
  if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
    __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_19);
    if (likely(__pyx_t_3)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
      __Pyx_INCREF(__pyx_t_3);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_19, function);
      __pyx_t_15 = 1;
    }
  }
  __pyx_t_17 = PyTuple_New(2+__pyx_t_15); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 361, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_17);
  if (__pyx_t_3) {
    __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_t_3); __pyx_t_3 = NULL;
  }
  __Pyx_INCREF(__pyx_v___pred_exons);
  __Pyx_GIVEREF(__pyx_v___pred_exons);
  PyTuple_SET_ITEM(__pyx_t_17, 0+__pyx_t_15, __pyx_v___pred_exons);
  __Pyx_INCREF(__pyx_v___ref_exons);
  __Pyx_GIVEREF(__pyx_v___ref_exons);
  PyTuple_SET_ITEM(__pyx_t_17, 1+__pyx_t_15, __pyx_v___ref_exons);
  __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_17, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 361, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_18);
  __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
  __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
  __pyx_t_15 = PyObject_Length(__pyx_t_18); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 361, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
  __pyx_v_recalled_exons = __pyx_t_15;

  /* "Mikado/scales/contrast.pyx":362
 * 
 *     recalled_exons = len(set.intersection(__pred_exons, __ref_exons))
 *     exon_recall = recalled_exons / r_exon_num             # <<<<<<<<<<<<<<
 *     exon_precision = recalled_exons / p_exon_num
 *     exon_f1 = calc_f1(exon_recall, exon_precision)
 */
  __pyx_v_exon_recall = (__pyx_v_recalled_exons / __pyx_v_r_exon_num);

  /* "Mikado/scales/contrast.pyx":363
 *     recalled_exons = len(set.intersection(__pred_exons, __ref_exons))
 *     exon_recall = recalled_exons / r_exon_num
 *     exon_precision = recalled_exons / p_exon_num             # <<<<<<<<<<<<<<
 *     exon_f1 = calc_f1(exon_recall, exon_precision)
 * 
 */
  __pyx_v_exon_precision = (__pyx_v_recalled_exons / __pyx_v_p_exon_num);

  /* "Mikado/scales/contrast.pyx":364
 *     exon_recall = recalled_exons / r_exon_num
 *     exon_precision = recalled_exons / p_exon_num
 *     exon_f1 = calc_f1(exon_recall, exon_precision)             # <<<<<<<<<<<<<<
 * 
 *     reference_exon = None
 */
  __pyx_v_exon_f1 = __pyx_f_6Mikado_6scales_2f1_calc_f1(__pyx_v_exon_recall, __pyx_v_exon_precision, 0);

  /* "Mikado/scales/contrast.pyx":366
 *     exon_f1 = calc_f1(exon_recall, exon_precision)
 * 
 *     reference_exon = None             # <<<<<<<<<<<<<<
 * 
 *     # Both multiexonic
 */
  __Pyx_INCREF(Py_None);
  __pyx_v_reference_exon = Py_None;

  /* "Mikado/scales/contrast.pyx":369
 * 
 *     # Both multiexonic
 *     if p_exon_num > 1 and r_exon_num > 1:             # <<<<<<<<<<<<<<
 *         r_splices, p_splices = reference.splices, prediction.splices
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)
 */
  __pyx_t_20 = ((__pyx_v_p_exon_num > 1) != 0);
  if (__pyx_t_20) {
  } else {
    __pyx_t_10 = __pyx_t_20;
    goto __pyx_L16_bool_binop_done;
  }
  __pyx_t_20 = ((__pyx_v_r_exon_num > 1) != 0);
  __pyx_t_10 = __pyx_t_20;
  __pyx_L16_bool_binop_done:;
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":370
 *     # Both multiexonic
 *     if p_exon_num > 1 and r_exon_num > 1:
 *         r_splices, p_splices = reference.splices, prediction.splices             # <<<<<<<<<<<<<<
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)
 *         junction_overlap = len(set.intersection(p_splices, r_splices))
 */
    __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_splices); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 370, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    if (!(likely(PySet_CheckExact(__pyx_t_18))||((__pyx_t_18) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_18)->tp_name), 0))) __PYX_ERR(0, 370, __pyx_L1_error)
    __pyx_t_19 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_splices); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 370, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    if (!(likely(PySet_CheckExact(__pyx_t_19))||((__pyx_t_19) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "set", Py_TYPE(__pyx_t_19)->tp_name), 0))) __PYX_ERR(0, 370, __pyx_L1_error)
    __pyx_v_r_splices = ((PyObject*)__pyx_t_18);
    __pyx_t_18 = 0;
    __pyx_v_p_splices = ((PyObject*)__pyx_t_19);
    __pyx_t_19 = 0;

    /* "Mikado/scales/contrast.pyx":371
 *     if p_exon_num > 1 and r_exon_num > 1:
 *         r_splices, p_splices = reference.splices, prediction.splices
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)             # <<<<<<<<<<<<<<
 *         junction_overlap = len(set.intersection(p_splices, r_splices))
 *         junction_recall = junction_overlap / len_rsplices
 */
    if (unlikely(__pyx_v_r_splices == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
      __PYX_ERR(0, 371, __pyx_L1_error)
    }
    __pyx_t_15 = PySet_GET_SIZE(__pyx_v_r_splices); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 371, __pyx_L1_error)
    __pyx_t_19 = PyInt_FromSsize_t(__pyx_t_15); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 371, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    if (unlikely(__pyx_v_p_splices == Py_None)) {
      PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
      __PYX_ERR(0, 371, __pyx_L1_error)
    }
    __pyx_t_15 = PySet_GET_SIZE(__pyx_v_p_splices); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 371, __pyx_L1_error)
    __pyx_t_18 = PyInt_FromSsize_t(__pyx_t_15); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 371, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __pyx_v_len_rsplices = __pyx_t_19;
    __pyx_t_19 = 0;
    __pyx_v_len_psplices = __pyx_t_18;
    __pyx_t_18 = 0;

    /* "Mikado/scales/contrast.pyx":372
 *         r_splices, p_splices = reference.splices, prediction.splices
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)
 *         junction_overlap = len(set.intersection(p_splices, r_splices))             # <<<<<<<<<<<<<<
 *         junction_recall = junction_overlap / len_rsplices
 *         junction_precision = junction_overlap / len_psplices
 */
    __pyx_t_19 = __Pyx_PyObject_GetAttrStr(((PyObject *)(&PySet_Type)), __pyx_n_s_intersection); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 372, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    __pyx_t_17 = NULL;
    __pyx_t_15 = 0;
    if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_19))) {
      __pyx_t_17 = PyMethod_GET_SELF(__pyx_t_19);
      if (likely(__pyx_t_17)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_19);
        __Pyx_INCREF(__pyx_t_17);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_19, function);
        __pyx_t_15 = 1;
      }
    }
    __pyx_t_3 = PyTuple_New(2+__pyx_t_15); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 372, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_3);
    if (__pyx_t_17) {
      __Pyx_GIVEREF(__pyx_t_17); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_17); __pyx_t_17 = NULL;
    }
    __Pyx_INCREF(__pyx_v_p_splices);
    __Pyx_GIVEREF(__pyx_v_p_splices);
    PyTuple_SET_ITEM(__pyx_t_3, 0+__pyx_t_15, __pyx_v_p_splices);
    __Pyx_INCREF(__pyx_v_r_splices);
    __Pyx_GIVEREF(__pyx_v_r_splices);
    PyTuple_SET_ITEM(__pyx_t_3, 1+__pyx_t_15, __pyx_v_r_splices);
    __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_19, __pyx_t_3, NULL); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 372, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
    __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
    __pyx_t_15 = PyObject_Length(__pyx_t_18); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 372, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __pyx_v_junction_overlap = __pyx_t_15;

    /* "Mikado/scales/contrast.pyx":373
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)
 *         junction_overlap = len(set.intersection(p_splices, r_splices))
 *         junction_recall = junction_overlap / len_rsplices             # <<<<<<<<<<<<<<
 *         junction_precision = junction_overlap / len_psplices
 *         junction_f1 = calc_f1(junction_recall, junction_precision)
 */
    __pyx_t_18 = __Pyx_PyInt_From_long(__pyx_v_junction_overlap); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 373, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __pyx_t_19 = __Pyx_PyNumber_Divide(__pyx_t_18, __pyx_v_len_rsplices); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 373, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_19); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 373, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
    __pyx_v_junction_recall = __pyx_t_5;

    /* "Mikado/scales/contrast.pyx":374
 *         junction_overlap = len(set.intersection(p_splices, r_splices))
 *         junction_recall = junction_overlap / len_rsplices
 *         junction_precision = junction_overlap / len_psplices             # <<<<<<<<<<<<<<
 *         junction_f1 = calc_f1(junction_recall, junction_precision)
 * 
 */
    __pyx_t_19 = __Pyx_PyInt_From_long(__pyx_v_junction_overlap); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 374, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    __pyx_t_18 = __Pyx_PyNumber_Divide(__pyx_t_19, __pyx_v_len_psplices); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 374, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
    __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_18); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 374, __pyx_L1_error)
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __pyx_v_junction_precision = __pyx_t_5;

    /* "Mikado/scales/contrast.pyx":375
 *         junction_recall = junction_overlap / len_rsplices
 *         junction_precision = junction_overlap / len_psplices
 *         junction_f1 = calc_f1(junction_recall, junction_precision)             # <<<<<<<<<<<<<<
 * 
 *     elif p_exon_num == r_exon_num == 1 and nucl_f1 > 0:
 */
    __pyx_v_junction_f1 = __pyx_f_6Mikado_6scales_2f1_calc_f1(__pyx_v_junction_recall, __pyx_v_junction_precision, 0);

    /* "Mikado/scales/contrast.pyx":369
 * 
 *     # Both multiexonic
 *     if p_exon_num > 1 and r_exon_num > 1:             # <<<<<<<<<<<<<<
 *         r_splices, p_splices = reference.splices, prediction.splices
 *         len_rsplices, len_psplices = len(r_splices), len(p_splices)
 */
    goto __pyx_L15;
  }

  /* "Mikado/scales/contrast.pyx":377
 *         junction_f1 = calc_f1(junction_recall, junction_precision)
 * 
 *     elif p_exon_num == r_exon_num == 1 and nucl_f1 > 0:             # <<<<<<<<<<<<<<
 *         # junction_overlap = junction_f1 = junction_precision = junction_recall = 1
 *         junction_f1 = junction_precision = junction_recall = 1
 */
  __pyx_t_20 = (__pyx_v_p_exon_num == __pyx_v_r_exon_num);
  if (__pyx_t_20) {
    __pyx_t_20 = (__pyx_v_r_exon_num == 1);
  }
  __pyx_t_11 = (__pyx_t_20 != 0);
  if (__pyx_t_11) {
  } else {
    __pyx_t_10 = __pyx_t_11;
    goto __pyx_L18_bool_binop_done;
  }
  __pyx_t_11 = ((__pyx_v_nucl_f1 > 0.0) != 0);
  __pyx_t_10 = __pyx_t_11;
  __pyx_L18_bool_binop_done:;
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":379
 *     elif p_exon_num == r_exon_num == 1 and nucl_f1 > 0:
 *         # junction_overlap = junction_f1 = junction_precision = junction_recall = 1
 *         junction_f1 = junction_precision = junction_recall = 1             # <<<<<<<<<<<<<<
 *     else:
 *         # junction_overlap = junction_f1 = junction_precision = junction_recall = 0
 */
    __pyx_v_junction_f1 = 1.0;
    __pyx_v_junction_precision = 1.0;
    __pyx_v_junction_recall = 1.0;

    /* "Mikado/scales/contrast.pyx":377
 *         junction_f1 = calc_f1(junction_recall, junction_precision)
 * 
 *     elif p_exon_num == r_exon_num == 1 and nucl_f1 > 0:             # <<<<<<<<<<<<<<
 *         # junction_overlap = junction_f1 = junction_precision = junction_recall = 1
 *         junction_f1 = junction_precision = junction_recall = 1
 */
    goto __pyx_L15;
  }

  /* "Mikado/scales/contrast.pyx":382
 *     else:
 *         # junction_overlap = junction_f1 = junction_precision = junction_recall = 0
 *         junction_f1 = junction_precision = junction_recall = 0             # <<<<<<<<<<<<<<
 * 
 *     ccode = ""
 */
  /*else*/ {
    __pyx_v_junction_f1 = 0.0;
    __pyx_v_junction_precision = 0.0;
    __pyx_v_junction_recall = 0.0;
  }
  __pyx_L15:;

  /* "Mikado/scales/contrast.pyx":384
 *         junction_f1 = junction_precision = junction_recall = 0
 * 
 *     ccode = ""             # <<<<<<<<<<<<<<
 *     distance = 0
 *     if junction_f1 == 1 and p_exon_num > 1:
 */
  __Pyx_INCREF(__pyx_kp_s_);
  __pyx_v_ccode = __pyx_kp_s_;

  /* "Mikado/scales/contrast.pyx":385
 * 
 *     ccode = ""
 *     distance = 0             # <<<<<<<<<<<<<<
 *     if junction_f1 == 1 and p_exon_num > 1:
 *         if p_strand == r_strand:
 */
  __pyx_v_distance = 0;

  /* "Mikado/scales/contrast.pyx":386
 *     ccode = ""
 *     distance = 0
 *     if junction_f1 == 1 and p_exon_num > 1:             # <<<<<<<<<<<<<<
 *         if p_strand == r_strand:
 *             ccode = "="  # We have recovered all the junctions
 */
  __pyx_t_11 = ((__pyx_v_junction_f1 == 1.0) != 0);
  if (__pyx_t_11) {
  } else {
    __pyx_t_10 = __pyx_t_11;
    goto __pyx_L21_bool_binop_done;
  }
  __pyx_t_11 = ((__pyx_v_p_exon_num > 1) != 0);
  __pyx_t_10 = __pyx_t_11;
  __pyx_L21_bool_binop_done:;
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":387
 *     distance = 0
 *     if junction_f1 == 1 and p_exon_num > 1:
 *         if p_strand == r_strand:             # <<<<<<<<<<<<<<
 *             ccode = "="  # We have recovered all the junctions
 *         else:
 */
    __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_v_p_strand, __pyx_v_r_strand, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 387, __pyx_L1_error)
    __pyx_t_11 = (__pyx_t_10 != 0);
    if (__pyx_t_11) {

      /* "Mikado/scales/contrast.pyx":388
 *     if junction_f1 == 1 and p_exon_num > 1:
 *         if p_strand == r_strand:
 *             ccode = "="  # We have recovered all the junctions             # <<<<<<<<<<<<<<
 *         else:
 *             ccode = "c"  # We will set this to x at the end of the function
 */
      __Pyx_INCREF(__pyx_kp_s__3);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_kp_s__3);

      /* "Mikado/scales/contrast.pyx":387
 *     distance = 0
 *     if junction_f1 == 1 and p_exon_num > 1:
 *         if p_strand == r_strand:             # <<<<<<<<<<<<<<
 *             ccode = "="  # We have recovered all the junctions
 *         else:
 */
      goto __pyx_L23;
    }

    /* "Mikado/scales/contrast.pyx":390
 *             ccode = "="  # We have recovered all the junctions
 *         else:
 *             ccode = "c"  # We will set this to x at the end of the function             # <<<<<<<<<<<<<<
 * 
 *     elif junction_f1 == 1 and nucl_f1 >= 0.80:
 */
    /*else*/ {
      __Pyx_INCREF(__pyx_n_s_c);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_c);
    }
    __pyx_L23:;

    /* "Mikado/scales/contrast.pyx":386
 *     ccode = ""
 *     distance = 0
 *     if junction_f1 == 1 and p_exon_num > 1:             # <<<<<<<<<<<<<<
 *         if p_strand == r_strand:
 *             ccode = "="  # We have recovered all the junctions
 */
    goto __pyx_L20;
  }

  /* "Mikado/scales/contrast.pyx":392
 *             ccode = "c"  # We will set this to x at the end of the function
 * 
 *     elif junction_f1 == 1 and nucl_f1 >= 0.80:             # <<<<<<<<<<<<<<
 *         reference_exon = reference.exons[0]
 *         ccode = "_"  # We have recovered all the junctions
 */
  __pyx_t_10 = ((__pyx_v_junction_f1 == 1.0) != 0);
  if (__pyx_t_10) {
  } else {
    __pyx_t_11 = __pyx_t_10;
    goto __pyx_L24_bool_binop_done;
  }
  __pyx_t_10 = ((__pyx_v_nucl_f1 >= 0.80) != 0);
  __pyx_t_11 = __pyx_t_10;
  __pyx_L24_bool_binop_done:;
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":393
 * 
 *     elif junction_f1 == 1 and nucl_f1 >= 0.80:
 *         reference_exon = reference.exons[0]             # <<<<<<<<<<<<<<
 *         ccode = "_"  # We have recovered all the junctions
 * 
 */
    __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 393, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __pyx_t_19 = __Pyx_GetItemInt(__pyx_t_18, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 393, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __Pyx_DECREF_SET(__pyx_v_reference_exon, __pyx_t_19);
    __pyx_t_19 = 0;

    /* "Mikado/scales/contrast.pyx":394
 *     elif junction_f1 == 1 and nucl_f1 >= 0.80:
 *         reference_exon = reference.exons[0]
 *         ccode = "_"  # We have recovered all the junctions             # <<<<<<<<<<<<<<
 * 
 *     # Outside the transcript - polymerase run-on
 */
    __Pyx_INCREF(__pyx_n_s__2);
    __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s__2);

    /* "Mikado/scales/contrast.pyx":392
 *             ccode = "c"  # We will set this to x at the end of the function
 * 
 *     elif junction_f1 == 1 and nucl_f1 >= 0.80:             # <<<<<<<<<<<<<<
 *         reference_exon = reference.exons[0]
 *         ccode = "_"  # We have recovered all the junctions
 */
    goto __pyx_L20;
  }

  /* "Mikado/scales/contrast.pyx":397
 * 
 *     # Outside the transcript - polymerase run-on
 *     elif p_start > r_end or p_end < r_start:             # <<<<<<<<<<<<<<
 *         if r_strand == p_strand:
 *             ccode = "p"
 */
  __pyx_t_10 = ((__pyx_v_p_start > __pyx_v_r_end) != 0);
  if (!__pyx_t_10) {
  } else {
    __pyx_t_11 = __pyx_t_10;
    goto __pyx_L26_bool_binop_done;
  }
  __pyx_t_10 = ((__pyx_v_p_end < __pyx_v_r_start) != 0);
  __pyx_t_11 = __pyx_t_10;
  __pyx_L26_bool_binop_done:;
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":398
 *     # Outside the transcript - polymerase run-on
 *     elif p_start > r_end or p_end < r_start:
 *         if r_strand == p_strand:             # <<<<<<<<<<<<<<
 *             ccode = "p"
 *         else:
 */
    __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_v_r_strand, __pyx_v_p_strand, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 398, __pyx_L1_error)
    __pyx_t_10 = (__pyx_t_11 != 0);
    if (__pyx_t_10) {

      /* "Mikado/scales/contrast.pyx":399
 *     elif p_start > r_end or p_end < r_start:
 *         if r_strand == p_strand:
 *             ccode = "p"             # <<<<<<<<<<<<<<
 *         else:
 *             ccode = "P"
 */
      __Pyx_INCREF(__pyx_n_s_p);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_p);

      /* "Mikado/scales/contrast.pyx":398
 *     # Outside the transcript - polymerase run-on
 *     elif p_start > r_end or p_end < r_start:
 *         if r_strand == p_strand:             # <<<<<<<<<<<<<<
 *             ccode = "p"
 *         else:
 */
      goto __pyx_L28;
    }

    /* "Mikado/scales/contrast.pyx":401
 *             ccode = "p"
 *         else:
 *             ccode = "P"             # <<<<<<<<<<<<<<
 *         distance = long_max(p_start - r_end, r_start - p_end)
 * 
 */
    /*else*/ {
      __Pyx_INCREF(__pyx_n_s_P);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_P);
    }
    __pyx_L28:;

    /* "Mikado/scales/contrast.pyx":402
 *         else:
 *             ccode = "P"
 *         distance = long_max(p_start - r_end, r_start - p_end)             # <<<<<<<<<<<<<<
 * 
 *     elif nucl_precision == 1:
 */
    __pyx_v_distance = __pyx_f_6Mikado_6scales_8contrast_long_max((__pyx_v_p_start - __pyx_v_r_end), (__pyx_v_r_start - __pyx_v_p_end));

    /* "Mikado/scales/contrast.pyx":397
 * 
 *     # Outside the transcript - polymerase run-on
 *     elif p_start > r_end or p_end < r_start:             # <<<<<<<<<<<<<<
 *         if r_strand == p_strand:
 *             ccode = "p"
 */
    goto __pyx_L20;
  }

  /* "Mikado/scales/contrast.pyx":404
 *         distance = long_max(p_start - r_end, r_start - p_end)
 * 
 *     elif nucl_precision == 1:             # <<<<<<<<<<<<<<
 *         if p_exon_num == 1 or (p_exon_num > 1 and junction_precision == 1):
 *             ccode = "c"
 */
  __pyx_t_10 = ((__pyx_v_nucl_precision == 1.0) != 0);
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":405
 * 
 *     elif nucl_precision == 1:
 *         if p_exon_num == 1 or (p_exon_num > 1 and junction_precision == 1):             # <<<<<<<<<<<<<<
 *             ccode = "c"
 * 
 */
    __pyx_t_11 = ((__pyx_v_p_exon_num == 1) != 0);
    if (!__pyx_t_11) {
    } else {
      __pyx_t_10 = __pyx_t_11;
      goto __pyx_L30_bool_binop_done;
    }
    __pyx_t_11 = ((__pyx_v_p_exon_num > 1) != 0);
    if (__pyx_t_11) {
    } else {
      __pyx_t_10 = __pyx_t_11;
      goto __pyx_L30_bool_binop_done;
    }
    __pyx_t_11 = ((__pyx_v_junction_precision == 1.0) != 0);
    __pyx_t_10 = __pyx_t_11;
    __pyx_L30_bool_binop_done:;
    if (__pyx_t_10) {

      /* "Mikado/scales/contrast.pyx":406
 *     elif nucl_precision == 1:
 *         if p_exon_num == 1 or (p_exon_num > 1 and junction_precision == 1):
 *             ccode = "c"             # <<<<<<<<<<<<<<
 * 
 *     if ccode == "":
 */
      __Pyx_INCREF(__pyx_n_s_c);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_c);

      /* "Mikado/scales/contrast.pyx":405
 * 
 *     elif nucl_precision == 1:
 *         if p_exon_num == 1 or (p_exon_num > 1 and junction_precision == 1):             # <<<<<<<<<<<<<<
 *             ccode = "c"
 * 
 */
    }

    /* "Mikado/scales/contrast.pyx":404
 *         distance = long_max(p_start - r_end, r_start - p_end)
 * 
 *     elif nucl_precision == 1:             # <<<<<<<<<<<<<<
 *         if p_exon_num == 1 or (p_exon_num > 1 and junction_precision == 1):
 *             ccode = "c"
 */
  }
  __pyx_L20:;

  /* "Mikado/scales/contrast.pyx":408
 *             ccode = "c"
 * 
 *     if ccode == "":             # <<<<<<<<<<<<<<
 *         # stats = (nucl_recall, nucl_precision, nucl_f1,
 *         #         exon_recall, exon_precision, exon_f1,
 */
  __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_v_ccode, __pyx_kp_s_, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 408, __pyx_L1_error)
  if (__pyx_t_10) {

    /* "Mikado/scales/contrast.pyx":412
 *         #         exon_recall, exon_precision, exon_f1,
 *         #          junction_recall, junction_precision, junction_f1)
 *         stats[0] = nucl_recall             # <<<<<<<<<<<<<<
 *         stats[1] = nucl_precision
 *         stats[2] = nucl_f1
 */
    (__pyx_v_stats[0]) = __pyx_v_nucl_recall;

    /* "Mikado/scales/contrast.pyx":413
 *         #          junction_recall, junction_precision, junction_f1)
 *         stats[0] = nucl_recall
 *         stats[1] = nucl_precision             # <<<<<<<<<<<<<<
 *         stats[2] = nucl_f1
 *         stats[3] = exon_recall
 */
    (__pyx_v_stats[1]) = __pyx_v_nucl_precision;

    /* "Mikado/scales/contrast.pyx":414
 *         stats[0] = nucl_recall
 *         stats[1] = nucl_precision
 *         stats[2] = nucl_f1             # <<<<<<<<<<<<<<
 *         stats[3] = exon_recall
 *         stats[4] = exon_precision
 */
    (__pyx_v_stats[2]) = __pyx_v_nucl_f1;

    /* "Mikado/scales/contrast.pyx":415
 *         stats[1] = nucl_precision
 *         stats[2] = nucl_f1
 *         stats[3] = exon_recall             # <<<<<<<<<<<<<<
 *         stats[4] = exon_precision
 *         stats[5] = exon_f1
 */
    (__pyx_v_stats[3]) = __pyx_v_exon_recall;

    /* "Mikado/scales/contrast.pyx":416
 *         stats[2] = nucl_f1
 *         stats[3] = exon_recall
 *         stats[4] = exon_precision             # <<<<<<<<<<<<<<
 *         stats[5] = exon_f1
 *         stats[6] = junction_recall
 */
    (__pyx_v_stats[4]) = __pyx_v_exon_precision;

    /* "Mikado/scales/contrast.pyx":417
 *         stats[3] = exon_recall
 *         stats[4] = exon_precision
 *         stats[5] = exon_f1             # <<<<<<<<<<<<<<
 *         stats[6] = junction_recall
 *         stats[7] = junction_precision
 */
    (__pyx_v_stats[5]) = __pyx_v_exon_f1;

    /* "Mikado/scales/contrast.pyx":418
 *         stats[4] = exon_precision
 *         stats[5] = exon_f1
 *         stats[6] = junction_recall             # <<<<<<<<<<<<<<
 *         stats[7] = junction_precision
 *         stats[8] = junction_f1
 */
    (__pyx_v_stats[6]) = __pyx_v_junction_recall;

    /* "Mikado/scales/contrast.pyx":419
 *         stats[5] = exon_f1
 *         stats[6] = junction_recall
 *         stats[7] = junction_precision             # <<<<<<<<<<<<<<
 *         stats[8] = junction_f1
 * 
 */
    (__pyx_v_stats[7]) = __pyx_v_junction_precision;

    /* "Mikado/scales/contrast.pyx":420
 *         stats[6] = junction_recall
 *         stats[7] = junction_precision
 *         stats[8] = junction_f1             # <<<<<<<<<<<<<<
 * 
 * 
 */
    (__pyx_v_stats[8]) = __pyx_v_junction_f1;

    /* "Mikado/scales/contrast.pyx":423
 * 
 * 
 *         if double_min(p_exon_num, r_exon_num) > 1:             # <<<<<<<<<<<<<<
 *             ccode = __assign_multiexonic_ccode(prediction, reference,
 *                                                nucl_overlap, stats)
 */
    __pyx_t_10 = ((__pyx_f_6Mikado_6scales_8contrast_double_min(__pyx_v_p_exon_num, __pyx_v_r_exon_num) > 1.0) != 0);
    if (__pyx_t_10) {

      /* "Mikado/scales/contrast.pyx":424
 * 
 *         if double_min(p_exon_num, r_exon_num) > 1:
 *             ccode = __assign_multiexonic_ccode(prediction, reference,             # <<<<<<<<<<<<<<
 *                                                nucl_overlap, stats)
 *         else:
 */
      __pyx_t_19 = __pyx_f_6Mikado_6scales_8contrast___assign_multiexonic_ccode(__pyx_v_prediction, __pyx_v_reference, __pyx_v_nucl_overlap, __pyx_v_stats); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 424, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_t_19);
      __pyx_t_19 = 0;

      /* "Mikado/scales/contrast.pyx":423
 * 
 * 
 *         if double_min(p_exon_num, r_exon_num) > 1:             # <<<<<<<<<<<<<<
 *             ccode = __assign_multiexonic_ccode(prediction, reference,
 *                                                nucl_overlap, stats)
 */
      goto __pyx_L34;
    }

    /* "Mikado/scales/contrast.pyx":427
 *                                                nucl_overlap, stats)
 *         else:
 *             ccode = __assign_monoexonic_ccode(prediction, reference,             # <<<<<<<<<<<<<<
 *                                               nucl_overlap, stats)
 * 
 */
    /*else*/ {

      /* "Mikado/scales/contrast.pyx":428
 *         else:
 *             ccode = __assign_monoexonic_ccode(prediction, reference,
 *                                               nucl_overlap, stats)             # <<<<<<<<<<<<<<
 * 
 *     if (p_strand != r_strand):
 */
      __pyx_t_19 = __pyx_f_6Mikado_6scales_8contrast___assign_monoexonic_ccode(__pyx_v_prediction, __pyx_v_reference, __pyx_v_nucl_overlap, __pyx_v_stats); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 427, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_t_19);
      __pyx_t_19 = 0;
    }
    __pyx_L34:;

    /* "Mikado/scales/contrast.pyx":408
 *             ccode = "c"
 * 
 *     if ccode == "":             # <<<<<<<<<<<<<<
 *         # stats = (nucl_recall, nucl_precision, nucl_f1,
 *         #         exon_recall, exon_precision, exon_f1,
 */
  }

  /* "Mikado/scales/contrast.pyx":430
 *                                               nucl_overlap, stats)
 * 
 *     if (p_strand != r_strand):             # <<<<<<<<<<<<<<
 * 
 *         if (p_strand != "" and r_strand != ""):
 */
  __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_v_p_strand, __pyx_v_r_strand, Py_NE)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 430, __pyx_L1_error)
  __pyx_t_11 = (__pyx_t_10 != 0);
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":432
 *     if (p_strand != r_strand):
 * 
 *         if (p_strand != "" and r_strand != ""):             # <<<<<<<<<<<<<<
 *             if ccode in ("e", "g", "c", "m", "_", "C"):
 *                 ccode = "x"  # "x{0}".format(ccode)
 */
    __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_v_p_strand, __pyx_kp_s_, Py_NE)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 432, __pyx_L1_error)
    __pyx_t_20 = (__pyx_t_10 != 0);
    if (__pyx_t_20) {
    } else {
      __pyx_t_11 = __pyx_t_20;
      goto __pyx_L37_bool_binop_done;
    }
    __pyx_t_20 = (__Pyx_PyString_Equals(__pyx_v_r_strand, __pyx_kp_s_, Py_NE)); if (unlikely(__pyx_t_20 < 0)) __PYX_ERR(0, 432, __pyx_L1_error)
    __pyx_t_10 = (__pyx_t_20 != 0);
    __pyx_t_11 = __pyx_t_10;
    __pyx_L37_bool_binop_done:;
    if (__pyx_t_11) {

      /* "Mikado/scales/contrast.pyx":433
 * 
 *         if (p_strand != "" and r_strand != ""):
 *             if ccode in ("e", "g", "c", "m", "_", "C"):             # <<<<<<<<<<<<<<
 *                 ccode = "x"  # "x{0}".format(ccode)
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):
 */
      __Pyx_INCREF(__pyx_v_ccode);
      __pyx_t_19 = __pyx_v_ccode;
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_e, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      if (!__pyx_t_10) {
      } else {
        __pyx_t_11 = __pyx_t_10;
        goto __pyx_L40_bool_binop_done;
      }
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_g, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      if (!__pyx_t_10) {
      } else {
        __pyx_t_11 = __pyx_t_10;
        goto __pyx_L40_bool_binop_done;
      }
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_c, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      if (!__pyx_t_10) {
      } else {
        __pyx_t_11 = __pyx_t_10;
        goto __pyx_L40_bool_binop_done;
      }
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_m, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      if (!__pyx_t_10) {
      } else {
        __pyx_t_11 = __pyx_t_10;
        goto __pyx_L40_bool_binop_done;
      }
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s__2, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      if (!__pyx_t_10) {
      } else {
        __pyx_t_11 = __pyx_t_10;
        goto __pyx_L40_bool_binop_done;
      }
      __pyx_t_10 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_C, Py_EQ)); if (unlikely(__pyx_t_10 < 0)) __PYX_ERR(0, 433, __pyx_L1_error)
      __pyx_t_11 = __pyx_t_10;
      __pyx_L40_bool_binop_done:;
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_10 = (__pyx_t_11 != 0);
      if (__pyx_t_10) {

        /* "Mikado/scales/contrast.pyx":434
 *         if (p_strand != "" and r_strand != ""):
 *             if ccode in ("e", "g", "c", "m", "_", "C"):
 *                 ccode = "x"  # "x{0}".format(ccode)             # <<<<<<<<<<<<<<
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):
 *                 ccode = "X"  # "X{0}".format(ccode)
 */
        __Pyx_INCREF(__pyx_n_s_x);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_x);

        /* "Mikado/scales/contrast.pyx":433
 * 
 *         if (p_strand != "" and r_strand != ""):
 *             if ccode in ("e", "g", "c", "m", "_", "C"):             # <<<<<<<<<<<<<<
 *                 ccode = "x"  # "x{0}".format(ccode)
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):
 */
        goto __pyx_L39;
      }

      /* "Mikado/scales/contrast.pyx":435
 *             if ccode in ("e", "g", "c", "m", "_", "C"):
 *                 ccode = "x"  # "x{0}".format(ccode)
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):             # <<<<<<<<<<<<<<
 *                 ccode = "X"  # "X{0}".format(ccode)
 *         reference_exon = None
 */
      __Pyx_INCREF(__pyx_v_ccode);
      __pyx_t_19 = __pyx_v_ccode;
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_u, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      if (__pyx_t_11) {
      } else {
        __pyx_t_10 = __pyx_t_11;
        goto __pyx_L46_bool_binop_done;
      }
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_i, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      if (__pyx_t_11) {
      } else {
        __pyx_t_10 = __pyx_t_11;
        goto __pyx_L46_bool_binop_done;
      }
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_I, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      if (__pyx_t_11) {
      } else {
        __pyx_t_10 = __pyx_t_11;
        goto __pyx_L46_bool_binop_done;
      }
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_p, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      if (__pyx_t_11) {
      } else {
        __pyx_t_10 = __pyx_t_11;
        goto __pyx_L46_bool_binop_done;
      }
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_P, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      if (__pyx_t_11) {
      } else {
        __pyx_t_10 = __pyx_t_11;
        goto __pyx_L46_bool_binop_done;
      }
      __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_t_19, __pyx_n_s_x, Py_NE)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 435, __pyx_L1_error)
      __pyx_t_10 = __pyx_t_11;
      __pyx_L46_bool_binop_done:;
      __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
      __pyx_t_11 = (__pyx_t_10 != 0);
      if (__pyx_t_11) {

        /* "Mikado/scales/contrast.pyx":436
 *                 ccode = "x"  # "x{0}".format(ccode)
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):
 *                 ccode = "X"  # "X{0}".format(ccode)             # <<<<<<<<<<<<<<
 *         reference_exon = None
 * 
 */
        __Pyx_INCREF(__pyx_n_s_X);
        __Pyx_DECREF_SET(__pyx_v_ccode, __pyx_n_s_X);

        /* "Mikado/scales/contrast.pyx":435
 *             if ccode in ("e", "g", "c", "m", "_", "C"):
 *                 ccode = "x"  # "x{0}".format(ccode)
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):             # <<<<<<<<<<<<<<
 *                 ccode = "X"  # "X{0}".format(ccode)
 *         reference_exon = None
 */
      }
      __pyx_L39:;

      /* "Mikado/scales/contrast.pyx":432
 *     if (p_strand != r_strand):
 * 
 *         if (p_strand != "" and r_strand != ""):             # <<<<<<<<<<<<<<
 *             if ccode in ("e", "g", "c", "m", "_", "C"):
 *                 ccode = "x"  # "x{0}".format(ccode)
 */
    }

    /* "Mikado/scales/contrast.pyx":437
 *             elif ccode not in ("u", "i", "I", "p", "P", "x"):
 *                 ccode = "X"  # "X{0}".format(ccode)
 *         reference_exon = None             # <<<<<<<<<<<<<<
 * 
 *     result = ResultStorer(reference.id,
 */
    __Pyx_INCREF(Py_None);
    __Pyx_DECREF_SET(__pyx_v_reference_exon, Py_None);

    /* "Mikado/scales/contrast.pyx":430
 *                                               nucl_overlap, stats)
 * 
 *     if (p_strand != r_strand):             # <<<<<<<<<<<<<<
 * 
 *         if (p_strand != "" and r_strand != ""):
 */
  }

  /* "Mikado/scales/contrast.pyx":439
 *         reference_exon = None
 * 
 *     result = ResultStorer(reference.id,             # <<<<<<<<<<<<<<
 *                           ",".join(reference.parent),
 *                           ccode, prediction.id,
 */
  __pyx_t_18 = __Pyx_GetModuleGlobalName(__pyx_n_s_ResultStorer); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 439, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_18);
  __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_id); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 439, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);

  /* "Mikado/scales/contrast.pyx":440
 * 
 *     result = ResultStorer(reference.id,
 *                           ",".join(reference.parent),             # <<<<<<<<<<<<<<
 *                           ccode, prediction.id,
 *                           ",".join(prediction.parent),
 */
  __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_parent); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 440, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_17);
  __pyx_t_1 = __Pyx_PyString_Join(__pyx_kp_s__4, __pyx_t_17); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 440, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_1);
  __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;

  /* "Mikado/scales/contrast.pyx":441
 *     result = ResultStorer(reference.id,
 *                           ",".join(reference.parent),
 *                           ccode, prediction.id,             # <<<<<<<<<<<<<<
 *                           ",".join(prediction.parent),
 *                           len(prediction.exons),
 */
  __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_id); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 441, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_17);

  /* "Mikado/scales/contrast.pyx":442
 *                           ",".join(reference.parent),
 *                           ccode, prediction.id,
 *                           ",".join(prediction.parent),             # <<<<<<<<<<<<<<
 *                           len(prediction.exons),
 *                           len(reference.exons),
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_parent); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 442, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_21 = __Pyx_PyString_Join(__pyx_kp_s__4, __pyx_t_2); if (unlikely(!__pyx_t_21)) __PYX_ERR(0, 442, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_21);
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;

  /* "Mikado/scales/contrast.pyx":443
 *                           ccode, prediction.id,
 *                           ",".join(prediction.parent),
 *                           len(prediction.exons),             # <<<<<<<<<<<<<<
 *                           len(reference.exons),
 *                           # Nucleotide stats
 */
  __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_prediction, __pyx_n_s_exons); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 443, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);
  __pyx_t_15 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 443, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_15); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 443, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_2);

  /* "Mikado/scales/contrast.pyx":444
 *                           ",".join(prediction.parent),
 *                           len(prediction.exons),
 *                           len(reference.exons),             # <<<<<<<<<<<<<<
 *                           # Nucleotide stats
 *                           round(nucl_precision * 100, 2),
 */
  __pyx_t_22 = __Pyx_PyObject_GetAttrStr(__pyx_v_reference, __pyx_n_s_exons); if (unlikely(!__pyx_t_22)) __PYX_ERR(0, 444, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_22);
  __pyx_t_15 = PyObject_Length(__pyx_t_22); if (unlikely(__pyx_t_15 == -1)) __PYX_ERR(0, 444, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
  __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_15); if (unlikely(!__pyx_t_22)) __PYX_ERR(0, 444, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_22);

  /* "Mikado/scales/contrast.pyx":446
 *                           len(reference.exons),
 *                           # Nucleotide stats
 *                           round(nucl_precision * 100, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * nucl_recall, 2),
 *                           round(100 * nucl_f1, 2),
 */
  __pyx_t_23 = PyFloat_FromDouble((__pyx_v_nucl_precision * 100.0)); if (unlikely(!__pyx_t_23)) __PYX_ERR(0, 446, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_23);
  __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) __PYX_ERR(0, 446, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_24);
  __Pyx_GIVEREF(__pyx_t_23);
  PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_23);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_int_2);
  __pyx_t_23 = 0;
  __pyx_t_23 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_24, NULL); if (unlikely(!__pyx_t_23)) __PYX_ERR(0, 446, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_23);
  __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;

  /* "Mikado/scales/contrast.pyx":447
 *                           # Nucleotide stats
 *                           round(nucl_precision * 100, 2),
 *                           round(100 * nucl_recall, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * nucl_f1, 2),
 *                           # Junction stats
 */
  __pyx_t_24 = PyFloat_FromDouble((100.0 * __pyx_v_nucl_recall)); if (unlikely(!__pyx_t_24)) __PYX_ERR(0, 447, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_24);
  __pyx_t_25 = PyTuple_New(2); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 447, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_25);
  __Pyx_GIVEREF(__pyx_t_24);
  PyTuple_SET_ITEM(__pyx_t_25, 0, __pyx_t_24);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_25, 1, __pyx_int_2);
  __pyx_t_24 = 0;
  __pyx_t_24 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_25, NULL); if (unlikely(!__pyx_t_24)) __PYX_ERR(0, 447, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_24);
  __Pyx_DECREF(__pyx_t_25); __pyx_t_25 = 0;

  /* "Mikado/scales/contrast.pyx":448
 *                           round(nucl_precision * 100, 2),
 *                           round(100 * nucl_recall, 2),
 *                           round(100 * nucl_f1, 2),             # <<<<<<<<<<<<<<
 *                           # Junction stats
 *                           round(junction_precision * 100, 2),
 */
  __pyx_t_25 = PyFloat_FromDouble((100.0 * __pyx_v_nucl_f1)); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 448, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_25);
  __pyx_t_26 = PyTuple_New(2); if (unlikely(!__pyx_t_26)) __PYX_ERR(0, 448, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_26);
  __Pyx_GIVEREF(__pyx_t_25);
  PyTuple_SET_ITEM(__pyx_t_26, 0, __pyx_t_25);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_26, 1, __pyx_int_2);
  __pyx_t_25 = 0;
  __pyx_t_25 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_26, NULL); if (unlikely(!__pyx_t_25)) __PYX_ERR(0, 448, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_25);
  __Pyx_DECREF(__pyx_t_26); __pyx_t_26 = 0;

  /* "Mikado/scales/contrast.pyx":450
 *                           round(100 * nucl_f1, 2),
 *                           # Junction stats
 *                           round(junction_precision * 100, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * junction_recall, 2),
 *                           round(100 * junction_f1, 2),
 */
  __pyx_t_26 = PyFloat_FromDouble((__pyx_v_junction_precision * 100.0)); if (unlikely(!__pyx_t_26)) __PYX_ERR(0, 450, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_26);
  __pyx_t_27 = PyTuple_New(2); if (unlikely(!__pyx_t_27)) __PYX_ERR(0, 450, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_27);
  __Pyx_GIVEREF(__pyx_t_26);
  PyTuple_SET_ITEM(__pyx_t_27, 0, __pyx_t_26);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_27, 1, __pyx_int_2);
  __pyx_t_26 = 0;
  __pyx_t_26 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_27, NULL); if (unlikely(!__pyx_t_26)) __PYX_ERR(0, 450, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_26);
  __Pyx_DECREF(__pyx_t_27); __pyx_t_27 = 0;

  /* "Mikado/scales/contrast.pyx":451
 *                           # Junction stats
 *                           round(junction_precision * 100, 2),
 *                           round(100 * junction_recall, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * junction_f1, 2),
 *                           # Exonic stats
 */
  __pyx_t_27 = PyFloat_FromDouble((100.0 * __pyx_v_junction_recall)); if (unlikely(!__pyx_t_27)) __PYX_ERR(0, 451, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_27);
  __pyx_t_28 = PyTuple_New(2); if (unlikely(!__pyx_t_28)) __PYX_ERR(0, 451, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_28);
  __Pyx_GIVEREF(__pyx_t_27);
  PyTuple_SET_ITEM(__pyx_t_28, 0, __pyx_t_27);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_28, 1, __pyx_int_2);
  __pyx_t_27 = 0;
  __pyx_t_27 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_28, NULL); if (unlikely(!__pyx_t_27)) __PYX_ERR(0, 451, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_27);
  __Pyx_DECREF(__pyx_t_28); __pyx_t_28 = 0;

  /* "Mikado/scales/contrast.pyx":452
 *                           round(junction_precision * 100, 2),
 *                           round(100 * junction_recall, 2),
 *                           round(100 * junction_f1, 2),             # <<<<<<<<<<<<<<
 *                           # Exonic stats
 *                           round(exon_precision * 100, 2),
 */
  __pyx_t_28 = PyFloat_FromDouble((100.0 * __pyx_v_junction_f1)); if (unlikely(!__pyx_t_28)) __PYX_ERR(0, 452, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_28);
  __pyx_t_29 = PyTuple_New(2); if (unlikely(!__pyx_t_29)) __PYX_ERR(0, 452, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_29);
  __Pyx_GIVEREF(__pyx_t_28);
  PyTuple_SET_ITEM(__pyx_t_29, 0, __pyx_t_28);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_29, 1, __pyx_int_2);
  __pyx_t_28 = 0;
  __pyx_t_28 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_29, NULL); if (unlikely(!__pyx_t_28)) __PYX_ERR(0, 452, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_28);
  __Pyx_DECREF(__pyx_t_29); __pyx_t_29 = 0;

  /* "Mikado/scales/contrast.pyx":454
 *                           round(100 * junction_f1, 2),
 *                           # Exonic stats
 *                           round(exon_precision * 100, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * exon_recall, 2),
 *                           round(100 * exon_f1, 2),
 */
  __pyx_t_29 = PyFloat_FromDouble((__pyx_v_exon_precision * 100.0)); if (unlikely(!__pyx_t_29)) __PYX_ERR(0, 454, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_29);
  __pyx_t_30 = PyTuple_New(2); if (unlikely(!__pyx_t_30)) __PYX_ERR(0, 454, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_30);
  __Pyx_GIVEREF(__pyx_t_29);
  PyTuple_SET_ITEM(__pyx_t_30, 0, __pyx_t_29);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_30, 1, __pyx_int_2);
  __pyx_t_29 = 0;
  __pyx_t_29 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_30, NULL); if (unlikely(!__pyx_t_29)) __PYX_ERR(0, 454, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_29);
  __Pyx_DECREF(__pyx_t_30); __pyx_t_30 = 0;

  /* "Mikado/scales/contrast.pyx":455
 *                           # Exonic stats
 *                           round(exon_precision * 100, 2),
 *                           round(100 * exon_recall, 2),             # <<<<<<<<<<<<<<
 *                           round(100 * exon_f1, 2),
 *                           distance)
 */
  __pyx_t_30 = PyFloat_FromDouble((100.0 * __pyx_v_exon_recall)); if (unlikely(!__pyx_t_30)) __PYX_ERR(0, 455, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_30);
  __pyx_t_31 = PyTuple_New(2); if (unlikely(!__pyx_t_31)) __PYX_ERR(0, 455, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_31);
  __Pyx_GIVEREF(__pyx_t_30);
  PyTuple_SET_ITEM(__pyx_t_31, 0, __pyx_t_30);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_31, 1, __pyx_int_2);
  __pyx_t_30 = 0;
  __pyx_t_30 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_31, NULL); if (unlikely(!__pyx_t_30)) __PYX_ERR(0, 455, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_30);
  __Pyx_DECREF(__pyx_t_31); __pyx_t_31 = 0;

  /* "Mikado/scales/contrast.pyx":456
 *                           round(exon_precision * 100, 2),
 *                           round(100 * exon_recall, 2),
 *                           round(100 * exon_f1, 2),             # <<<<<<<<<<<<<<
 *                           distance)
 * 
 */
  __pyx_t_31 = PyFloat_FromDouble((100.0 * __pyx_v_exon_f1)); if (unlikely(!__pyx_t_31)) __PYX_ERR(0, 456, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_31);
  __pyx_t_32 = PyTuple_New(2); if (unlikely(!__pyx_t_32)) __PYX_ERR(0, 456, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_32);
  __Pyx_GIVEREF(__pyx_t_31);
  PyTuple_SET_ITEM(__pyx_t_32, 0, __pyx_t_31);
  __Pyx_INCREF(__pyx_int_2);
  __Pyx_GIVEREF(__pyx_int_2);
  PyTuple_SET_ITEM(__pyx_t_32, 1, __pyx_int_2);
  __pyx_t_31 = 0;
  __pyx_t_31 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_32, NULL); if (unlikely(!__pyx_t_31)) __PYX_ERR(0, 456, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_31);
  __Pyx_DECREF(__pyx_t_32); __pyx_t_32 = 0;

  /* "Mikado/scales/contrast.pyx":457
 *                           round(100 * exon_recall, 2),
 *                           round(100 * exon_f1, 2),
 *                           distance)             # <<<<<<<<<<<<<<
 * 
 *     if ccode == "":
 */
  __pyx_t_32 = __Pyx_PyInt_From_long(__pyx_v_distance); if (unlikely(!__pyx_t_32)) __PYX_ERR(0, 457, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_32);
  __pyx_t_33 = NULL;
  __pyx_t_15 = 0;
  if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_18))) {
    __pyx_t_33 = PyMethod_GET_SELF(__pyx_t_18);
    if (likely(__pyx_t_33)) {
      PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_18);
      __Pyx_INCREF(__pyx_t_33);
      __Pyx_INCREF(function);
      __Pyx_DECREF_SET(__pyx_t_18, function);
      __pyx_t_15 = 1;
    }
  }
  __pyx_t_34 = PyTuple_New(17+__pyx_t_15); if (unlikely(!__pyx_t_34)) __PYX_ERR(0, 439, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_34);
  if (__pyx_t_33) {
    __Pyx_GIVEREF(__pyx_t_33); PyTuple_SET_ITEM(__pyx_t_34, 0, __pyx_t_33); __pyx_t_33 = NULL;
  }
  __Pyx_GIVEREF(__pyx_t_3);
  PyTuple_SET_ITEM(__pyx_t_34, 0+__pyx_t_15, __pyx_t_3);
  __Pyx_GIVEREF(__pyx_t_1);
  PyTuple_SET_ITEM(__pyx_t_34, 1+__pyx_t_15, __pyx_t_1);
  __Pyx_INCREF(__pyx_v_ccode);
  __Pyx_GIVEREF(__pyx_v_ccode);
  PyTuple_SET_ITEM(__pyx_t_34, 2+__pyx_t_15, __pyx_v_ccode);
  __Pyx_GIVEREF(__pyx_t_17);
  PyTuple_SET_ITEM(__pyx_t_34, 3+__pyx_t_15, __pyx_t_17);
  __Pyx_GIVEREF(__pyx_t_21);
  PyTuple_SET_ITEM(__pyx_t_34, 4+__pyx_t_15, __pyx_t_21);
  __Pyx_GIVEREF(__pyx_t_2);
  PyTuple_SET_ITEM(__pyx_t_34, 5+__pyx_t_15, __pyx_t_2);
  __Pyx_GIVEREF(__pyx_t_22);
  PyTuple_SET_ITEM(__pyx_t_34, 6+__pyx_t_15, __pyx_t_22);
  __Pyx_GIVEREF(__pyx_t_23);
  PyTuple_SET_ITEM(__pyx_t_34, 7+__pyx_t_15, __pyx_t_23);
  __Pyx_GIVEREF(__pyx_t_24);
  PyTuple_SET_ITEM(__pyx_t_34, 8+__pyx_t_15, __pyx_t_24);
  __Pyx_GIVEREF(__pyx_t_25);
  PyTuple_SET_ITEM(__pyx_t_34, 9+__pyx_t_15, __pyx_t_25);
  __Pyx_GIVEREF(__pyx_t_26);
  PyTuple_SET_ITEM(__pyx_t_34, 10+__pyx_t_15, __pyx_t_26);
  __Pyx_GIVEREF(__pyx_t_27);
  PyTuple_SET_ITEM(__pyx_t_34, 11+__pyx_t_15, __pyx_t_27);
  __Pyx_GIVEREF(__pyx_t_28);
  PyTuple_SET_ITEM(__pyx_t_34, 12+__pyx_t_15, __pyx_t_28);
  __Pyx_GIVEREF(__pyx_t_29);
  PyTuple_SET_ITEM(__pyx_t_34, 13+__pyx_t_15, __pyx_t_29);
  __Pyx_GIVEREF(__pyx_t_30);
  PyTuple_SET_ITEM(__pyx_t_34, 14+__pyx_t_15, __pyx_t_30);
  __Pyx_GIVEREF(__pyx_t_31);
  PyTuple_SET_ITEM(__pyx_t_34, 15+__pyx_t_15, __pyx_t_31);
  __Pyx_GIVEREF(__pyx_t_32);
  PyTuple_SET_ITEM(__pyx_t_34, 16+__pyx_t_15, __pyx_t_32);
  __pyx_t_3 = 0;
  __pyx_t_1 = 0;
  __pyx_t_17 = 0;
  __pyx_t_21 = 0;
  __pyx_t_2 = 0;
  __pyx_t_22 = 0;
  __pyx_t_23 = 0;
  __pyx_t_24 = 0;
  __pyx_t_25 = 0;
  __pyx_t_26 = 0;
  __pyx_t_27 = 0;
  __pyx_t_28 = 0;
  __pyx_t_29 = 0;
  __pyx_t_30 = 0;
  __pyx_t_31 = 0;
  __pyx_t_32 = 0;
  __pyx_t_19 = __Pyx_PyObject_Call(__pyx_t_18, __pyx_t_34, NULL); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 439, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_19);
  __Pyx_DECREF(__pyx_t_34); __pyx_t_34 = 0;
  __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
  __pyx_v_result = __pyx_t_19;
  __pyx_t_19 = 0;

  /* "Mikado/scales/contrast.pyx":459
 *                           distance)
 * 
 *     if ccode == "":             # <<<<<<<<<<<<<<
 *         raise ValueError("Ccode is null;\n{0}".format(repr(result)))
 * 
 */
  __pyx_t_11 = (__Pyx_PyString_Equals(__pyx_v_ccode, __pyx_kp_s_, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) __PYX_ERR(0, 459, __pyx_L1_error)
  if (__pyx_t_11) {

    /* "Mikado/scales/contrast.pyx":460
 * 
 *     if ccode == "":
 *         raise ValueError("Ccode is null;\n{0}".format(repr(result)))             # <<<<<<<<<<<<<<
 * 
 *     return (result, reference_exon)
 */
    __pyx_t_18 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Ccode_is_null_0, __pyx_n_s_format); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 460, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __pyx_t_34 = PyObject_Repr(__pyx_v_result); if (unlikely(!__pyx_t_34)) __PYX_ERR(0, 460, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_34);
    __pyx_t_32 = NULL;
    if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_18))) {
      __pyx_t_32 = PyMethod_GET_SELF(__pyx_t_18);
      if (likely(__pyx_t_32)) {
        PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_18);
        __Pyx_INCREF(__pyx_t_32);
        __Pyx_INCREF(function);
        __Pyx_DECREF_SET(__pyx_t_18, function);
      }
    }
    if (!__pyx_t_32) {
      __pyx_t_19 = __Pyx_PyObject_CallOneArg(__pyx_t_18, __pyx_t_34); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_DECREF(__pyx_t_34); __pyx_t_34 = 0;
      __Pyx_GOTREF(__pyx_t_19);
    } else {
      __pyx_t_31 = PyTuple_New(1+1); if (unlikely(!__pyx_t_31)) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_31);
      __Pyx_GIVEREF(__pyx_t_32); PyTuple_SET_ITEM(__pyx_t_31, 0, __pyx_t_32); __pyx_t_32 = NULL;
      __Pyx_GIVEREF(__pyx_t_34);
      PyTuple_SET_ITEM(__pyx_t_31, 0+1, __pyx_t_34);
      __pyx_t_34 = 0;
      __pyx_t_19 = __Pyx_PyObject_Call(__pyx_t_18, __pyx_t_31, NULL); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 460, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_19);
      __Pyx_DECREF(__pyx_t_31); __pyx_t_31 = 0;
    }
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 460, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_18);
    __Pyx_GIVEREF(__pyx_t_19);
    PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_t_19);
    __pyx_t_19 = 0;
    __pyx_t_19 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_18, NULL); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 460, __pyx_L1_error)
    __Pyx_GOTREF(__pyx_t_19);
    __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
    __Pyx_Raise(__pyx_t_19, 0, 0, 0);
    __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
    __PYX_ERR(0, 460, __pyx_L1_error)

    /* "Mikado/scales/contrast.pyx":459
 *                           distance)
 * 
 *     if ccode == "":             # <<<<<<<<<<<<<<
 *         raise ValueError("Ccode is null;\n{0}".format(repr(result)))
 * 
 */
  }

  /* "Mikado/scales/contrast.pyx":462
 *         raise ValueError("Ccode is null;\n{0}".format(repr(result)))
 * 
 *     return (result, reference_exon)             # <<<<<<<<<<<<<<
 */
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_19 = PyTuple_New(2); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 462, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_19);
  __Pyx_INCREF(__pyx_v_result);
  __Pyx_GIVEREF(__pyx_v_result);
  PyTuple_SET_ITEM(__pyx_t_19, 0, __pyx_v_result);
  __Pyx_INCREF(__pyx_v_reference_exon);
  __Pyx_GIVEREF(__pyx_v_reference_exon);
  PyTuple_SET_ITEM(__pyx_t_19, 1, __pyx_v_reference_exon);
  __pyx_r = ((PyObject*)__pyx_t_19);
  __pyx_t_19 = 0;
  goto __pyx_L0;

  /* "Mikado/scales/contrast.pyx":231
 * @cython.profile(True)
 * @cython.cdivision(True)
 * cpdef tuple compare(prediction, reference, bint lenient=False):             # <<<<<<<<<<<<<<
 * 
 *     """Cython function to compare two transcripts and determine a ccode.
 */

  /* 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_17);
  __Pyx_XDECREF(__pyx_t_18);
  __Pyx_XDECREF(__pyx_t_19);
  __Pyx_XDECREF(__pyx_t_21);
  __Pyx_XDECREF(__pyx_t_22);
  __Pyx_XDECREF(__pyx_t_23);
  __Pyx_XDECREF(__pyx_t_24);
  __Pyx_XDECREF(__pyx_t_25);
  __Pyx_XDECREF(__pyx_t_26);
  __Pyx_XDECREF(__pyx_t_27);
  __Pyx_XDECREF(__pyx_t_28);
  __Pyx_XDECREF(__pyx_t_29);
  __Pyx_XDECREF(__pyx_t_30);
  __Pyx_XDECREF(__pyx_t_31);
  __Pyx_XDECREF(__pyx_t_32);
  __Pyx_XDECREF(__pyx_t_33);
  __Pyx_XDECREF(__pyx_t_34);
  __Pyx_AddTraceback("Mikado.scales.contrast.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = 0;
  __pyx_L0:;
  __Pyx_XDECREF(__pyx_v___pred_exons);
  __Pyx_XDECREF(__pyx_v___ref_exons);
  __Pyx_XDECREF(__pyx_v_r_splices);
  __Pyx_XDECREF(__pyx_v_p_splices);
  __Pyx_XDECREF(__pyx_v_r_strand);
  __Pyx_XDECREF(__pyx_v_p_strand);
  __Pyx_XDECREF(__pyx_v_exon);
  __Pyx_XDECREF(__pyx_v_other_exon);
  __Pyx_XDECREF(__pyx_v_reference_exon);
  __Pyx_XDECREF(__pyx_v_len_rsplices);
  __Pyx_XDECREF(__pyx_v_len_psplices);
  __Pyx_XDECREF(__pyx_v_ccode);
  __Pyx_XDECREF(__pyx_v_result);
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_TraceReturn(__pyx_r, 0);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

/* Python wrapper */
static PyObject *__pyx_pw_6Mikado_6scales_8contrast_1compare(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_6Mikado_6scales_8contrast_compare[] = "Cython function to compare two transcripts and determine a ccode.\n\n    :param prediction: the transcript query\n    :type prediction: Transcript\n\n    :param reference: the reference transcript against which we desire to\n    calculate the ccode and other stats.\n    :type reference: Transcript\n    \n    :param lenient: a boolean flag that indicates whether the exon-level features should be calculated\n    leniently or not.\n    :type lenient: bool\n\n    :rtype (ResultStorer, (int,int)) | (ResultStorer, None)\n\n    Available ccodes (from Cufflinks documentation):\n\n    - =    Complete intron chain match\n    - c    Contained (perfect junction recall and precision, imperfect recall)\n    - j    Potentially novel isoform (fragment): at least one splice junction is shared\n    with a reference transcript\n    - e    Single exon transfrag overlapping a reference exon and at least\n    10 bp of a reference intron, indicating a possible pre-mRNA fragment.\n    - i    A *monoexonic* transfrag falling entirely within a reference intron\n    - o    Generic exonic overlap with a reference transcript\n    - p    Possible polymerase run-on fragment (within 2Kbases of a reference transcript)\n    - u    Unknown, intergenic transcript\n    - x    Exonic overlap with reference on the opposite strand (class codes e, o, m, c, _)\n    - X    Overlap on the opposite strand, with some junctions in common (probably a serious mistake,\n           unless non-canonical splicing junctions are involved).\n\n    Please note that the description for i is changed from Cufflinks.\n\n    We also provide the following additional classifications:\n\n    - f    gene fusion - in this case, this ccode will be followed by the ccodes of the matches for each gene, separated by comma\n    - _    Complete match, for monoexonic transcripts (nucleotide F1>=80% - i.e. min(precision,recall)>=66.7%\n    - m    Exon overlap between two monoexonic transcripts\n    - n    Potential extension of the referenc""e - we have added new splice junctions *outside* the boundaries of the transcript itself\n    - C    Contained transcript with overextensions on either side (perfect junction recall, imperfect nucleotide specificity)\n    - J    Potentially novel isoform, where all the known junctions have been confirmed and we have added others as well *externally*\n    - I    *multiexonic* transcript falling completely inside a known transcript\n    - h    AS event in which at least a couple of introns overlaps but without any\n           junction in common.\n    - G    Reverse generic overlap - the reference is monoexonic while the prediction isn't\n    - P    Possible polymerase run-on fragment\n    - g   Monoexonic overlap - the prediction is monoexonic and the reference is multiexonic\n    (within 2K bases of a reference transcript), on the opposite strand\n\n    This is a class method, and can therefore be used outside of a class instance.\n    ";
static PyObject *__pyx_pw_6Mikado_6scales_8contrast_1compare(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
  PyObject *__pyx_v_prediction = 0;
  PyObject *__pyx_v_reference = 0;
  int __pyx_v_lenient;
  PyObject *__pyx_r = 0;
  __Pyx_RefNannyDeclarations
  __Pyx_RefNannySetupContext("compare (wrapper)", 0);
  {
    static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_prediction,&__pyx_n_s_reference,&__pyx_n_s_lenient,0};
    PyObject* values[3] = {0,0,0};
    if (unlikely(__pyx_kwds)) {
      Py_ssize_t kw_args;
      const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
      switch (pos_args) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        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_prediction)) != 0)) kw_args--;
        else goto __pyx_L5_argtuple_error;
        case  1:
        if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_reference)) != 0)) kw_args--;
        else {
          __Pyx_RaiseArgtupleInvalid("compare", 0, 2, 3, 1); __PYX_ERR(0, 231, __pyx_L3_error)
        }
        case  2:
        if (kw_args > 0) {
          PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lenient);
          if (value) { values[2] = value; kw_args--; }
        }
      }
      if (unlikely(kw_args > 0)) {
        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compare") < 0)) __PYX_ERR(0, 231, __pyx_L3_error)
      }
    } else {
      switch (PyTuple_GET_SIZE(__pyx_args)) {
        case  3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
        case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
        values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
        break;
        default: goto __pyx_L5_argtuple_error;
      }
    }
    __pyx_v_prediction = values[0];
    __pyx_v_reference = values[1];
    if (values[2]) {
      __pyx_v_lenient = __Pyx_PyObject_IsTrue(values[2]); if (unlikely((__pyx_v_lenient == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 231, __pyx_L3_error)
    } else {
      __pyx_v_lenient = ((int)0);
    }
  }
  goto __pyx_L4_argument_unpacking_done;
  __pyx_L5_argtuple_error:;
  __Pyx_RaiseArgtupleInvalid("compare", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 231, __pyx_L3_error)
  __pyx_L3_error:;
  __Pyx_AddTraceback("Mikado.scales.contrast.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __Pyx_RefNannyFinishContext();
  return NULL;
  __pyx_L4_argument_unpacking_done:;
  __pyx_r = __pyx_pf_6Mikado_6scales_8contrast_compare(__pyx_self, __pyx_v_prediction, __pyx_v_reference, __pyx_v_lenient);

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

static PyObject *__pyx_pf_6Mikado_6scales_8contrast_compare(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_prediction, PyObject *__pyx_v_reference, int __pyx_v_lenient) {
  PyObject *__pyx_r = NULL;
  __Pyx_TraceDeclarations
  __Pyx_RefNannyDeclarations
  PyObject *__pyx_t_1 = NULL;
  struct __pyx_opt_args_6Mikado_6scales_8contrast_compare __pyx_t_2;
  __Pyx_RefNannySetupContext("compare", 0);
  __Pyx_TraceCall("compare (wrapper)", __pyx_f[0], 231, 0, __PYX_ERR(0, 231, __pyx_L1_error));
  __Pyx_XDECREF(__pyx_r);
  __pyx_t_2.__pyx_n = 1;
  __pyx_t_2.lenient = __pyx_v_lenient;
  __pyx_t_1 = __pyx_f_6Mikado_6scales_8contrast_compare(__pyx_v_prediction, __pyx_v_reference, 0, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 231, __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("Mikado.scales.contrast.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
  __pyx_r = NULL;
  __pyx_L0:;
  __Pyx_XGIVEREF(__pyx_r);
  __Pyx_TraceReturn(__pyx_r, 0);
  __Pyx_RefNannyFinishContext();
  return __pyx_r;
}

static PyMethodDef __pyx_methods[] = {
  {"compare", (PyCFunction)__pyx_pw_6Mikado_6scales_8contrast_1compare, METH_VARARGS|METH_KEYWORDS, __pyx_doc_6Mikado_6scales_8contrast_compare},
  {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
    "contrast",
    0, /* m_doc */
    -1, /* m_size */
    __pyx_methods /* m_methods */,
    NULL, /* m_reload */
    NULL, /* m_traverse */
    NULL, /* m_clear */
    NULL /* m_free */
};
#endif

static __Pyx_StringTabEntry __pyx_string_tab[] = {
  {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0},
  {&__pyx_n_s_C, __pyx_k_C, sizeof(__pyx_k_C), 0, 0, 1, 1},
  {&__pyx_kp_s_Ccode_is_null_0, __pyx_k_Ccode_is_null_0, sizeof(__pyx_k_Ccode_is_null_0), 0, 0, 1, 0},
  {&__pyx_n_s_G, __pyx_k_G, sizeof(__pyx_k_G), 0, 0, 1, 1},
  {&__pyx_n_s_I, __pyx_k_I, sizeof(__pyx_k_I), 0, 0, 1, 1},
  {&__pyx_n_s_J, __pyx_k_J, sizeof(__pyx_k_J), 0, 0, 1, 1},
  {&__pyx_kp_s_Luca_Venturini, __pyx_k_Luca_Venturini, sizeof(__pyx_k_Luca_Venturini), 0, 0, 1, 0},
  {&__pyx_n_s_P, __pyx_k_P, sizeof(__pyx_k_P), 0, 0, 1, 1},
  {&__pyx_n_s_ResultStorer, __pyx_k_ResultStorer, sizeof(__pyx_k_ResultStorer), 0, 0, 1, 1},
  {&__pyx_n_s_Transcript, __pyx_k_Transcript, sizeof(__pyx_k_Transcript), 0, 0, 1, 1},
  {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
  {&__pyx_n_s_X, __pyx_k_X, sizeof(__pyx_k_X), 0, 0, 1, 1},
  {&__pyx_n_s__2, __pyx_k__2, sizeof(__pyx_k__2), 0, 0, 1, 1},
  {&__pyx_kp_s__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 0, 1, 0},
  {&__pyx_kp_s__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 0, 1, 0},
  {&__pyx_n_s_author, __pyx_k_author, sizeof(__pyx_k_author), 0, 0, 1, 1},
  {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1},
  {&__pyx_n_s_cdna_length, __pyx_k_cdna_length, sizeof(__pyx_k_cdna_length), 0, 0, 1, 1},
  {&__pyx_n_s_copy, __pyx_k_copy, sizeof(__pyx_k_copy), 0, 0, 1, 1},
  {&__pyx_n_s_e, __pyx_k_e, sizeof(__pyx_k_e), 0, 0, 1, 1},
  {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1},
  {&__pyx_n_s_exon_num, __pyx_k_exon_num, sizeof(__pyx_k_exon_num), 0, 0, 1, 1},
  {&__pyx_n_s_exons, __pyx_k_exons, sizeof(__pyx_k_exons), 0, 0, 1, 1},
  {&__pyx_n_s_finalize, __pyx_k_finalize, sizeof(__pyx_k_finalize), 0, 0, 1, 1},
  {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1},
  {&__pyx_n_s_g, __pyx_k_g, sizeof(__pyx_k_g), 0, 0, 1, 1},
  {&__pyx_n_s_h, __pyx_k_h, sizeof(__pyx_k_h), 0, 0, 1, 1},
  {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1},
  {&__pyx_n_s_id, __pyx_k_id, sizeof(__pyx_k_id), 0, 0, 1, 1},
  {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
  {&__pyx_n_s_intersection, __pyx_k_intersection, sizeof(__pyx_k_intersection), 0, 0, 1, 1},
  {&__pyx_n_s_introns, __pyx_k_introns, sizeof(__pyx_k_introns), 0, 0, 1, 1},
  {&__pyx_n_s_j, __pyx_k_j, sizeof(__pyx_k_j), 0, 0, 1, 1},
  {&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1},
  {&__pyx_n_s_lenient, __pyx_k_lenient, sizeof(__pyx_k_lenient), 0, 0, 1, 1},
  {&__pyx_n_s_loci, __pyx_k_loci, sizeof(__pyx_k_loci), 0, 0, 1, 1},
  {&__pyx_n_s_m, __pyx_k_m, sizeof(__pyx_k_m), 0, 0, 1, 1},
  {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
  {&__pyx_n_s_max, __pyx_k_max, sizeof(__pyx_k_max), 0, 0, 1, 1},
  {&__pyx_n_s_min, __pyx_k_min, sizeof(__pyx_k_min), 0, 0, 1, 1},
  {&__pyx_n_s_n, __pyx_k_n, sizeof(__pyx_k_n), 0, 0, 1, 1},
  {&__pyx_n_s_o, __pyx_k_o, sizeof(__pyx_k_o), 0, 0, 1, 1},
  {&__pyx_n_s_p, __pyx_k_p, sizeof(__pyx_k_p), 0, 0, 1, 1},
  {&__pyx_n_s_parent, __pyx_k_parent, sizeof(__pyx_k_parent), 0, 0, 1, 1},
  {&__pyx_n_s_prediction, __pyx_k_prediction, sizeof(__pyx_k_prediction), 0, 0, 1, 1},
  {&__pyx_n_s_rI, __pyx_k_rI, sizeof(__pyx_k_rI), 0, 0, 1, 1},
  {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1},
  {&__pyx_n_s_remove, __pyx_k_remove, sizeof(__pyx_k_remove), 0, 0, 1, 1},
  {&__pyx_n_s_resultstorer, __pyx_k_resultstorer, sizeof(__pyx_k_resultstorer), 0, 0, 1, 1},
  {&__pyx_n_s_ri, __pyx_k_ri, sizeof(__pyx_k_ri), 0, 0, 1, 1},
  {&__pyx_n_s_round, __pyx_k_round, sizeof(__pyx_k_round), 0, 0, 1, 1},
  {&__pyx_n_s_splices, __pyx_k_splices, sizeof(__pyx_k_splices), 0, 0, 1, 1},
  {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
  {&__pyx_n_s_strand, __pyx_k_strand, sizeof(__pyx_k_strand), 0, 0, 1, 1},
  {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
  {&__pyx_n_s_u, __pyx_k_u, sizeof(__pyx_k_u), 0, 0, 1, 1},
  {&__pyx_n_s_x, __pyx_k_x, sizeof(__pyx_k_x), 0, 0, 1, 1},
  {0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
  __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) __PYX_ERR(0, 167, __pyx_L1_error)
  __pyx_builtin_min = __Pyx_GetBuiltinName(__pyx_n_s_min); if (!__pyx_builtin_min) __PYX_ERR(0, 168, __pyx_L1_error)
  __pyx_builtin_round = __Pyx_GetBuiltinName(__pyx_n_s_round); if (!__pyx_builtin_round) __PYX_ERR(0, 446, __pyx_L1_error)
  __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 460, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

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

static int __Pyx_InitGlobals(void) {
  if (__Pyx_InitStrings(__pyx_string_tab) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) __PYX_ERR(0, 1, __pyx_L1_error)
  return 0;
  __pyx_L1_error:;
  return -1;
}

#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC initcontrast(void); /*proto*/
PyMODINIT_FUNC initcontrast(void)
#else
PyMODINIT_FUNC PyInit_contrast(void); /*proto*/
PyMODINIT_FUNC PyInit_contrast(void)
#endif
{
  PyObject *__pyx_t_1 = NULL;
  PyObject *__pyx_t_2 = NULL;
  PyObject *__pyx_t_3 = NULL;
  PyObject *__pyx_t_4 = NULL;
  __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_contrast(void)", 0);
  if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
  #ifdef __Pyx_CyFunction_USED
  if (__pyx_CyFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_FusedFunction_USED
  if (__pyx_FusedFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Coroutine_USED
  if (__pyx_Coroutine_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_Generator_USED
  if (__pyx_Generator_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  #ifdef __Pyx_StopAsyncIteration_USED
  if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  /*--- Library function declarations ---*/
  /*--- Threads initialization code ---*/
  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
  #ifdef WITH_THREAD /* Python build with threading support? */
  PyEval_InitThreads();
  #endif
  #endif
  /*--- Module creation code ---*/
  #if PY_MAJOR_VERSION < 3
  __pyx_m = Py_InitModule4("contrast", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
  #else
  __pyx_m = PyModule_Create(&__pyx_moduledef);
  #endif
  if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
  __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_INCREF(__pyx_d);
  __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
  #if CYTHON_COMPILING_IN_PYPY
  Py_INCREF(__pyx_b);
  #endif
  if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error);
  /*--- Initialize various global constants etc. ---*/
  if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
  if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif
  if (__pyx_module_is_main_Mikado__scales__contrast) {
    if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  }
  #if PY_MAJOR_VERSION >= 3
  {
    PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
    if (!PyDict_GetItemString(modules, "Mikado.scales.contrast")) {
      if (unlikely(PyDict_SetItemString(modules, "Mikado.scales.contrast", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
    }
  }
  #endif
  /*--- Builtin init code ---*/
  if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Constants init code ---*/
  if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Global init code ---*/
  /*--- Variable export code ---*/
  /*--- Function export code ---*/
  if (__Pyx_ExportFunction("compare", (void (*)(void))__pyx_f_6Mikado_6scales_8contrast_compare, "PyObject *(PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_6Mikado_6scales_8contrast_compare *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ExportFunction("__assign_multiexonic_ccode", (void (*)(void))__pyx_f_6Mikado_6scales_8contrast___assign_multiexonic_ccode, "PyObject *(PyObject *, PyObject *, long, double *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ExportFunction("__assign_monoexonic_ccode", (void (*)(void))__pyx_f_6Mikado_6scales_8contrast___assign_monoexonic_ccode, "PyObject *(PyObject *, PyObject *, long, double *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  /*--- Type init code ---*/
  /*--- Type import code ---*/
  /*--- Variable import code ---*/
  /*--- Function import code ---*/
  __pyx_t_1 = __Pyx_ImportModule("Mikado.utilities.overlap"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_1, "c_overlap", (void (**)(void))&__pyx_f_6Mikado_9utilities_7overlap_c_overlap, "long (long, long, long, long, long, int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_DECREF(__pyx_t_1); __pyx_t_1 = 0;
  __pyx_t_2 = __Pyx_ImportModule("Mikado.scales.f1"); if (!__pyx_t_2) __PYX_ERR(0, 1, __pyx_L1_error)
  if (__Pyx_ImportFunction(__pyx_t_2, "calc_f1", (void (**)(void))&__pyx_f_6Mikado_6scales_2f1_calc_f1, "double (double, double, int __pyx_skip_dispatch)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  Py_DECREF(__pyx_t_2); __pyx_t_2 = 0;
  /*--- Execution code ---*/
  #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
  if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  #endif

  /* "Mikado/scales/contrast.pyx":1
 * from .resultstorer import ResultStorer             # <<<<<<<<<<<<<<
 * from ..loci import Transcript
 * from ..utilities.overlap cimport c_overlap
 */
  __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_INCREF(__pyx_n_s_ResultStorer);
  __Pyx_GIVEREF(__pyx_n_s_ResultStorer);
  PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_ResultStorer);
  __pyx_t_4 = __Pyx_Import(__pyx_n_s_resultstorer, __pyx_t_3, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __pyx_t_3 = __Pyx_ImportFrom(__pyx_t_4, __pyx_n_s_ResultStorer); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_ResultStorer, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;

  /* "Mikado/scales/contrast.pyx":2
 * from .resultstorer import ResultStorer
 * from ..loci import Transcript             # <<<<<<<<<<<<<<
 * from ..utilities.overlap cimport c_overlap
 * from .f1 cimport calc_f1
 */
  __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  __Pyx_INCREF(__pyx_n_s_Transcript);
  __Pyx_GIVEREF(__pyx_n_s_Transcript);
  PyList_SET_ITEM(__pyx_t_4, 0, __pyx_n_s_Transcript);
  __pyx_t_3 = __Pyx_Import(__pyx_n_s_loci, __pyx_t_4, 2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __pyx_t_4 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_Transcript); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_4);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_Transcript, __pyx_t_4) < 0) __PYX_ERR(0, 2, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

  /* "Mikado/scales/contrast.pyx":8
 * 
 * 
 * __author__ = 'Luca Venturini'             # <<<<<<<<<<<<<<
 * 
 * cdef inline long long_max(long a, long b): return a if a >= b else b
 */
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_author, __pyx_kp_s_Luca_Venturini) < 0) __PYX_ERR(0, 8, __pyx_L1_error)

  /* "Mikado/scales/contrast.pyx":1
 * from .resultstorer import ResultStorer             # <<<<<<<<<<<<<<
 * from ..loci import Transcript
 * from ..utilities.overlap cimport c_overlap
 */
  __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_3);
  if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;

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

  goto __pyx_L0;
  __pyx_L1_error:;
  __Pyx_XDECREF(__pyx_t_1);
  __Pyx_XDECREF(__pyx_t_2);
  __Pyx_XDECREF(__pyx_t_3);
  __Pyx_XDECREF(__pyx_t_4);
  if (__pyx_m) {
    if (__pyx_d) {
      __Pyx_AddTraceback("init Mikado.scales.contrast", __pyx_clineno, __pyx_lineno, __pyx_filename);
    }
    Py_DECREF(__pyx_m); __pyx_m = 0;
  } else if (!PyErr_Occurred()) {
    PyErr_SetString(PyExc_ImportError, "init Mikado.scales.contrast");
  }
  __pyx_L0:;
  __Pyx_RefNannyFinishContext();
  #if PY_MAJOR_VERSION < 3
  return;
  #else
  return __pyx_m;
  #endif
}

/* --- Runtime support code --- */
/* Refnanny */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
    PyObject *m = NULL, *p = NULL;
    void *r = NULL;
    m = PyImport_ImportModule((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

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

/* Profile */
#if CYTHON_PROFILE
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
                                   PyFrameObject** frame,
                                   const char *funcname,
                                   const char *srcfile,
                                   int firstlineno) {
    PyObject *type, *value, *traceback;
    int retval;
    PyThreadState* tstate = PyThreadState_GET();
    if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) {
        if (*code == NULL) {
            *code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno);
            if (*code == NULL) return 0;
        }
        *frame = PyFrame_New(
            tstate,                          /*PyThreadState *tstate*/
            *code,                           /*PyCodeObject *code*/
            __pyx_d,                  /*PyObject *globals*/
            0                                /*PyObject *locals*/
        );
        if (*frame == NULL) return 0;
        if (CYTHON_TRACE && (*frame)->f_trace == NULL) {
            Py_INCREF(Py_None);
            (*frame)->f_trace = Py_None;
        }
#if PY_VERSION_HEX < 0x030400B1
    } else {
        (*frame)->f_tstate = tstate;
#endif
    }
    (*frame)->f_lineno = firstlineno;
    retval = 1;
    tstate->tracing++;
    tstate->use_tracing = 0;
    PyErr_Fetch(&type, &value, &traceback);
    #if CYTHON_TRACE
    if (tstate->c_tracefunc)
        retval = tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL) == 0;
    if (retval && tstate->c_profilefunc)
    #endif
        retval = tstate->c_profilefunc(tstate->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
    tstate->use_tracing = (tstate->c_profilefunc ||
                           (CYTHON_TRACE && tstate->c_tracefunc));
    tstate->tracing--;
    if (retval) {
        PyErr_Restore(type, value, traceback);
        return tstate->use_tracing && retval;
    } else {
        Py_XDECREF(type);
        Py_XDECREF(value);
        Py_XDECREF(traceback);
        return -1;
    }
}
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
    PyObject *py_srcfile = 0;
    PyObject *py_funcname = 0;
    PyCodeObject *py_code = 0;
    #if PY_MAJOR_VERSION < 3
    py_funcname = PyString_FromString(funcname);
    py_srcfile = PyString_FromString(srcfile);
    #else
    py_funcname = PyUnicode_FromString(funcname);
    py_srcfile = PyUnicode_FromString(srcfile);
    #endif
    if (!py_funcname | !py_srcfile) goto bad;
    py_code = PyCode_New(
        0,
        #if PY_MAJOR_VERSION >= 3
        0,
        #endif
        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,*/
        firstlineno,
        __pyx_empty_bytes      /*PyObject *lnotab*/
    );
bad:
    Py_XDECREF(py_srcfile);
    Py_XDECREF(py_funcname);
    return py_code;
}
#endif

/* GetItemInt */
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,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED 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,
                                                              CYTHON_NCP_UNUSED int wraparound,
                                                              CYTHON_NCP_UNUSED 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,
                                                     CYTHON_NCP_UNUSED int wraparound,
                                                     CYTHON_NCP_UNUSED 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))
                        return NULL;
                    PyErr_Clear();
                }
            }
            return m->sq_item(o, i);
        }
    }
#else
    if (is_list || PySequence_Check(o)) {
        return PySequence_GetItem(o, i);
    }
#endif
    return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}

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

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

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

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

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

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

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

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

/* PyObjectCallOneArg */
#if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
    PyObject *result;
    PyObject *args = PyTuple_New(1);
    if (unlikely(!args)) return NULL;
    Py_INCREF(arg);
    PyTuple_SET_ITEM(args, 0, arg);
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
#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 *result;
    PyObject *args = PyTuple_Pack(1, arg);
    if (unlikely(!args)) return NULL;
    result = __Pyx_PyObject_Call(func, args, NULL);
    Py_DECREF(args);
    return result;
}
#endif

/* PyObjectCallNoArg */
  #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

/* PyIntBinop */
    #if CYTHON_COMPILING_IN_CPYTHON
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
    #if PY_MAJOR_VERSION < 3
    if (likely(PyInt_CheckExact(op1))) {
        const long b = intval;
        long x;
        long a = PyInt_AS_LONG(op1);
            x = (long)((unsigned long)a + b);
            if (likely((x^a) >= 0 || (x^b) >= 0))
                return PyInt_FromLong(x);
            return PyLong_Type.tp_as_number->nb_add(op1, op2);
    }
    #endif
    #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
    if (likely(PyLong_CheckExact(op1))) {
        const long b = intval;
        long a, x;
        const PY_LONG_LONG llb = intval;
        PY_LONG_LONG lla, llx;
        const digit* digits = ((PyLongObject*)op1)->ob_digit;
        const Py_ssize_t size = Py_SIZE(op1);
        if (likely(__Pyx_sst_abs(size) <= 1)) {
            a = likely(size) ? digits[0] : 0;
            if (size == -1) a = -a;
        } else {
            switch (size) {
                case -2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                case 2:
                    if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
                        a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                case -3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                case 3:
                    if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
                        a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                case -4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                case 4:
                    if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
                        a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
                        break;
                    } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
                        lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
                        goto long_long;
                    }
                default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
            }
        }
                x = a + b;
            return PyLong_FromLong(x);
        long_long:
                llx = lla + llb;
            return PyLong_FromLongLong(llx);
    }
    #endif
    if (PyFloat_CheckExact(op1)) {
        const long b = intval;
        double a = PyFloat_AS_DOUBLE(op1);
            double result;
            PyFPE_START_PROTECT("add", return NULL)
            result = ((double)a) + (double)b;
            PyFPE_END_PROTECT(result)
            return PyFloat_FromDouble(result);
    }
    return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2);
}
#endif

/* GetModuleGlobalName */
    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;
}

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

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

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

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

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

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

/* Import */
        static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
    PyObject *empty_list = 0;
    PyObject *module = 0;
    PyObject *global_dict = 0;
    PyObject *empty_dict = 0;
    PyObject *list;
    #if PY_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;
}

/* ImportFrom */
        static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
    PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
    if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
        PyErr_Format(PyExc_ImportError,
        #if PY_MAJOR_VERSION < 3
            "cannot import name %.230s", PyString_AS_STRING(name));
        #else
            "cannot import name %S", name);
        #endif
    }
    return value;
}

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

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

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

/* CIntToPy */
        static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
    const long neg_one = (long) -1, const_zero = (long) 0;
    const int is_unsigned = neg_one > const_zero;
    if (is_unsigned) {
        if (sizeof(long) < sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(long) <= sizeof(unsigned long)) {
            return PyLong_FromUnsignedLong((unsigned long) value);
        } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
            return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
        }
    } else {
        if (sizeof(long) <= sizeof(long)) {
            return PyInt_FromLong((long) value);
        } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
            return PyLong_FromLongLong((PY_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);
    }
}

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

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

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

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

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

/* ModuleImport */
        #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

/* FunctionImport */
        #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

/* InitStrings */
        static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
    while (t->p) {
        #if PY_MAJOR_VERSION < 3
        if (t->is_unicode) {
            *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
        } else if (t->intern) {
            *t->p = PyString_InternFromString(t->s);
        } else {
            *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
        }
        #else
        if (t->is_unicode | t->is_str) {
            if (t->intern) {
                *t->p = PyUnicode_InternFromString(t->s);
            } else if (t->encoding) {
                *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
            } else {
                *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
            }
        } else {
            *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
        }
        #endif
        if (!*t->p)
            return -1;
        ++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 CYTHON_COMPILING_IN_CPYTHON && (__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) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
    if (PyByteArray_Check(o)) {
        *length = PyByteArray_GET_SIZE(o);
        return PyByteArray_AS_STRING(o);
    } else
#endif
    {
        char* result;
        int r = PyBytes_AsStringAndSize(o, &result, length);
        if (unlikely(r < 0)) {
            return NULL;
        } else {
            return result;
        }
    }
}
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
   int is_true = x == Py_True;
   if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
   else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(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 __Pyx_NewRef(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))) {
    if (sizeof(Py_ssize_t) >= sizeof(long))
        return PyInt_AS_LONG(b);
    else
        return PyInt_AsSsize_t(x);
  }
#endif
  if (likely(PyLong_CheckExact(b))) {
    #if CYTHON_USE_PYLONG_INTERNALS
    const digit* digits = ((PyLongObject*)b)->ob_digit;
    const Py_ssize_t size = Py_SIZE(b);
    if (likely(__Pyx_sst_abs(size) <= 1)) {
        ival = likely(size) ? digits[0] : 0;
        if (size == -1) ival = -ival;
        return ival;
    } else {
      switch (size) {
         case 2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -2:
           if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -3:
           if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case 4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
         case -4:
           if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
             return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
           }
           break;
      }
    }
    #endif
    return PyLong_AsSsize_t(b);
  }
  x = PyNumber_Index(b);
  if (!x) return -1;
  ival = PyInt_AsSsize_t(x);
  Py_DECREF(x);
  return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
    return PyInt_FromSize_t(ival);
}


#endif /* Py_PYTHON_H */
