[med-svn] [macs] 01/03: Imported Upstream version 2.1.1.20160309
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue May 24 11:02:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository macs.
commit 88a91b9934f5d8fd0fd9158caf8583d77e329d03
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Fri May 13 09:45:21 2016 -0700
Imported Upstream version 2.1.1.20160309
---
ChangeLog | 15 +
MACS2.egg-info/PKG-INFO | 2 +-
MACS2/Constants.py | 2 +-
MACS2/IO/FixWidthTrack.c | 3157 +++++++++++++++++-------
MACS2/IO/FixWidthTrack.pyx | 2 +-
MACS2/IO/Parser.c | 5823 ++++++++++++++++++++++++++++----------------
MACS2/IO/Parser.pyx | 13 +-
MACS2/PeakModel.c | 2703 ++++++++++++++------
MACS2/PeakModel.pyx | 2 +-
PKG-INFO | 2 +-
bin/macs2 | 26 +-
setup.py | 4 +-
setup_w_cython.py | 4 +-
13 files changed, 7941 insertions(+), 3814 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 1e26e7c..dc2f0e7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,18 @@
+2016-03-09 Tao Liu <vladimir.liu at gmail.com>
+ MACS version 2.1.1 20160309
+
+ * Retire the tag:rc.
+
+ * Fixed spelling. Merged pull request #120. Thank @mr-c!
+
+ * Change filtering criteria for reading BAM/SAM files
+
+ Related to callpeak and filterdup commands. Now the
+ reads/alignments flagged with 1028 or 'PCR/Optical duplicate' will
+ still be read although MACS2 may decide them as duplicates
+ later. Related to old issue #33. Sorry I forgot to address it for
+ years!
+
2016-02-26 Tao Liu <vladimir.liu at gmail.com>
MACS version 2.1.1 20160226 (tag:rc Zhengyue)
diff --git a/MACS2.egg-info/PKG-INFO b/MACS2.egg-info/PKG-INFO
index cf74d85..a5c58f7 100644
--- a/MACS2.egg-info/PKG-INFO
+++ b/MACS2.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.1.20160226
+Version: 2.1.1.20160309
Summary: Model Based Analysis for ChIP-Seq data
Home-page: http://github.com/taoliu/MACS/
Author: Tao Liu
diff --git a/MACS2/Constants.py b/MACS2/Constants.py
index 6afe067..90559f9 100644
--- a/MACS2/Constants.py
+++ b/MACS2/Constants.py
@@ -1,4 +1,4 @@
-MACS_VERSION = "2.1.1.20160226"
+MACS_VERSION = "2.1.1.20160309"
#MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"
FILTERDUP_VERSION = "1.0.0 20140616"
RANDSAMPLE_VERSION = "1.0.0 20120703"
diff --git a/MACS2/IO/FixWidthTrack.c b/MACS2/IO/FixWidthTrack.c
index d86a8e6..c63e59f 100644
--- a/MACS2/IO/FixWidthTrack.c
+++ b/MACS2/IO/FixWidthTrack.c
@@ -1,25 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.23.4 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
#error Cython requires Python 2.6+ or Python 3.2+.
#else
-#define CYTHON_ABI "0_22"
+#define CYTHON_ABI "0_23_4"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -54,6 +42,9 @@
#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_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
#define Py_OptimizeFlag 0
#endif
@@ -61,26 +52,30 @@
#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) \
+ #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) \
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#define __Pyx_DefaultClassType PyType_Type
#endif
-#if PY_MAJOR_VERSION >= 3
+#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
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
+#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)) ? \
+ #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)
@@ -99,12 +94,13 @@
#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)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
#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)) ? \
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
+ #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
#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))
@@ -169,16 +165,18 @@
#else
#define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
-#ifndef CYTHON_INLINE
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- #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
+#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__)
@@ -191,35 +189,33 @@
#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() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
float value;
memset(&value, 0xFF, sizeof(value));
return value;
}
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
-#endif
#if PY_MAJOR_VERSION >= 3
@@ -238,10 +234,6 @@ class __Pyx_FakeReference {
#endif
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
#define __PYX_HAVE__MACS2__IO__FixWidthTrack
#define __PYX_HAVE_API__MACS2__IO__FixWidthTrack
#include "stdint.h"
@@ -272,6 +264,13 @@ class __Pyx_FakeReference {
# 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; char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
@@ -280,16 +279,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
+#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))
@@ -324,8 +341,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+#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_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
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- PyGILState_Release(__pyx_gilstate_save); \
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+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\
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- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
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__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
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#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); \
+#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); \
+#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)
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static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
const char* function_name);
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
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#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
#endif
-#if PY_MAJOR_VERSION >= 3
+#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
value = PyDict_GetItemWithError(d, key);
@@ -1046,20 +1064,20 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
+#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) : \
+#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);
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- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, 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);
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static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
-#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \
+#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\
__Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
int is_list, int wraparound, int boundscheck);
-static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */
-
-#ifndef __PYX_FORCE_INIT_THREADS
- #define __PYX_FORCE_INIT_THREADS 0
-#endif
+static CYTHON_INLINE long __Pyx_mod_long(long, long);
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
+#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
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb);
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb);
@@ -1103,13 +1124,31 @@ static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* o
__Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);
-
static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d);
+typedef struct {
+ PyObject *type;
+ PyObject **method_name;
+ PyCFunction func;
+ PyObject *method;
+ int flag;
+} __Pyx_CachedCFunction;
+
+static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self);
+#if CYTHON_COMPILING_IN_CPYTHON
+#define __Pyx_CallUnboundCMethod0(cfunc, self)\
+ ((likely((cfunc)->func)) ?\
+ (likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\
+ (likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\
+ ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) : __Pyx__CallUnboundCMethod0(cfunc, self)))) :\
+ __Pyx__CallUnboundCMethod0(cfunc, self))
+#else
+#define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self)
+#endif
+
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename,
- int full_traceback);
+ int full_traceback, int nogil);
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
@@ -1130,7 +1169,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
static void __Pyx_RaiseBufferFallbackError(void);
#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+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));
}
@@ -1161,12 +1200,14 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
static void __Pyx_RaiseBufferIndexError(int axis);
-static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */
+static CYTHON_INLINE long __Pyx_div_long(long, long);
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
typedef struct {
@@ -1211,8 +1252,6 @@ typedef struct {
static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
-
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *);
@@ -1343,7 +1382,9 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value);
-static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value);
+
+static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *);
static int __Pyx_check_binary_version(void);
@@ -1386,6 +1427,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_pileup_a_chromosome
/* Module declarations from 'cpython.version' */
+/* Module declarations from '__builtin__' */
+
+/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
+
+/* Module declarations from 'libc.string' */
+
+/* Module declarations from 'libc.stdio' */
+
+/* Module declarations from 'cpython.object' */
+
/* Module declarations from 'cpython.ref' */
/* Module declarations from 'cpython.exc' */
@@ -1398,23 +1450,12 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_pileup_a_chromosome
/* Module declarations from 'cpython.list' */
-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from 'cpython.object' */
-
/* Module declarations from 'cpython.sequence' */
/* Module declarations from 'cpython.mapping' */
/* Module declarations from 'cpython.iterator' */
-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
-
/* Module declarations from 'cpython.number' */
/* Module declarations from 'cpython.int' */
@@ -1501,45 +1542,6 @@ static PyObject *__pyx_builtin_file;
static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack___init__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_fw, char *__pyx_v_anno, long __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_2destroy(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4add_loc(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome, int32_t __pyx_v_fiveendpos, int __pyx_v_strand); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_6finalize(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_8set_rlengths(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_rlengths); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10get_rlengths(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_12get_locations_by_chr(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_14get_chr_names(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_16sort(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_18separate_dups(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_maxint); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_20addback_dups(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_22filter_dup(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_maxnum); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_24filter_dup_dryrun(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_maxnum); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_26sample_percent(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, float __pyx_v_percent, int __pyx_v_seed); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_28sample_num(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, uint64_t __pyx_v_samplesize, int __pyx_v_seed); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_30print_to_bed(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_fhd); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_32extract_region_tags(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome, int32_t __pyx_v_startpos, int32_t __pyx_v_endpos); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_34compute_region_tags_from_peaks(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_peaks, PyObject *__pyx_v_func, int __pyx_v_window_size, float __pyx_v_cutoff); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_36refine_peak_from_tags_distribution(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_peaks, int __pyx_v_window_size, float __pyx_v_cutoff); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_38pileup_a_chromosome(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_ds, PyObject *__pyx_v_scale_factor_s, float __pyx_v_baseline_value, int __pyx_v_directional, int __pyx_v_end_shift); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_11buffer_size___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_11buffer_size_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_5total___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_5total_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_9dup_total___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_9dup_total_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation_4__del__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4dups___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4dups_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4dups_4__del__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_2fw___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_2fw_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_6length___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_6length_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_5MACS2_2IO_13FixWidthTrack_FWTrack(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_[] = "";
static char __pyx_k_B[] = "B";
static char __pyx_k_H[] = "H";
@@ -1809,6 +1811,46 @@ static PyObject *__pyx_n_s_version;
static PyObject *__pyx_n_s_window_size;
static PyObject *__pyx_n_s_write;
static PyObject *__pyx_n_s_zeros;
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack___init__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_fw, char *__pyx_v_anno, long __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_2destroy(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4add_loc(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome, int32_t __pyx_v_fiveendpos, int __pyx_v_strand); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_6finalize(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_8set_rlengths(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_rlengths); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10get_rlengths(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_12get_locations_by_chr(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_14get_chr_names(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_16sort(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_18separate_dups(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_maxint); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_20addback_dups(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_22filter_dup(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_maxnum); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_24filter_dup_dryrun(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, int32_t __pyx_v_maxnum); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_26sample_percent(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, float __pyx_v_percent, int __pyx_v_seed); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_28sample_num(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, uint64_t __pyx_v_samplesize, int __pyx_v_seed); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_30print_to_bed(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_fhd); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_32extract_region_tags(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chromosome, int32_t __pyx_v_startpos, int32_t __pyx_v_endpos); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_34compute_region_tags_from_peaks(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_peaks, PyObject *__pyx_v_func, int __pyx_v_window_size, float __pyx_v_cutoff); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_36refine_peak_from_tags_distribution(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_peaks, int __pyx_v_window_size, float __pyx_v_cutoff); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_38pileup_a_chromosome(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_ds, PyObject *__pyx_v_scale_factor_s, float __pyx_v_baseline_value, int __pyx_v_directional, int __pyx_v_end_shift); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_11buffer_size___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_11buffer_size_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_5total___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_5total_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_9dup_total___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_9dup_total_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_10annotation_4__del__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4dups___get__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_13FixWidthTrack_7FWTrack_4dups_2__set__(struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
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static PyObject *__pyx_int_1;
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+ * self.__locations[chromosome][0].resize( 0, refcheck=False )
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__Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
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- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = NULL;
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__Pyx_INCREF(__pyx_v_chromosome);
- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_chromosome);
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if (__pyx_t_6) {
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
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__Pyx_INCREF(__pyx_v_chromosome);
- PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_v_chromosome);
__Pyx_GIVEREF(__pyx_v_chromosome);
- PyTuple_SET_ITEM(__pyx_t_8, 1+__pyx_t_7, __pyx_t_3);
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@@ -2928,11 +2982,11 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_add_loc(struct __py
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goto __pyx_L3;
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PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero");
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@@ -3056,9 +3112,15 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_add_loc(struct __py
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@@ -6198,9 +6330,9 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
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+ __pyx_t_26 = 0;
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* p = minus[ i_old ]
* if p == current_loc:
*/
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- for (__pyx_t_26 = 1; __pyx_t_26 < __pyx_t_25; __pyx_t_26+=1) {
- __pyx_v_i_old = __pyx_t_26;
+ __pyx_t_19 = __pyx_v_size;
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@@ -6250,17 +6382,25 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* current_loc = p
*/
__pyx_v_n = (__pyx_v_n + 1);
+
+ /* "MACS2/IO/FixWidthTrack.pyx":349
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goto __pyx_L14;
}
- /*else*/ {
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* n += 1
* else:
* current_loc = p # <<<<<<<<<<<<<<
* n = 1
* if n > maxint:
*/
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__pyx_v_current_loc = __pyx_v_p;
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* new_minus[ i_new ] = p
*/
__pyx_v_i_dup = (__pyx_v_i_dup + 1);
+
+ /* "MACS2/IO/FixWidthTrack.pyx":354
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+ * n = 1
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goto __pyx_L15;
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__Pyx_GOTREF(__pyx_t_2);
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__Pyx_GIVEREF(__pyx_t_5);
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__Pyx_GOTREF(__pyx_t_2);
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__Pyx_GIVEREF(__pyx_t_5);
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__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
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- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_new_plus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_new_plus));
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_new_plus));
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- PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_new_minus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_new_minus));
+ PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_new_minus));
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_dup_plus));
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_dup_plus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_dup_plus));
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_dup_plus));
__Pyx_INCREF(((PyObject *)__pyx_v_dup_minus));
- PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_dup_minus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_dup_minus));
+ PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_dup_minus));
if (unlikely(__pyx_v_self->__pyx___dup_locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6831,9 +6979,15 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_addback_dups(struct
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__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L3;
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+ /* "MACS2/IO/FixWidthTrack.pyx":397
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+ *
+ * if not self.__sorted: # <<<<<<<<<<<<<<
+ * self.sort()
+ *
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}
- __pyx_L3:;
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_plus));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_plus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_plus));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_plus));
__Pyx_INCREF(((PyObject *)__pyx_v_dup_plus));
- PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_dup_plus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_dup_plus));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_dup_plus));
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if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_3))) {
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@@ -7105,9 +7259,9 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_addback_dups(struct
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__pyx_t_14 = PyTuple_New(1+1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
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- PyTuple_SET_ITEM(__pyx_t_14, 0+1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_4); __pyx_t_4 = NULL;
__Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_14, 0+1, __pyx_t_2);
__pyx_t_2 = 0;
__pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_14, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7151,11 +7305,11 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_addback_dups(struct
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__Pyx_GOTREF(__pyx_t_3);
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- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_minus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_minus));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_minus));
__Pyx_INCREF(((PyObject *)__pyx_v_dup_minus));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_v_dup_minus));
__Pyx_GIVEREF(((PyObject *)__pyx_v_dup_minus));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_v_dup_minus));
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_14))) {
__pyx_t_2 = PyMethod_GET_SELF(__pyx_t_14);
@@ -7173,9 +7327,9 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_addback_dups(struct
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__pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
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- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __pyx_t_2 = NULL;
__Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_3);
__pyx_t_3 = 0;
__pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_14, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7217,8 +7371,8 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_addback_dups(struct
__Pyx_GOTREF(__pyx_t_14);
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__Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
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__Pyx_GOTREF(__pyx_t_3);
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__Pyx_GIVEREF(__pyx_t_14);
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__pyx_t_14 = PyDict_New(); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_14);
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__pyx_t_14 = PyDict_New(); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_4);
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__Pyx_GIVEREF(__pyx_t_14);
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Py_ssize_t __pyx_t_16;
- unsigned long __pyx_t_17;
- unsigned long __pyx_t_18;
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int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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__Pyx_GIVEREF(__pyx_t_3);
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+ * self.sort()
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Py_ssize_t __pyx_t_16;
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*/
goto __pyx_L9_continue;
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*/
goto __pyx_L10_break;
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- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL;
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float __pyx_v_cutoff = ((float)5.0);
int32_t __pyx_v_m;
int32_t __pyx_v_i;
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int32_t __pyx_t_18;
int32_t __pyx_t_19;
npy_intp __pyx_t_20;
- int32_t __pyx_t_21;
+ Py_ssize_t __pyx_t_21;
int __pyx_t_22;
- int32_t __pyx_t_23;
- long __pyx_t_24;
- int32_t __pyx_t_25;
- long __pyx_t_26;
- int32_t __pyx_t_27;
+ Py_ssize_t __pyx_t_23;
+ Py_ssize_t __pyx_t_24;
+ Py_ssize_t __pyx_t_25;
+ Py_ssize_t __pyx_t_26;
+ Py_ssize_t __pyx_t_27;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
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- PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_v_peaks);
__Pyx_GIVEREF(__pyx_v_peaks);
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__Pyx_GIVEREF(__pyx_v_func);
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- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
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goto __pyx_L10_continue;
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*/
goto __pyx_L11_break;
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* break
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@@ -12807,8 +13104,8 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_compute_region_tags
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__Pyx_GIVEREF(__pyx_v_temp);
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@@ -13020,18 +13333,18 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_compute_region_tags
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float __pyx_v_cutoff = ((float)5.0);
int32_t __pyx_v_m;
int32_t __pyx_v_i;
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int32_t __pyx_t_20;
npy_intp __pyx_t_21;
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- int32_t __pyx_t_23;
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Py_ssize_t __pyx_t_25;
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const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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- PyTuple_SET_ITEM(__pyx_t_8, 2+__pyx_t_7, __pyx_t_4);
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if (!(likely(PyString_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(__pyx_v_chrom);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2);
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__Pyx_INCREF(__pyx_v_chrom);
- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
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*/
goto __pyx_L11_break;
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__pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(__pyx_v_temp);
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*/
goto __pyx_L14_break;
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*
*/
goto __pyx_L22_break;
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__pyx_L22_break:;
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goto __pyx_L25_break;
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__pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
__pyx_r = 0;
goto __pyx_L0;
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}
- /*else*/ {
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* info.format[0] = c'^' # Native data types, manual alignment
* offset = 0
*/
- __pyx_v_info->format = ((char *)malloc(255));
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/* "numpy.pxd":281
* else:
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+ __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* stdlib.free(info.strides)
*/
free(__pyx_v_info->format);
- goto __pyx_L3;
+
+ /* "numpy.pxd":289
+ *
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}
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/* "numpy.pxd":291
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*
*/
free(__pyx_v_info->strides);
- goto __pyx_L4;
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+ /* "numpy.pxd":291
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+ __Pyx_GOTREF(__pyx_t_3);
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__Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3);
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "numpy.pxd":798
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__pyx_t_6 = __pyx_t_7;
__pyx_L7_bool_binop_done:;
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+ /* "numpy.pxd":801
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@@ -18479,6 +18979,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "numpy.pxd":801
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -18607,7 +19123,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -18625,14 +19141,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 104;
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goto __pyx_L15;
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- __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -18661,14 +19177,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 105;
+ (__pyx_v_f[0]) = 0x69;
goto __pyx_L15;
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@@ -18679,7 +19195,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -18697,14 +19213,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 108;
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goto __pyx_L15;
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -18733,14 +19249,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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- (__pyx_v_f[0]) = 100;
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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goto __pyx_L15;
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
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__pyx_v_f = (__pyx_v_f + 1);
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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__Pyx_GOTREF(__pyx_t_3);
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__Pyx_GIVEREF(__pyx_t_5);
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__pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_f = (__pyx_v_f + 1);
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*/
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__pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
__pyx_v_baseptr = NULL;
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+ /* "numpy.pxd":967
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goto __pyx_L3;
}
- /*else*/ {
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* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
*/
+ /*else*/ {
Py_INCREF(__pyx_v_base);
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__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
+
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__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_v_arr->base));
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#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
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static int
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if (all == NULL) {
if (!PyErr_ExceptionMatches(PyExc_AttributeError))
- return -1; /* Unexpected error */
+ return -1;
PyErr_Clear();
dict = PyObject_GetAttrString(v, "__dict__");
if (dict == NULL) {
@@ -19640,6 +20298,7 @@ bad:
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#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
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@@ -20019,6 +20678,7 @@ static int __Pyx_InitCachedConstants(void) {
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static int __Pyx_InitGlobals(void) {
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if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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#endif
+ #ifdef __Pyx_Coroutine_USED
+ if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
#ifdef __Pyx_Generator_USED
if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
+ #ifdef __Pyx_StopAsyncIteration_USED
+ if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
#if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
@@ -20087,12 +20753,12 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
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/*--- Initialize various global constants etc. ---*/
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+ if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
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+ if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
- if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
__pyx_v_5MACS2_2IO_13FixWidthTrack_INT_MAX = Py_None; Py_INCREF(Py_None);
/*--- Variable export code ---*/
@@ -20165,6 +20831,9 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
+ #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
+ if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/* "MACS2/IO/FixWidthTrack.pyx":20
* # python modules
@@ -20200,8 +20869,8 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s_copy);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_copy);
__Pyx_GIVEREF(__pyx_n_s_copy);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_copy);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_copy, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -20221,8 +20890,8 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s_Counter);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_Counter);
__Pyx_GIVEREF(__pyx_n_s_Counter);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_Counter);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -20242,8 +20911,8 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s__24);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s__24);
__Pyx_GIVEREF(__pyx_n_s__24);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s__24);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_MACS2_Constants, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -20260,8 +20929,8 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s__24);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s__24);
__Pyx_GIVEREF(__pyx_n_s__24);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s__24);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_MACS2_Signal, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -20278,8 +20947,8 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s_PeakIO);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PeakIO);
__Pyx_GIVEREF(__pyx_n_s_PeakIO);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PeakIO);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_MACS2_IO_PeakIO, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -20299,11 +20968,11 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s_se_all_in_one_pileup);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_se_all_in_one_pileup);
__Pyx_GIVEREF(__pyx_n_s_se_all_in_one_pileup);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_se_all_in_one_pileup);
__Pyx_INCREF(__pyx_n_s_max_over_two_pv_array);
- PyList_SET_ITEM(__pyx_t_2, 1, __pyx_n_s_max_over_two_pv_array);
__Pyx_GIVEREF(__pyx_n_s_max_over_two_pv_array);
+ PyList_SET_ITEM(__pyx_t_2, 1, __pyx_n_s_max_over_two_pv_array);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_MACS2_Pileup, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -20363,7 +21032,7 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
*
* # ------------------------------------
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(((int)(((unsigned int)-1) >> 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(((int)(((unsigned int)-1L) >> 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XGOTREF(__pyx_v_5MACS2_2IO_13FixWidthTrack_INT_MAX);
__Pyx_DECREF_SET(__pyx_v_5MACS2_2IO_13FixWidthTrack_INT_MAX, __pyx_t_1);
@@ -20643,8 +21312,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject* args = PyTuple_Pack(1, arg);
- return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
+ 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
@@ -20671,7 +21344,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -20685,7 +21359,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -20698,8 +21373,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
return PySequence_GetItem(o, i);
#endif
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
+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);
@@ -20765,8 +21441,8 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb
Py_DECREF(j);
return r;
}
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck) {
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, 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) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
@@ -20824,6 +21500,107 @@ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
return 0;
}
+#if CYTHON_USE_PYLONG_INTERNALS
+ #include "longintrepr.h"
+#endif
+
+#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
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
@@ -21017,10 +21794,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (value && PyExceptionInstance_Check(value)) {
instance_class = (PyObject*) Py_TYPE(value);
if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
+ 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;
}
}
}
@@ -21080,7 +21860,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (tb) {
#if CYTHON_COMPILING_IN_PYPY
PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(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);
@@ -21675,49 +22455,60 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
__Pyx_ReleaseBuffer(info);
}
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
- PyObject *method, *result = NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
+static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) {
+ PyObject *method;
+ method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name);
+ if (unlikely(!method))
+ return -1;
+ target->method = method;
#if CYTHON_COMPILING_IN_CPYTHON
- if (likely(PyMethod_Check(method))) {
- PyObject *self = PyMethod_GET_SELF(method);
- if (likely(self)) {
- PyObject *args;
- PyObject *function = PyMethod_GET_FUNCTION(method);
- args = PyTuple_New(2);
- if (unlikely(!args)) goto bad;
- Py_INCREF(self);
- PyTuple_SET_ITEM(args, 0, self);
- Py_INCREF(arg);
- PyTuple_SET_ITEM(args, 1, arg);
- Py_INCREF(function);
- Py_DECREF(method); method = NULL;
- result = __Pyx_PyObject_Call(function, args, NULL);
- Py_DECREF(args);
- Py_DECREF(function);
- return result;
- }
+ #if PY_MAJOR_VERSION >= 3
+ if (likely(PyObject_TypeCheck(method, &PyMethodDescr_Type)))
+ #endif
+ {
+ PyMethodDescrObject *descr = (PyMethodDescrObject*) method;
+ target->func = descr->d_method->ml_meth;
+ target->flag = descr->d_method->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_O | METH_NOARGS);
}
#endif
- result = __Pyx_PyObject_CallOneArg(method, arg);
+ return 0;
+}
+
+static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) {
+ PyObject *args, *result = NULL;
+ if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL;
+#if CYTHON_COMPILING_IN_CPYTHON
+ args = PyTuple_New(1);
+ if (unlikely(!args)) goto bad;
+ Py_INCREF(self);
+ PyTuple_SET_ITEM(args, 0, self);
+#else
+ args = PyTuple_Pack(1, self);
+ if (unlikely(!args)) goto bad;
+#endif
+ result = __Pyx_PyObject_Call(cfunc->method, args, NULL);
+ Py_DECREF(args);
bad:
- Py_XDECREF(method);
return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) {
if (PY_MAJOR_VERSION >= 3)
- return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d);
+ return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_keys, d);
else
return PyDict_Keys(d);
}
static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
- int full_traceback) {
+ int full_traceback, CYTHON_UNUSED int nogil) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
+#ifdef WITH_THREAD
+ PyGILState_STATE state;
+ if (nogil)
+ state = PyGILState_Ensure();
+#endif
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
if (full_traceback) {
Py_XINCREF(old_exc);
@@ -21738,6 +22529,10 @@ static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
PyErr_WriteUnraisable(ctx);
Py_DECREF(ctx);
}
+#ifdef WITH_THREAD
+ if (nogil)
+ PyGILState_Release(state);
+#endif
}
static void __Pyx_RaiseBufferFallbackError(void) {
@@ -21834,6 +22629,79 @@ bad:
return -1;
}
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ {
+ #if PY_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;
+}
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
@@ -21853,7 +22721,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co
return count;
}
while (start < end) {
- mid = (start + end) / 2;
+ mid = start + (end - start) / 2;
if (code_line < entries[mid].code_line) {
end = mid;
} else if (code_line > entries[mid].code_line) {
@@ -22027,95 +22895,22 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) {
#endif
- 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;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
+ const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(int) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(int) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(int) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22126,29 +22921,29 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
}
}
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
+#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;\
+ }
static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) {
- const int32_t neg_one = (int32_t) -1, const_zero = 0;
+ const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
@@ -22165,36 +22960,125 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int32_t, digit, ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (int32_t) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(int32_t, digit, digits[0])
+ case 2:
+ if (8 * sizeof(int32_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) >= 2 * PyLong_SHIFT) {
+ return (int32_t) (((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(int32_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) >= 3 * PyLong_SHIFT) {
+ return (int32_t) (((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(int32_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, 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(int32_t) >= 4 * PyLong_SHIFT) {
+ return (int32_t) (((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
+ }
+ }
+ break;
}
- #endif
#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 (int32_t) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
if (sizeof(int32_t) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int32_t) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
}
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int32_t, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int32_t, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (int32_t) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(int32_t, sdigit, -(sdigit) digits[0])
+ case 1: __PYX_VERIFY_RETURN_INT(int32_t, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(int32_t) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT) {
+ return (int32_t) (((int32_t)-1)*(((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(int32_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT) {
+ return (int32_t) ((((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT) {
+ return (int32_t) (((int32_t)-1)*(((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(int32_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT) {
+ return (int32_t) ((((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, 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(int32_t) - 1 > 4 * PyLong_SHIFT) {
+ return (int32_t) (((int32_t)-1)*(((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(int32_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(int32_t, 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(int32_t) - 1 > 4 * PyLong_SHIFT) {
+ return (int32_t) ((((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
+ }
+ }
+ break;
}
- #endif
#endif
if (sizeof(int32_t) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, long, PyLong_AsLong(x))
- } else if (sizeof(int32_t) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, long long, PyLong_AsLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(int32_t, long, PyLong_AsLong(x))
+ } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(int32_t, PY_LONG_LONG, PyLong_AsLongLong(x))
}
}
{
@@ -22243,7 +23127,7 @@ raise_neg_overflow:
}
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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))) {
@@ -22260,36 +23144,125 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (long) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(long, 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
#endif
if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -22338,7 +23311,7 @@ raise_neg_overflow:
}
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
+ 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))) {
@@ -22355,36 +23328,125 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (int) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(int, 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
#endif
if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -22433,7 +23495,7 @@ raise_neg_overflow:
}
static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
- const uint64_t neg_one = (uint64_t) -1, const_zero = 0;
+ const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
@@ -22450,36 +23512,125 @@ static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (uint64_t) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, digits[0])
+ case 2:
+ if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) >= 2 * PyLong_SHIFT) {
+ return (uint64_t) (((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) >= 3 * PyLong_SHIFT) {
+ return (uint64_t) (((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, 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(uint64_t) >= 4 * PyLong_SHIFT) {
+ return (uint64_t) (((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]));
+ }
+ }
+ break;
}
- #endif
#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 (uint64_t) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
if (sizeof(uint64_t) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(uint64_t) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
}
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(uint64_t, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (uint64_t) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(uint64_t, sdigit, -(sdigit) digits[0])
+ case 1: __PYX_VERIFY_RETURN_INT(uint64_t, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(uint64_t) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
+ return (uint64_t) (((uint64_t)-1)*(((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(uint64_t) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
+ return (uint64_t) ((((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
+ return (uint64_t) (((uint64_t)-1)*(((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(uint64_t) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
+ return (uint64_t) ((((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, 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(uint64_t) - 1 > 4 * PyLong_SHIFT) {
+ return (uint64_t) (((uint64_t)-1)*(((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(uint64_t) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(uint64_t, 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(uint64_t) - 1 > 4 * PyLong_SHIFT) {
+ return (uint64_t) ((((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])));
+ }
+ }
+ break;
}
- #endif
#endif
if (sizeof(uint64_t) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(uint64_t, long, PyLong_AsLong(x))
- } else if (sizeof(uint64_t) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(uint64_t, long long, PyLong_AsLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x))
+ } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
}
}
{
@@ -22528,21 +23679,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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 long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long 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(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22554,21 +23705,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) {
- const int32_t neg_one = (int32_t) -1, const_zero = 0;
+ const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(int32_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(int32_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int32_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(int32_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(int32_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22685,21 +23836,21 @@ bad:
#endif
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long value) {
- const unsigned long neg_one = (unsigned long) -1, const_zero = 0;
+ const unsigned long neg_one = (unsigned long) -1, const_zero = (unsigned long) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(unsigned long) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(unsigned long) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(unsigned long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(unsigned long) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(unsigned long) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(unsigned long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(unsigned long) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22711,7 +23862,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long valu
}
static CYTHON_INLINE unsigned long __Pyx_PyInt_As_unsigned_long(PyObject *x) {
- const unsigned long neg_one = (unsigned long) -1, const_zero = 0;
+ const unsigned long neg_one = (unsigned long) -1, const_zero = (unsigned long) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_Check(x))) {
@@ -22728,36 +23879,125 @@ static CYTHON_INLINE unsigned long __Pyx_PyInt_As_unsigned_long(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (unsigned long) 0;
+ case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, digits[0])
+ case 2:
+ if (8 * sizeof(unsigned long) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) >= 2 * PyLong_SHIFT) {
+ return (unsigned long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) >= 3 * PyLong_SHIFT) {
+ return (unsigned long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) >= 4 * PyLong_SHIFT) {
+ return (unsigned long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
+ }
+ }
+ break;
}
- #endif
#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 (unsigned long) -1;
+ if (unlikely(result == 1))
+ goto raise_neg_overflow;
+ }
+#endif
if (sizeof(unsigned long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(unsigned long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(unsigned long, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(unsigned long) <= sizeof(unsigned PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(unsigned long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
}
} else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(unsigned long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (unsigned long) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(unsigned long, sdigit, -(sdigit) digits[0])
+ case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, +digits[0])
+ case -2:
+ if (8 * sizeof(unsigned long) - 1 > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) {
+ return (unsigned long) (((unsigned long)-1)*(((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
+ case 2:
+ if (8 * sizeof(unsigned long) > 1 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) {
+ return (unsigned long) ((((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
+ case -3:
+ if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) {
+ return (unsigned long) (((unsigned long)-1)*(((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
+ case 3:
+ if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
+ } else if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) {
+ return (unsigned long) ((((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
+ case -4:
+ if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) - 1 > 4 * PyLong_SHIFT) {
+ return (unsigned long) (((unsigned long)-1)*(((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
+ case 4:
+ if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) {
+ if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) {
+ __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) - 1 > 4 * PyLong_SHIFT) {
+ return (unsigned long) ((((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])));
+ }
+ }
+ break;
}
- #endif
#endif
if (sizeof(unsigned long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(unsigned long, long, PyLong_AsLong(x))
- } else if (sizeof(unsigned long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(unsigned long, long long, PyLong_AsLongLong(x))
+ __PYX_VERIFY_RETURN_INT_EXC(unsigned long, long, PyLong_AsLong(x))
+ } else if (sizeof(unsigned long) <= sizeof(PY_LONG_LONG)) {
+ __PYX_VERIFY_RETURN_INT_EXC(unsigned long, PY_LONG_LONG, PyLong_AsLongLong(x))
}
}
{
@@ -22806,21 +24046,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) {
- const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = 0;
+ const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(Py_intptr_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(Py_intptr_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(Py_intptr_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22832,21 +24072,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) {
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
- const uint64_t neg_one = (uint64_t) -1, const_zero = 0;
+ const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(uint64_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(uint64_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(uint64_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(uint64_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(uint64_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -22858,21 +24098,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int32(npy_int32 value) {
- const npy_int32 neg_one = (npy_int32) -1, const_zero = 0;
+ const npy_int32 neg_one = (npy_int32) -1, const_zero = (npy_int32) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(npy_int32) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(npy_int32) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(npy_int32) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(npy_int32) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(npy_int32) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(npy_int32) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(npy_int32) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -23124,21 +24364,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int32(npy_int32 value) {
#endif
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
- const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = 0;
+ const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = (ptrdiff_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(ptrdiff_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(ptrdiff_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(ptrdiff_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -23149,9 +24389,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
}
}
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
+ const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(enum NPY_TYPES) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+ }
+ } else {
+ if (sizeof(enum NPY_TYPES) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= 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(enum NPY_TYPES),
+ little, !is_unsigned);
+ }
+}
+
static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
- while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
- return *s1 == *s2;
+ while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
+ return *s1 == *s2;
}
static int __Pyx_check_binary_version(void) {
@@ -23288,7 +24554,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+#if 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 &&
@@ -23329,7 +24595,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_
#endif
} else
#endif
-#if !CYTHON_COMPILING_IN_PYPY
+#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);
@@ -23359,7 +24625,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
#else
if (PyLong_Check(x))
#endif
- return Py_INCREF(x), x;
+ return __Pyx_NewRef(x);
m = Py_TYPE(x)->tp_as_number;
#if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
@@ -23399,18 +24665,55 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject *x;
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
+ 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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
+ #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);
}
diff --git a/MACS2/IO/FixWidthTrack.pyx b/MACS2/IO/FixWidthTrack.pyx
index a294a09..142e7de 100644
--- a/MACS2/IO/FixWidthTrack.pyx
+++ b/MACS2/IO/FixWidthTrack.pyx
@@ -954,7 +954,7 @@ cdef class FWTrack:
values. Final pileup will the maximum.
scale_factor_s : linearly scale the pileup value applied to each d in ds. The list should have the same length as ds.
baseline_value : a value to be filled for missing values, and will be the minimum pileup.
- directional : if False, the strand or direction of tag will be ignored, so that extenstion will be both sides with d/2.
+ directional : if False, the strand or direction of tag will be ignored, so that extension will be both sides with d/2.
end_shift : move cutting ends towards 5->3 direction if value is positive, or towards 3->5 direction if negative. Default is 0 -- no shift at all.
diff --git a/MACS2/IO/Parser.c b/MACS2/IO/Parser.c
index 4bd0b03..d239896 100644
--- a/MACS2/IO/Parser.c
+++ b/MACS2/IO/Parser.c
@@ -1,25 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.23.4 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
#error Cython requires Python 2.6+ or Python 3.2+.
#else
-#define CYTHON_ABI "0_22"
+#define CYTHON_ABI "0_23_4"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -54,6 +42,9 @@
#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_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
#define Py_OptimizeFlag 0
#endif
@@ -61,26 +52,30 @@
#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) \
+ #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) \
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#define __Pyx_DefaultClassType PyType_Type
#endif
-#if PY_MAJOR_VERSION >= 3
+#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
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
+#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)) ? \
+ #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)
@@ -99,12 +94,13 @@
#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)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
#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)) ? \
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
+ #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
#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))
@@ -169,16 +165,18 @@
#else
#define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
+#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__)
@@ -191,35 +189,33 @@
#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() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
float value;
memset(&value, 0xFF, sizeof(value));
return value;
}
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
-#endif
#if PY_MAJOR_VERSION >= 3
@@ -238,10 +234,6 @@ class __Pyx_FakeReference {
#endif
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
#define __PYX_HAVE__MACS2__IO__Parser
#define __PYX_HAVE_API__MACS2__IO__Parser
#include "string.h"
@@ -271,6 +263,13 @@ class __Pyx_FakeReference {
# 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; char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
@@ -279,16 +278,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
+#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))
@@ -323,8 +340,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+#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_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
@@ -731,7 +749,7 @@ struct __pyx_opt_args_5MACS2_2IO_6Parser_guess_parser {
long buffer_size;
};
-/* "MACS2/IO/Parser.pyx":1168
+/* "MACS2/IO/Parser.pyx":1171
* return ret
*
* cdef struct _BAMPEParsed: # <<<<<<<<<<<<<<
@@ -836,7 +854,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_SAMParser {
};
-/* "MACS2/IO/Parser.pyx":735
+/* "MACS2/IO/Parser.pyx":736
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -848,7 +866,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser {
};
-/* "MACS2/IO/Parser.pyx":994
+/* "MACS2/IO/Parser.pyx":996
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMPEParser(BAMParser): # <<<<<<<<<<<<<<
@@ -862,7 +880,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser {
};
-/* "MACS2/IO/Parser.pyx":1175
+/* "MACS2/IO/Parser.pyx":1178
* ### End ###
*
* cdef class BowtieParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -982,7 +1000,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_SAMParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_SAMParser *__pyx_vtabptr_5MACS2_2IO_6Parser_SAMParser;
-/* "MACS2/IO/Parser.pyx":735
+/* "MACS2/IO/Parser.pyx":736
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -998,7 +1016,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser;
-/* "MACS2/IO/Parser.pyx":994
+/* "MACS2/IO/Parser.pyx":996
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMPEParser(BAMParser): # <<<<<<<<<<<<<<
@@ -1015,7 +1033,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMPEParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMPEParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser;
-/* "MACS2/IO/Parser.pyx":1175
+/* "MACS2/IO/Parser.pyx":1178
* ### End ###
*
* cdef class BowtieParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -1045,19 +1063,19 @@ static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BowtieParser *__pyx_vtabptr_5M
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__); \
+ #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) \
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)\
__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
#endif
- #define __Pyx_RefNannyFinishContext() \
+ #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__)
@@ -1080,13 +1098,13 @@ static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BowtieParser *__pyx_vtabptr_5M
#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); \
+#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); \
+#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)
@@ -1143,8 +1161,8 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
const char* function_name);
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
@@ -1181,17 +1199,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
#endif
-static CYTHON_INLINE int __Pyx_div_int(int, int); /* proto */
-
-#ifndef __PYX_FORCE_INIT_THREADS
- #define __PYX_FORCE_INIT_THREADS 0
-#endif
+static CYTHON_INLINE int __Pyx_div_int(int, int);
-#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x)))
+#define UNARY_NEG_WOULD_OVERFLOW(x)\
+ (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x)))
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename,
- int full_traceback);
+ int full_traceback, int nogil);
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
@@ -1201,20 +1216,34 @@ static CYTHON_INLINE int __Pyx_IterFinish(void);
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
-#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) : \
+#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
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
+#else
+#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\
+ PyObject_RichCompare(op1, op2, Py_EQ)
+ #endif
+
+#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
__Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
+#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) : \
+#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);
@@ -1222,13 +1251,20 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
int is_list, int wraparound, int boundscheck);
-static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */
+static CYTHON_INLINE long __Pyx_mod_long(long, long);
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
int has_cstart, int has_cstop, int wraparound);
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
+#else
+#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\
+ (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2))
+#endif
+
#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))
@@ -1282,6 +1318,8 @@ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases);
@@ -1293,13 +1331,13 @@ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
#define __Pyx_CYFUNCTION_CCLASS 0x04
-#define __Pyx_CyFunction_GetClosure(f) \
+#define __Pyx_CyFunction_GetClosure(f)\
(((__pyx_CyFunctionObject *) (f))->func_closure)
-#define __Pyx_CyFunction_GetClassObj(f) \
+#define __Pyx_CyFunction_GetClassObj(f)\
(((__pyx_CyFunctionObject *) (f))->func_classobj)
-#define __Pyx_CyFunction_Defaults(type, f) \
+#define __Pyx_CyFunction_Defaults(type, f)\
((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\
((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
typedef struct {
PyCFunctionObject func;
@@ -1323,7 +1361,7 @@ typedef struct {
PyObject *func_annotations;
} __pyx_CyFunctionObject;
static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code) \
+#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\
__Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code)
static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
int flags, PyObject* qualname,
@@ -1339,7 +1377,7 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
PyObject *dict);
static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
PyObject *dict);
-static int __Pyx_CyFunction_init(void);
+static int __pyx_CyFunction_init(void);
static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname,
PyObject *mkw, PyObject *modname, PyObject *doc);
@@ -1363,8 +1401,6 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
static void __Pyx_AddTraceback(const char *funcname, int c_line,
int py_line, const char *filename);
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
-
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
@@ -1477,7 +1513,9 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value);
-static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value);
+
+static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *);
static int __Pyx_check_binary_version(void);
@@ -1529,6 +1567,17 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___fw_parse_line(CYTHO
/* Module declarations from 'cpython.version' */
+/* Module declarations from '__builtin__' */
+
+/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
+
+/* Module declarations from 'libc.string' */
+
+/* Module declarations from 'libc.stdio' */
+
+/* Module declarations from 'cpython.object' */
+
/* Module declarations from 'cpython.ref' */
/* Module declarations from 'cpython.exc' */
@@ -1541,23 +1590,12 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___fw_parse_line(CYTHO
/* Module declarations from 'cpython.list' */
-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from 'cpython.object' */
-
/* Module declarations from 'cpython.sequence' */
/* Module declarations from 'cpython.mapping' */
/* Module declarations from 'cpython.iterator' */
-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
-
/* Module declarations from 'cpython.number' */
/* Module declarations from 'cpython.int' */
@@ -1647,45 +1685,6 @@ static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_guess_parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fhd, long __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_17StrandFormatError___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_string, PyObject *__pyx_v_strand); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_17StrandFormatError_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_13GenericParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_2tsize(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_4build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_6append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_8sniff(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_10close(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_2append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_petrack); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_9BAMParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_2sniff(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_4tsize(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_6get_references(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_8build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_10append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_2append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_petrack); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_GenericParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDResultParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDMultiParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDExportParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_SAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BowtieParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_B[] = "<B";
static char __pyx_k_F[] = "F";
static char __pyx_k_H[] = "H";
@@ -1950,6 +1949,45 @@ static PyObject *__pyx_n_s_tsize;
static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
static PyObject *__pyx_n_s_unpack;
static PyObject *__pyx_n_s_version;
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_guess_parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fhd, long __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_17StrandFormatError___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_string, PyObject *__pyx_v_strand); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_17StrandFormatError_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_13GenericParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_2tsize(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_4build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_6append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_8sniff(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_10close(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_2append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_petrack); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_9BAMParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_2sniff(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_4tsize(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_6get_references(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_8build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_10append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_2append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_petrack); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_GenericParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDResultParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDMultiParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDExportParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_SAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BowtieParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_3;
@@ -2065,7 +2103,7 @@ static PyObject *__pyx_codeobj__98;
static PyObject *__pyx_pw_5MACS2_2IO_6Parser_1guess_parser(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_6Parser_guess_parser *__pyx_optional_args) {
- long __pyx_v_buffer_size = ((long)100000);
+ long __pyx_v_buffer_size = ((long)0x186A0);
PyObject *__pyx_v_order_list = NULL;
PyObject *__pyx_v_f = NULL;
struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_p = NULL;
@@ -2114,6 +2152,7 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
__pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
__pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
#endif
__Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_3);
__pyx_t_3 = 0;
@@ -2138,20 +2177,28 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_fhd);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fhd);
__Pyx_GIVEREF(__pyx_v_fhd);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fhd);
__pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_buffer_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_buffer_size, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5MACS2_2IO_6Parser_BEDParser)), __pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5MACS2_2IO_6Parser_BEDParser), __pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF_SET(__pyx_v_p, ((struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *)__pyx_t_6));
__pyx_t_6 = 0;
+
+ /* "MACS2/IO/Parser.pyx":70
+ *
+ * for f in order_list:
+ * if f == 'BED': # <<<<<<<<<<<<<<
+ * p = BEDParser( fhd, buffer_size = buffer_size )
+ * elif f == "ELAND":
+ */
goto __pyx_L5;
}
@@ -2175,20 +2222,28 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
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__Pyx_XDECREF_SET(__pyx_v_p, ((struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *)__pyx_t_3));
__pyx_t_3 = 0;
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__Pyx_GIVEREF(__pyx_v_fhd);
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__Pyx_XDECREF_SET(__pyx_v_p, ((struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *)__pyx_t_6));
__pyx_t_6 = 0;
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__Pyx_XDECREF_SET(__pyx_v_p, ((struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *)__pyx_t_3));
__pyx_t_3 = 0;
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__Pyx_GIVEREF(__pyx_v_fhd);
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__Pyx_XDECREF_SET(__pyx_v_p, ((struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *)__pyx_t_6));
__pyx_t_6 = 0;
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goto __pyx_L4_argument_unpacking_done;
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__Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
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__Pyx_GIVEREF(__pyx_t_2);
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- __pyx_v_buffer_size = ((long)100000);
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goto __pyx_L4_argument_unpacking_done;
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- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "MACS2/IO/Parser.pyx":142
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}
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
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}
goto __pyx_L5_except_error;
__pyx_L5_except_error:;
+
+ /* "MACS2/IO/Parser.pyx":142
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+ * f = gzip.open( filename )
+ * try: # <<<<<<<<<<<<<<
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__pyx_t_1 = PyTuple_New(1+1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
__pyx_r = __pyx_v_self->tag_size;
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goto __pyx_L6_bool_binop_done;
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goto __pyx_L3_continue;
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@@ -4489,7 +4650,7 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_13GenericParser_append_fwtrack(struc
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*/
{
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+ if (__pyx_t_5||__pyx_t_6||__pyx_t_7); else {/*mark used*/}
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__pyx_v_t = ((struct __pyx_vtabstruct_5MACS2_2IO_6Parser_GenericParser *)__pyx_v_self->__pyx_vtab)->tsize(__pyx_v_self, 0);
+
+ /* "MACS2/IO/Parser.pyx":271
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+ *
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+ * t = self.tsize()
+ * except:
+ */
}
- /*else:*/ {
- /* "MACS2/IO/Parser.pyx":277
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* return False
* else:
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__pyx_t_8 = __pyx_t_9;
goto __pyx_L12_bool_binop_done;
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- __pyx_t_9 = ((__pyx_v_t >= 10000) != 0);
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__pyx_r = Py_False;
goto __pyx_L6_except_return;
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}
- /*else*/ {
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* else:
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*/
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__pyx_L4_bool_binop_done:;
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__pyx_L4_bool_binop_done:;
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
}
+
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+ * # pass
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+ * if not strcmp(thisfields[ 5 ],"+"):
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+ */
}
__pyx_L8_error:;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_15);
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}
goto __pyx_L10_except_error;
__pyx_L10_except_error:;
+
+ /* "MACS2/IO/Parser.pyx":327
+ * # pass
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+ * if not strcmp(thisfields[ 5 ],"+"):
+ * return ( chromname,
+ */
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__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
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__pyx_L4_bool_binop_done:;
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__pyx_r = __pyx_tuple__16;
goto __pyx_L0;
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+ * # skip track/browser/comment lines
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+ * or thisline[ :7 ] == "browser" \
+ * or thisline[ 0 ] == "#":
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/* "MACS2/IO/Parser.pyx":374
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__pyx_t_1 = 0;
goto __pyx_L12_try_return;
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__Pyx_GIVEREF(__pyx_t_2);
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}
goto __pyx_L10_except_error;
__pyx_L10_except_error:;
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+ /* "MACS2/IO/Parser.pyx":375
+ * # still only support tabular as delimiter.
+ * thisfields = thisline.split( '\t' )
+ * try: # <<<<<<<<<<<<<<
+ * return ( thisfields[ 0 ],
+ * atoi( thisfields[ 1 ] ),
+ */
__Pyx_XGIVEREF(__pyx_t_7);
__Pyx_XGIVEREF(__pyx_t_8);
__Pyx_XGIVEREF(__pyx_t_9);
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} else {
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+ __Pyx_GOTREF(__pyx_t_2);
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* assert right_pos > left_pos, "Right position must be larger than left position, check your BED file at line: %s" % thisline
*/
goto __pyx_L3_continue;
- }
+
+ /* "MACS2/IO/Parser.pyx":399
+ * for thisline in self.fhd:
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+ * if left_pos < 0 or not chromosome: # <<<<<<<<<<<<<<
+ * continue
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+ */
+ }
/* "MACS2/IO/Parser.pyx":402
* continue
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* logging.info( " %d" % ( m*1000000 ) )
*/
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@@ -6591,9 +6882,9 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack(struct _
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L10;
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__Pyx_GIVEREF(__pyx_v_chromosome);
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__Pyx_GIVEREF(__pyx_t_8);
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- PyTuple_SET_ITEM(__pyx_t_8, 0+1, __pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_GIVEREF(__pyx_v_petrack);
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@@ -9637,16 +10088,16 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___tlen_parse_line(CYTHON_
goto __pyx_L0;
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@@ -9655,43 +10106,43 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___tlen_parse_line(CYTHON_
goto __pyx_L0;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L6_bool_binop_done;
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goto __pyx_L6_bool_binop_done;
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goto __pyx_L0;
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goto __pyx_L0;
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+ if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* if thisline[ 0 ] == "@": return ( "", -1, -1 ) # header line started with '@' is skipped
* thisfields = thisline.split( '\t' )
* thistagname = thisfields[ 0 ] # name of tag # <<<<<<<<<<<<<<
@@ -9991,15 +10474,15 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line(CYTHON_UN
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_thistagname = ((PyObject*)__pyx_t_2);
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@@ -10008,51 +10491,51 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line(CYTHON_UN
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
if (unlikely(__pyx_v_thisfields == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (unlikely(__pyx_v_thisfields == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* bwflag = atoi( thisfields[ 1 ] )
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@@ -10062,32 +10545,26 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line(CYTHON_UN
__pyx_t_5 = __pyx_t_4;
goto __pyx_L6_bool_binop_done;
}
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+ __pyx_t_4 = ((__pyx_v_bwflag & 0x200) != 0);
if (!__pyx_t_4) {
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__pyx_t_5 = __pyx_t_4;
goto __pyx_L6_bool_binop_done;
}
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if (!__pyx_t_4) {
} else {
__pyx_t_5 = __pyx_t_4;
goto __pyx_L6_bool_binop_done;
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- goto __pyx_L6_bool_binop_done;
- }
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__pyx_t_5 = __pyx_t_4;
__pyx_L6_bool_binop_done:;
if (__pyx_t_5) {
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* CIGAR = thisfields[ 5 ]
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
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__Pyx_INCREF(__pyx_tuple__43);
__pyx_r = __pyx_tuple__43;
goto __pyx_L0;
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- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ /* "MACS2/IO/Parser.pyx":704
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@@ -10108,7 +10593,7 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line(CYTHON_UN
__pyx_t_5 = ((__pyx_v_bwflag & 1) != 0);
if (__pyx_t_5) {
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__Pyx_INCREF(__pyx_tuple__44);
__pyx_r = __pyx_tuple__44;
goto __pyx_L0;
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__pyx_t_5 = ((__pyx_v_bwflag & 8) != 0);
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__Pyx_INCREF(__pyx_tuple__45);
__pyx_r = __pyx_tuple__45;
goto __pyx_L0;
+
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+ */
}
- /* "MACS2/IO/Parser.pyx":711
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*/
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goto __pyx_L7_bool_binop_done;
}
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goto __pyx_L7_bool_binop_done;
}
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__pyx_L7_bool_binop_done:;
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- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
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__Pyx_INCREF(__pyx_tuple__72);
__pyx_r = __pyx_tuple__72;
goto __pyx_L0;
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+ * thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
+ * (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
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+ */
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if (__pyx_t_2) {
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__Pyx_INCREF(__pyx_tuple__73);
__pyx_r = __pyx_tuple__73;
goto __pyx_L0;
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__pyx_r = __pyx_tuple__74;
goto __pyx_L0;
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__pyx_r = __pyx_tuple__75;
goto __pyx_L0;
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__pyx_t_2 = __pyx_t_1;
- goto __pyx_L20_bool_binop_done;
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if (!__pyx_t_1) {
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__pyx_t_2 = __pyx_t_1;
- goto __pyx_L20_bool_binop_done;
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if (!__pyx_t_1) {
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__pyx_t_2 = __pyx_t_1;
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if (!__pyx_t_1) {
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__pyx_t_2 = __pyx_t_1;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = PySequence_GetSlice(__pyx_v_data, 12, 16); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -16088,18 +16789,18 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__pyx_t_7 = 1;
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+ __pyx_t_8 = PyTuple_New(2+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
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- PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_kp_s_HH);
__Pyx_GIVEREF(__pyx_kp_s_HH);
- PyTuple_SET_ITEM(__pyx_t_8, 1+__pyx_t_7, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_kp_s_HH);
__Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_8, 1+__pyx_t_7, __pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_8, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_8, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -16113,7 +16814,7 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (likely(PyTuple_CheckExact(sequence))) {
@@ -16126,15 +16827,15 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__Pyx_INCREF(__pyx_t_4);
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+ __pyx_t_8 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -16142,7 +16843,7 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__Pyx_GOTREF(__pyx_t_4);
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@@ -16150,20 +16851,20 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
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+ __pyx_t_11 = __Pyx_PyInt_As_short(__pyx_t_8); if (unlikely((__pyx_t_11 == (short)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_bwflag = __pyx_t_11;
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+ /* "MACS2/IO/Parser.pyx":1140
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- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048: # <<<<<<<<<<<<<<
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048: # <<<<<<<<<<<<<<
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@@ -16173,41 +16874,43 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__pyx_t_2 = __pyx_t_1;
goto __pyx_L7_bool_binop_done;
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- goto __pyx_L7_bool_binop_done;
- }
- __pyx_t_1 = ((__pyx_v_bwflag & 1024) != 0);
+ __pyx_t_1 = ((__pyx_v_bwflag & 0x200) != 0);
if (!__pyx_t_1) {
} else {
__pyx_t_2 = __pyx_t_1;
goto __pyx_L7_bool_binop_done;
}
- __pyx_t_1 = ((__pyx_v_bwflag & 256) != 0);
+ __pyx_t_1 = ((__pyx_v_bwflag & 0x100) != 0);
if (!__pyx_t_1) {
} else {
__pyx_t_2 = __pyx_t_1;
goto __pyx_L7_bool_binop_done;
}
- __pyx_t_1 = ((__pyx_v_bwflag & 2048) != 0);
+ __pyx_t_1 = ((__pyx_v_bwflag & 0x800) != 0);
__pyx_t_2 = __pyx_t_1;
__pyx_L7_bool_binop_done:;
if (__pyx_t_2) {
- /* "MACS2/IO/Parser.pyx":1138
+ /* "MACS2/IO/Parser.pyx":1141
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
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* #if bwflag & 256 or bwflag & 2048:
* # return ret # secondary or supplementary alignment
*/
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
+
+ /* "MACS2/IO/Parser.pyx":1140
+ *
+ * (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048: # <<<<<<<<<<<<<<
+ * return ret #unmapped sequence or bad sequence or 2nd or sup alignment
+ * #if bwflag & 256 or bwflag & 2048:
+ */
}
- /* "MACS2/IO/Parser.pyx":1141
+ /* "MACS2/IO/Parser.pyx":1144
* #if bwflag & 256 or bwflag & 2048:
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__pyx_t_2 = ((__pyx_v_bwflag & 1) != 0);
if (__pyx_t_2) {
- /* "MACS2/IO/Parser.pyx":1144
+ /* "MACS2/IO/Parser.pyx":1147
* # paired read. We should only keep sequence if the mate is mapped
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@@ -16227,7 +16930,7 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__pyx_t_2 = ((!((__pyx_v_bwflag & 2) != 0)) != 0);
if (__pyx_t_2) {
- /* "MACS2/IO/Parser.pyx":1145
+ /* "MACS2/IO/Parser.pyx":1148
* # and if this is the left mate, all is within the flag!
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@@ -16236,9 +16939,17 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
*/
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
+
+ /* "MACS2/IO/Parser.pyx":1147
+ * # paired read. We should only keep sequence if the mate is mapped
+ * # and if this is the left mate, all is within the flag!
+ * if not bwflag & 2: # <<<<<<<<<<<<<<
+ * return ret # not a proper pair
+ * if bwflag & 8:
+ */
}
- /* "MACS2/IO/Parser.pyx":1146
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__pyx_t_2 = ((__pyx_v_bwflag & 8) != 0);
if (__pyx_t_2) {
- /* "MACS2/IO/Parser.pyx":1147
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*/
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
+
+ /* "MACS2/IO/Parser.pyx":1149
+ * if not bwflag & 2:
+ * return ret # not a proper pair
+ * if bwflag & 8: # <<<<<<<<<<<<<<
+ * return ret # the mate is unmapped
+ * if bwflag & 128:
+ */
}
- /* "MACS2/IO/Parser.pyx":1148
+ /* "MACS2/IO/Parser.pyx":1151
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* return ret
*/
- __pyx_t_2 = ((__pyx_v_bwflag & 128) != 0);
+ __pyx_t_2 = ((__pyx_v_bwflag & 0x80) != 0);
if (__pyx_t_2) {
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*/
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
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}
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+ */
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- __pyx_L12:;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_13 = PyTuple_New(3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
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__Pyx_GIVEREF(__pyx_v_chromname);
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_15);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_v_chromname);
__Pyx_GIVEREF(__pyx_t_15);
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__Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_13, 2, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L8_except_return;
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+ /*else*/ {
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
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- PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_t_16); __Pyx_GIVEREF(__pyx_t_16); __pyx_t_16 = NULL;
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__Pyx_GIVEREF(__pyx_v_thisline);
- PyTuple_SET_ITEM(__pyx_t_17, 1+__pyx_t_9, __pyx_t_11);
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__Pyx_GIVEREF(__pyx_t_11);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
}
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goto __pyx_L7_except_error;
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+ * chromname = thisfields[ 2 ]
+ * try: # <<<<<<<<<<<<<<
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+ * except ValueError:
+ */
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_XGIVEREF(__pyx_t_7);
__Pyx_XGIVEREF(__pyx_t_8);
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__pyx_L12_try_end:;
}
- /* "MACS2/IO/Parser.pyx":1192
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* copy_shape = 0
*/
__pyx_v_copy_shape = 1;
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+ /* "numpy.pxd":208
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+ * else:
+ */
goto __pyx_L4;
}
- /*else*/ {
- /* "numpy.pxd":211
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__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
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+ /* "numpy.pxd":213
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+ */
if (__pyx_t_1) {
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "numpy.pxd":213
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__pyx_t_1 = __pyx_t_2;
__pyx_L9_bool_binop_done:;
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+ */
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "numpy.pxd":217
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*/
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}
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*/
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__pyx_t_1 = __pyx_t_2;
__pyx_L19_bool_binop_done:;
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__Pyx_GOTREF(__pyx_t_3);
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__Pyx_GIVEREF(__pyx_t_6);
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free(__pyx_v_info->format);
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free(__pyx_v_info->strides);
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "numpy.pxd":801
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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- (__pyx_v_f[0]) = 105;
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goto __pyx_L15;
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@@ -18825,7 +19707,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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- (__pyx_v_f[0]) = 108;
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goto __pyx_L15;
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -18879,14 +19761,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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if (__pyx_t_6) {
- (__pyx_v_f[0]) = 103;
+ (__pyx_v_f[0]) = 0x67;
goto __pyx_L15;
}
@@ -18969,7 +19851,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
*/
- __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -18977,7 +19859,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
- (__pyx_v_f[1]) = 102;
+ (__pyx_v_f[1]) = 0x66;
__pyx_v_f = (__pyx_v_f + 1);
goto __pyx_L15;
}
@@ -18989,7 +19871,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -18997,7 +19879,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
- (__pyx_v_f[1]) = 100;
+ (__pyx_v_f[1]) = 0x64;
__pyx_v_f = (__pyx_v_f + 1);
goto __pyx_L15;
}
@@ -19009,7 +19891,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
*/
- __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -19017,7 +19899,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
- (__pyx_v_f[1]) = 103;
+ (__pyx_v_f[1]) = 0x67;
__pyx_v_f = (__pyx_v_f + 1);
goto __pyx_L15;
}
@@ -19029,7 +19911,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
*/
- __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -19039,21 +19921,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
(__pyx_v_f[0]) = 79;
goto __pyx_L15;
}
- /*else*/ {
- /* "numpy.pxd":844
+ /* "numpy.pxd":844
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* f += 1
* else:
*/
+ /*else*/ {
__pyx_t_5 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
__pyx_t_5 = 0;
__pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
@@ -19072,17 +19954,25 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* # Cython ignores struct boundary information ("T{...}"),
*/
__pyx_v_f = (__pyx_v_f + 1);
+
+ /* "numpy.pxd":820
+ * offset[0] += child.itemsize
+ *
+ * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<<
+ * t = child.type_num
+ * if end - f < 5:
+ */
goto __pyx_L13;
}
- /*else*/ {
- /* "numpy.pxd":849
+ /* "numpy.pxd":849
* # Cython ignores struct boundary information ("T{...}"),
* # so don't output it
* f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<<
* return f
*
*/
+ /*else*/ {
__pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_9;
}
@@ -19168,17 +20058,25 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
* Py_INCREF(base) # important to do this before decref below!
*/
__pyx_v_baseptr = NULL;
+
+ /* "numpy.pxd":967
+ * cdef inline void set_array_base(ndarray arr, object base):
+ * cdef PyObject* baseptr
+ * if base is None: # <<<<<<<<<<<<<<
+ * baseptr = NULL
+ * else:
+ */
goto __pyx_L3;
}
- /*else*/ {
- /* "numpy.pxd":970
+ /* "numpy.pxd":970
* baseptr = NULL
* else:
* Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<<
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
*/
+ /*else*/ {
Py_INCREF(__pyx_v_base);
/* "numpy.pxd":971
@@ -19257,14 +20155,22 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
+
+ /* "numpy.pxd":976
+ *
+ * cdef inline object get_array_base(ndarray arr):
+ * if arr.base is NULL: # <<<<<<<<<<<<<<
+ * return None
+ * else:
+ */
}
- /*else*/ {
- /* "numpy.pxd":979
+ /* "numpy.pxd":979
* return None
* else:
* return <object>arr.base # <<<<<<<<<<<<<<
*/
+ /*else*/ {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_v_arr->base));
__pyx_r = ((PyObject *)__pyx_v_arr->base);
@@ -19362,8 +20268,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_GenericParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19429,8 +20336,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BEDParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19540,8 +20448,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BEDPEParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19611,8 +20520,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_ELANDResultParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19682,8 +20592,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19753,8 +20664,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_ELANDExportParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19824,8 +20736,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_SAMParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19838,7 +20751,7 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_SAMParser = {
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "File Parser Class for SAM File.\n\n Each line of the output file contains at least: \n 1. Sequence name \n 2. Bitwise flag\n 3. Reference name\n 4. 1-based leftmost position fo clipped alignment\n 5. Mapping quality\n 6. CIGAR string\n 7. Mate Reference Name\n 8. 1-based leftmost Mate Position\n 9. Inferred insert size\n 10. Query sequence on the same strand as the reference\n 11. Query quality\n \n The bitwise flag is made like this:\n dec [...]
+ "File Parser Class for SAM File.\n\n Each line of the output file contains at least: \n 1. Sequence name \n 2. Bitwise flag\n 3. Reference name\n 4. 1-based leftmost position fo clipped alignment\n 5. Mapping quality\n 6. CIGAR string\n 7. Mate Reference Name\n 8. 1-based leftmost Mate Position\n 9. Inferred insert size\n 10. Query sequence on the same strand as the reference\n 11. Query quality\n \n The bitwise flag is made like this:\n dec [...]
__pyx_tp_traverse_5MACS2_2IO_6Parser_GenericParser, /*tp_traverse*/
__pyx_tp_clear_5MACS2_2IO_6Parser_GenericParser, /*tp_clear*/
0, /*tp_richcompare*/
@@ -19904,8 +20817,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BAMParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -19918,7 +20832,7 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BAMParser = {
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "File Parser Class for BAM File.\n\n File is gzip-compatible and binary.\n Information available is the same that is in SAM format.\n \n The bitwise flag is made like this:\n dec\tmeaning\n ---\t-------\n 1\tpaired read\n 2\tproper pair\n 4\tquery unmapped\n 8\tmate unmapped\n 16\tstrand of the query (1 -> reverse)\n 32\tstrand of the mate\n 64\tfirst read in pair\n 128\tsecond read in pair\n 256\talignment is not primary\n 512\tdoes not [...]
+ "File Parser Class for BAM File.\n\n File is gzip-compatible and binary.\n Information available is the same that is in SAM format.\n \n The bitwise flag is made like this:\n dec\tmeaning\n ---\t-------\n 1\tpaired read\n 2\tproper pair\n 4\tquery unmapped\n 8\tmate unmapped\n 16\tstrand of the query (1 -> reverse)\n 32\tstrand of the mate\n 64\tfirst read in pair\n 128\tsecond read in pair\n 256\talignment is not primary\n 512\tdoes not [...]
__pyx_tp_traverse_5MACS2_2IO_6Parser_GenericParser, /*tp_traverse*/
__pyx_tp_clear_5MACS2_2IO_6Parser_GenericParser, /*tp_clear*/
0, /*tp_richcompare*/
@@ -20011,8 +20925,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BAMPEParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -20025,7 +20940,7 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BAMPEParser = {
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "File Parser Class for BAM File containing paired-end reads\n Only counts valid pairs, discards everything else\n Uses the midpoint of every read and calculates the average fragment size\n on the fly instead of modeling it\n\n File is gzip-compatible and binary.\n Information available is the same that is in SAM format.\n \n The bitwise flag is made like this:\n dec meaning\n --- -------\n 1 paired read\n 2 proper pair\n 4 query unmapp [...]
+ "File Parser Class for BAM File containing paired-end reads\n Only counts valid pairs, discards everything else\n Uses the midpoint of every read and calculates the average fragment size\n on the fly instead of modeling it\n\n File is gzip-compatible and binary.\n Information available is the same that is in SAM format.\n \n The bitwise flag is made like this:\n dec meaning\n --- -------\n 1 paired read\n 2 proper pair\n 4 query unmapp [...]
__pyx_tp_traverse_5MACS2_2IO_6Parser_GenericParser, /*tp_traverse*/
__pyx_tp_clear_5MACS2_2IO_6Parser_GenericParser, /*tp_clear*/
0, /*tp_richcompare*/
@@ -20082,8 +20997,9 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BowtieParser = {
0, /*tp_setattr*/
#if PY_MAJOR_VERSION < 3
0, /*tp_compare*/
- #else
- 0, /*reserved*/
+ #endif
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*tp_as_async*/
#endif
0, /*tp_repr*/
0, /*tp_as_number*/
@@ -20132,67 +21048,184 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BowtieParser = {
#endif
};
-static PyMethodDef __pyx_methods[] = {
- {"guess_parser", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_1guess_parser, METH_VARARGS|METH_KEYWORDS, 0},
- {0, 0, 0, 0}
-};
+static PyMethodDef __pyx_methods[] = {
+ {"guess_parser", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_1guess_parser, METH_VARARGS|METH_KEYWORDS, 0},
+ {0, 0, 0, 0}
+};
+
+static int __pyx_import_star_set(PyObject *o, PyObject* py_name, char *name) {
+ static const char* internal_type_names[] = {
+ "BAMPEParser",
+ "BAMParser",
+ "BEDPEParser",
+ "BEDParser",
+ "BowtieParser",
+ "ELANDExportParser",
+ "ELANDMultiParser",
+ "ELANDResultParser",
+ "GenericParser",
+ "SAMParser",
+ "_BAMPEParsed",
+ "__pyx_ctuple_char__ptr__and_int__and_long",
+ "__pyx_ctuple_char__ptr__and_int__and_long_struct",
+ "__pyx_ctuple_double",
+ "__pyx_ctuple_double_struct",
+ "__pyx_ctuple_float",
+ "__pyx_ctuple_float_struct",
+ "__pyx_ctuple_int",
+ "__pyx_ctuple_int__and_int__and_int",
+ "__pyx_ctuple_int__and_int__and_int_struct",
+ "__pyx_ctuple_int_struct",
+ "__pyx_ctuple_long",
+ "__pyx_ctuple_long__and_long",
+ "__pyx_ctuple_long__and_long__and_long",
+ "__pyx_ctuple_long__and_long__and_long_struct",
+ "__pyx_ctuple_long__and_long_struct",
+ "__pyx_ctuple_long_struct",
+ "__pyx_opt_args_5MACS2_2IO_6Parser_guess_parser",
+ "bool",
+ "int32_t",
+ "size_t",
+ "uint32_t",
+ "uint64_t",
+ 0
+ };
+ const char** type_name = internal_type_names;
+ while (*type_name) {
+ if (__Pyx_StrEq(name, *type_name)) {
+ PyErr_Format(PyExc_TypeError, "Cannot overwrite C type %s", name);
+ goto bad;
+ }
+ type_name++;
+ }
+ if (0);
+ else {
+ if (PyObject_SetAttr(__pyx_m, py_name, o) < 0) goto bad;
+ }
+ return 0;
+ bad:
+ return -1;
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-static int __pyx_import_star_set(PyObject *o, PyObject* py_name, char *name) {
- static const char* internal_type_names[] = {
- "BAMPEParser",
- "BAMParser",
- "BEDPEParser",
- "BEDParser",
- "BowtieParser",
- "ELANDExportParser",
- "ELANDMultiParser",
- "ELANDResultParser",
- "GenericParser",
- "SAMParser",
- "_BAMPEParsed",
- "__pyx_ctuple_char__ptr__and_int__and_long",
- "__pyx_ctuple_char__ptr__and_int__and_long_struct",
- "__pyx_ctuple_double",
- "__pyx_ctuple_double_struct",
- "__pyx_ctuple_float",
- "__pyx_ctuple_float_struct",
- "__pyx_ctuple_int",
- "__pyx_ctuple_int__and_int__and_int",
- "__pyx_ctuple_int__and_int__and_int_struct",
- "__pyx_ctuple_int_struct",
- "__pyx_ctuple_long",
- "__pyx_ctuple_long__and_long",
- "__pyx_ctuple_long__and_long__and_long",
- "__pyx_ctuple_long__and_long__and_long_struct",
- "__pyx_ctuple_long__and_long_struct",
- "__pyx_ctuple_long_struct",
- "__pyx_opt_args_5MACS2_2IO_6Parser_guess_parser",
- "bool",
- "int32_t",
- "size_t",
- "uint32_t",
- "uint64_t",
- 0
- };
- const char** type_name = internal_type_names;
- while (*type_name) {
- if (__Pyx_StrEq(name, *type_name)) {
- PyErr_Format(PyExc_TypeError, "Cannot overwrite C type %s", name);
- goto bad;
- }
- type_name++;
- }
- if (0);
- else {
- if (PyObject_SetAttr(__pyx_m, py_name, o) < 0) goto bad;
- }
- return 0;
- bad:
- return -1;
-}
-/* import_all_from is an unexposed function from ceval.c */
static int
__Pyx_import_all_from(PyObject *locals, PyObject *v)
@@ -20204,7 +21237,7 @@ __Pyx_import_all_from(PyObject *locals, PyObject *v)
if (all == NULL) {
if (!PyErr_ExceptionMatches(PyExc_AttributeError))
- return -1; /* Unexpected error */
+ return -1;
PyErr_Clear();
dict = PyObject_GetAttrString(v, "__dict__");
if (dict == NULL) {
@@ -20307,6 +21340,7 @@ bad:
}
+
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
#if PY_VERSION_HEX < 0x03020000
@@ -20459,7 +21493,7 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_map = __Pyx_GetBuiltinName(__pyx_n_s_map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
@@ -20811,542 +21845,542 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__37);
__Pyx_GIVEREF(__pyx_tuple__37);
- /* "MACS2/IO/Parser.pyx":670
+ /* "MACS2/IO/Parser.pyx":671
* if not thisline: return 0
* if thisline[ 0 ] == "@": return 0 # header line started with '@' is skipped
* thisfields = thisline.split( '\t' ) # <<<<<<<<<<<<<<
* bwflag = atoi( thisfields[ 1 ] )
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
*/
- __pyx_tuple__39 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__39 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__39);
__Pyx_GIVEREF(__pyx_tuple__39);
- /* "MACS2/IO/Parser.pyx":694
+ /* "MACS2/IO/Parser.pyx":695
*
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* if thisline[ 0 ] == "@": return ( "", -1, -1 ) # header line started with '@' is skipped
* thisfields = thisline.split( '\t' )
*/
- __pyx_tuple__40 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__40 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__40);
__Pyx_GIVEREF(__pyx_tuple__40);
- /* "MACS2/IO/Parser.pyx":695
+ /* "MACS2/IO/Parser.pyx":696
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ] == "@": return ( "", -1, -1 ) # header line started with '@' is skipped # <<<<<<<<<<<<<<
* thisfields = thisline.split( '\t' )
* thistagname = thisfields[ 0 ] # name of tag
*/
- __pyx_tuple__41 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__41 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__41);
__Pyx_GIVEREF(__pyx_tuple__41);
- /* "MACS2/IO/Parser.pyx":696
+ /* "MACS2/IO/Parser.pyx":697
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ] == "@": return ( "", -1, -1 ) # header line started with '@' is skipped
* thisfields = thisline.split( '\t' ) # <<<<<<<<<<<<<<
* thistagname = thisfields[ 0 ] # name of tag
* thisref = thisfields[ 2 ]
*/
- __pyx_tuple__42 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__42 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__42);
__Pyx_GIVEREF(__pyx_tuple__42);
- /* "MACS2/IO/Parser.pyx":702
+ /* "MACS2/IO/Parser.pyx":703
* CIGAR = thisfields[ 5 ]
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
* return ( "", -1, -1 ) #unmapped sequence or bad sequence or 2nd or sup alignment # <<<<<<<<<<<<<<
* if bwflag & 1:
* # paired read. We should only keep sequence if the mate is mapped
*/
- __pyx_tuple__43 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__43 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__43);
__Pyx_GIVEREF(__pyx_tuple__43);
- /* "MACS2/IO/Parser.pyx":707
+ /* "MACS2/IO/Parser.pyx":708
* # and if this is the left mate, all is within the flag!
* if not bwflag & 2:
* return ( "", -1, -1 ) # not a proper pair # <<<<<<<<<<<<<<
* if bwflag & 8:
* return ( "", -1, -1 ) # the mate is unmapped
*/
- __pyx_tuple__44 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__44 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__44);
__Pyx_GIVEREF(__pyx_tuple__44);
- /* "MACS2/IO/Parser.pyx":709
+ /* "MACS2/IO/Parser.pyx":710
* return ( "", -1, -1 ) # not a proper pair
* if bwflag & 8:
* return ( "", -1, -1 ) # the mate is unmapped # <<<<<<<<<<<<<<
* # From Benjamin Schiller https://github.com/benjschiller
* if bwflag & 128:
*/
- __pyx_tuple__45 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__45 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__45);
__Pyx_GIVEREF(__pyx_tuple__45);
- /* "MACS2/IO/Parser.pyx":713
+ /* "MACS2/IO/Parser.pyx":714
* if bwflag & 128:
* # this is not the first read in a pair
* return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* # end of the patch
* # In case of paired-end we have now skipped all possible "bad" pairs
*/
- __pyx_tuple__46 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__46 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__46);
__Pyx_GIVEREF(__pyx_tuple__46);
- /* "MACS2/IO/Parser.pyx":729
+ /* "MACS2/IO/Parser.pyx":730
*
* try:
* thisref = thisref[ :thisref.rindex( ".fa" ) ] # <<<<<<<<<<<<<<
* except ValueError:
* pass
*/
- __pyx_tuple__47 = PyTuple_Pack(1, __pyx_kp_s_fa); if (unlikely(!__pyx_tuple__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__47 = PyTuple_Pack(1, __pyx_kp_s_fa); if (unlikely(!__pyx_tuple__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__47);
__Pyx_GIVEREF(__pyx_tuple__47);
- /* "MACS2/IO/Parser.pyx":774
+ /* "MACS2/IO/Parser.pyx":776
* f = gzip.open( filename )
* try:
* f.read( 10 ) # <<<<<<<<<<<<<<
* except IOError:
* # not a gzipped file
*/
- __pyx_tuple__48 = PyTuple_Pack(1, __pyx_int_10); if (unlikely(!__pyx_tuple__48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__48 = PyTuple_Pack(1, __pyx_int_10); if (unlikely(!__pyx_tuple__48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__48);
__Pyx_GIVEREF(__pyx_tuple__48);
- /* "MACS2/IO/Parser.pyx":790
+ /* "MACS2/IO/Parser.pyx":792
*
* """
* magic_header = self.fhd.read( 3 ) # <<<<<<<<<<<<<<
* if magic_header == "BAM":
* tsize = self.tsize()
*/
- __pyx_tuple__49 = PyTuple_Pack(1, __pyx_int_3); if (unlikely(!__pyx_tuple__49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__49 = PyTuple_Pack(1, __pyx_int_3); if (unlikely(!__pyx_tuple__49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__49);
__Pyx_GIVEREF(__pyx_tuple__49);
- /* "MACS2/IO/Parser.pyx":794
+ /* "MACS2/IO/Parser.pyx":796
* tsize = self.tsize()
* if tsize > 0:
* self.fhd.seek( 0 ) # <<<<<<<<<<<<<<
* return True
* else:
*/
- __pyx_tuple__50 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__50 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__50);
__Pyx_GIVEREF(__pyx_tuple__50);
- /* "MACS2/IO/Parser.pyx":797
+ /* "MACS2/IO/Parser.pyx":799
* return True
* else:
* self.fhd.seek( 0 ) # <<<<<<<<<<<<<<
* raise Exception( "File is not of a valid BAM format! %d" % tsize )
* else:
*/
- __pyx_tuple__51 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__51 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__51);
__Pyx_GIVEREF(__pyx_tuple__51);
- /* "MACS2/IO/Parser.pyx":800
+ /* "MACS2/IO/Parser.pyx":802
* raise Exception( "File is not of a valid BAM format! %d" % tsize )
* else:
* self.fhd.seek( 0 ) # <<<<<<<<<<<<<<
* return False
*
*/
- __pyx_tuple__52 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__52 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__52);
__Pyx_GIVEREF(__pyx_tuple__52);
- /* "MACS2/IO/Parser.pyx":825
+ /* "MACS2/IO/Parser.pyx":827
* ftell = self.fhd.tell
* # move to pos 4, there starts something
* fseek( 4 ) # <<<<<<<<<<<<<<
* header_len = unpack( '<i', fread( 4 ) )[ 0 ]
* fseek( header_len + ftell() )
*/
- __pyx_tuple__53 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__53 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__53);
__Pyx_GIVEREF(__pyx_tuple__53);
- /* "MACS2/IO/Parser.pyx":826
+ /* "MACS2/IO/Parser.pyx":828
* # move to pos 4, there starts something
* fseek( 4 )
* header_len = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* fseek( header_len + ftell() )
* # get the number of chromosome
*/
- __pyx_tuple__54 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__54)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__54 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__54)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__54);
__Pyx_GIVEREF(__pyx_tuple__54);
- /* "MACS2/IO/Parser.pyx":829
+ /* "MACS2/IO/Parser.pyx":831
* fseek( header_len + ftell() )
* # get the number of chromosome
* nc = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* for x in range( nc ):
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*/
- __pyx_tuple__55 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__55 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__55);
__Pyx_GIVEREF(__pyx_tuple__55);
- /* "MACS2/IO/Parser.pyx":832
+ /* "MACS2/IO/Parser.pyx":834
* for x in range( nc ):
* # read each chromosome name
* nlength = unpack( '<i' , fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* # jump over chromosome size, we don't need it
* fread( nlength )
*/
- __pyx_tuple__56 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__56 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__56);
__Pyx_GIVEREF(__pyx_tuple__56);
- /* "MACS2/IO/Parser.pyx":837
+ /* "MACS2/IO/Parser.pyx":839
* fseek( ftell() + 4 )
* while n < 10:
* entrylength = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* data = fread( entrylength )
* a = unpack( '<i', data[16:20] )[ 0 ]
*/
- __pyx_tuple__57 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__57 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__57);
__Pyx_GIVEREF(__pyx_tuple__57);
- /* "MACS2/IO/Parser.pyx":839
+ /* "MACS2/IO/Parser.pyx":841
* entrylength = unpack( '<i', fread( 4 ) )[ 0 ]
* data = fread( entrylength )
* a = unpack( '<i', data[16:20] )[ 0 ] # <<<<<<<<<<<<<<
* s += a
* n += 1
*/
- __pyx_slice__58 = PySlice_New(__pyx_int_16, __pyx_int_20, Py_None); if (unlikely(!__pyx_slice__58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__58 = PySlice_New(__pyx_int_16, __pyx_int_20, Py_None); if (unlikely(!__pyx_slice__58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__58);
__Pyx_GIVEREF(__pyx_slice__58);
- /* "MACS2/IO/Parser.pyx":842
+ /* "MACS2/IO/Parser.pyx":844
* s += a
* n += 1
* fseek( 0 ) # <<<<<<<<<<<<<<
* self.tag_size = int( s/n )
* return self.tag_size
*/
- __pyx_tuple__59 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__59 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__59);
__Pyx_GIVEREF(__pyx_tuple__59);
- /* "MACS2/IO/Parser.pyx":863
+ /* "MACS2/IO/Parser.pyx":865
* ftell = self.fhd.tell
* # move to pos 4, there starts something
* fseek(4) # <<<<<<<<<<<<<<
* header_len = unpack( '<i', fread( 4 ) )[ 0 ]
* fseek( header_len + ftell() )
*/
- __pyx_tuple__60 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__60 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__60);
__Pyx_GIVEREF(__pyx_tuple__60);
- /* "MACS2/IO/Parser.pyx":864
+ /* "MACS2/IO/Parser.pyx":866
* # move to pos 4, there starts something
* fseek(4)
* header_len = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* fseek( header_len + ftell() )
* # get the number of chromosome
*/
- __pyx_tuple__61 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__61 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__61);
__Pyx_GIVEREF(__pyx_tuple__61);
- /* "MACS2/IO/Parser.pyx":867
+ /* "MACS2/IO/Parser.pyx":869
* fseek( header_len + ftell() )
* # get the number of chromosome
* nc = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* for x in range( nc ):
* # read each chromosome name
*/
- __pyx_tuple__62 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__62 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__62);
__Pyx_GIVEREF(__pyx_tuple__62);
- /* "MACS2/IO/Parser.pyx":870
+ /* "MACS2/IO/Parser.pyx":872
* for x in range( nc ):
* # read each chromosome name
* nlength = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* refname = fread( nlength )[ :-1 ]
* references.append( refname )
*/
- __pyx_tuple__63 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__63 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__63);
__Pyx_GIVEREF(__pyx_tuple__63);
- /* "MACS2/IO/Parser.pyx":871
+ /* "MACS2/IO/Parser.pyx":873
* # read each chromosome name
* nlength = unpack( '<i', fread( 4 ) )[ 0 ]
* refname = fread( nlength )[ :-1 ] # <<<<<<<<<<<<<<
* references.append( refname )
* # don't jump over chromosome size
*/
- __pyx_slice__64 = PySlice_New(Py_None, __pyx_int_neg_1, Py_None); if (unlikely(!__pyx_slice__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__64 = PySlice_New(Py_None, __pyx_int_neg_1, Py_None); if (unlikely(!__pyx_slice__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__64);
__Pyx_GIVEREF(__pyx_slice__64);
- /* "MACS2/IO/Parser.pyx":875
+ /* "MACS2/IO/Parser.pyx":877
* # don't jump over chromosome size
* # we can use it to avoid falling of chrom ends during peak calling
* rlengths[refname] = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* return (references, rlengths)
*
*/
- __pyx_tuple__65 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__65 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__65);
__Pyx_GIVEREF(__pyx_tuple__65);
- /* "MACS2/IO/Parser.pyx":898
+ /* "MACS2/IO/Parser.pyx":900
* while True:
* try:
* entrylength = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* except struct.error:
* break
*/
- __pyx_tuple__66 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__66 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__66);
__Pyx_GIVEREF(__pyx_tuple__66);
- /* "MACS2/IO/Parser.pyx":934
+ /* "MACS2/IO/Parser.pyx":936
* while True:
* try:
* entrylength = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* except struct.error:
* break
*/
- __pyx_tuple__67 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__67 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__67);
__Pyx_GIVEREF(__pyx_tuple__67);
- /* "MACS2/IO/Parser.pyx":958
+ /* "MACS2/IO/Parser.pyx":960
*
* # we skip lot of the available information in data (i.e. tag name, quality etc etc)
* if not data: return ( -1, -1, -1 ) # <<<<<<<<<<<<<<
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
*/
- __pyx_tuple__68 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__68 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__68);
__Pyx_GIVEREF(__pyx_tuple__68);
- /* "MACS2/IO/Parser.pyx":960
+ /* "MACS2/IO/Parser.pyx":962
* if not data: return ( -1, -1, -1 )
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ] # <<<<<<<<<<<<<<
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
*/
- __pyx_slice__69 = PySlice_New(__pyx_int_0, __pyx_int_4, Py_None); if (unlikely(!__pyx_slice__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__69 = PySlice_New(__pyx_int_0, __pyx_int_4, Py_None); if (unlikely(!__pyx_slice__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__69);
__Pyx_GIVEREF(__pyx_slice__69);
- /* "MACS2/IO/Parser.pyx":961
+ /* "MACS2/IO/Parser.pyx":963
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ] # <<<<<<<<<<<<<<
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
*/
- __pyx_slice__70 = PySlice_New(__pyx_int_4, __pyx_int_8, Py_None); if (unlikely(!__pyx_slice__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__70 = PySlice_New(__pyx_int_4, __pyx_int_8, Py_None); if (unlikely(!__pyx_slice__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__70);
__Pyx_GIVEREF(__pyx_slice__70);
- /* "MACS2/IO/Parser.pyx":962
+ /* "MACS2/IO/Parser.pyx":964
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] ) # <<<<<<<<<<<<<<
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
* return ( -1, -1, -1 ) #unmapped sequence or bad sequence or secondary or supplementary alignment
*/
- __pyx_slice__71 = PySlice_New(__pyx_int_12, __pyx_int_16, Py_None); if (unlikely(!__pyx_slice__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__71 = PySlice_New(__pyx_int_12, __pyx_int_16, Py_None); if (unlikely(!__pyx_slice__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__71);
__Pyx_GIVEREF(__pyx_slice__71);
- /* "MACS2/IO/Parser.pyx":964
+ /* "MACS2/IO/Parser.pyx":966
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ * if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
* return ( -1, -1, -1 ) #unmapped sequence or bad sequence or secondary or supplementary alignment # <<<<<<<<<<<<<<
* if bwflag & 1:
* # paired read. We should only keep sequence if the mate is mapped
*/
- __pyx_tuple__72 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__72 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__72);
__Pyx_GIVEREF(__pyx_tuple__72);
- /* "MACS2/IO/Parser.pyx":969
+ /* "MACS2/IO/Parser.pyx":971
* # and if this is the left mate, all is within the flag!
* if not bwflag & 2:
* return ( -1, -1, -1 ) # not a proper pair # <<<<<<<<<<<<<<
* if bwflag & 8:
* return ( -1, -1, -1 ) # the mate is unmapped
*/
- __pyx_tuple__73 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__73 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__73);
__Pyx_GIVEREF(__pyx_tuple__73);
- /* "MACS2/IO/Parser.pyx":971
+ /* "MACS2/IO/Parser.pyx":973
* return ( -1, -1, -1 ) # not a proper pair
* if bwflag & 8:
* return ( -1, -1, -1 ) # the mate is unmapped # <<<<<<<<<<<<<<
* # From Benjamin Schiller https://github.com/benjschiller
* if bwflag & 128:
*/
- __pyx_tuple__74 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__74 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__74);
__Pyx_GIVEREF(__pyx_tuple__74);
- /* "MACS2/IO/Parser.pyx":975
+ /* "MACS2/IO/Parser.pyx":977
* if bwflag & 128:
* # this is not the first read in a pair
* return ( -1, -1, -1 ) # <<<<<<<<<<<<<<
* # end of the patch
* # In case of paired-end we have now skipped all possible "bad" pairs
*/
- __pyx_tuple__75 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__75 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__75);
__Pyx_GIVEREF(__pyx_tuple__75);
- /* "MACS2/IO/Parser.pyx":983
+ /* "MACS2/IO/Parser.pyx":985
* if bwflag & 16:
* # read mapped to minus strand
* l_read_name = unpack( '<B', data[ 8:9 ] )[ 0 ] # <<<<<<<<<<<<<<
* # need to decipher CIGAR string
* for cigar_code in unpack( '<%dI' % (n_cigar_op) , data[ 32 + l_read_name : 32 + l_read_name + n_cigar_op*4 ] ):
*/
- __pyx_slice__76 = PySlice_New(__pyx_int_8, __pyx_int_9, Py_None); if (unlikely(!__pyx_slice__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__76 = PySlice_New(__pyx_int_8, __pyx_int_9, Py_None); if (unlikely(!__pyx_slice__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__76);
__Pyx_GIVEREF(__pyx_slice__76);
- /* "MACS2/IO/Parser.pyx":1048
+ /* "MACS2/IO/Parser.pyx":1051
* err = struct.error
* while True:
* try: entrylength = unpack('<i', fread(4))[0] # <<<<<<<<<<<<<<
* except err: break
* rawread = fread(32)
*/
- __pyx_tuple__77 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__77 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__77);
__Pyx_GIVEREF(__pyx_tuple__77);
- /* "MACS2/IO/Parser.pyx":1050
+ /* "MACS2/IO/Parser.pyx":1053
* try: entrylength = unpack('<i', fread(4))[0]
* except err: break
* rawread = fread(32) # <<<<<<<<<<<<<<
* # rawread = <bytes>fread(entrylength)
* read = self.__pe_binary_parse(rawread)
*/
- __pyx_tuple__78 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__78 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1053; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__78);
__Pyx_GIVEREF(__pyx_tuple__78);
- /* "MACS2/IO/Parser.pyx":1094
+ /* "MACS2/IO/Parser.pyx":1097
* err = struct.error
* while True:
* try: entrylength = unpack('<i', fread(4))[0] # <<<<<<<<<<<<<<
* except err: break
* rawread = fread(32)
*/
- __pyx_tuple__79 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__79 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__79);
__Pyx_GIVEREF(__pyx_tuple__79);
- /* "MACS2/IO/Parser.pyx":1096
+ /* "MACS2/IO/Parser.pyx":1099
* try: entrylength = unpack('<i', fread(4))[0]
* except err: break
* rawread = fread(32) # <<<<<<<<<<<<<<
* # rawread = <bytes>fread(entrylength)
* read = self.__pe_binary_parse(rawread)
*/
- __pyx_tuple__80 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__80 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__80);
__Pyx_GIVEREF(__pyx_tuple__80);
- /* "MACS2/IO/Parser.pyx":1187
+ /* "MACS2/IO/Parser.pyx":1190
*
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* if thisline[ 0 ]=="#": return ( "", -1 , -1 ) # comment line is skipped
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
*/
- __pyx_tuple__81 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__81 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__81);
__Pyx_GIVEREF(__pyx_tuple__81);
- /* "MACS2/IO/Parser.pyx":1188
+ /* "MACS2/IO/Parser.pyx":1191
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1 , -1 ) # comment line is skipped # <<<<<<<<<<<<<<
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
* return len( thisfields[ 4 ] )
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+ __pyx_tuple__82 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__82);
__Pyx_GIVEREF(__pyx_tuple__82);
- /* "MACS2/IO/Parser.pyx":1189
+ /* "MACS2/IO/Parser.pyx":1192
* if not thisline: return ( "", -1, -1 )
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+ __pyx_tuple__83 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__83);
__Pyx_GIVEREF(__pyx_tuple__83);
- /* "MACS2/IO/Parser.pyx":1238
+ /* "MACS2/IO/Parser.pyx":1241
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* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* if thisline[ 0 ]=="#": return ( "", -1, -1 ) # comment line is skipped
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*/
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+ __pyx_tuple__84 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__84);
__Pyx_GIVEREF(__pyx_tuple__84);
- /* "MACS2/IO/Parser.pyx":1239
+ /* "MACS2/IO/Parser.pyx":1242
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1, -1 ) # comment line is skipped # <<<<<<<<<<<<<<
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+ __pyx_tuple__85 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__85);
__Pyx_GIVEREF(__pyx_tuple__85);
- /* "MACS2/IO/Parser.pyx":1240
+ /* "MACS2/IO/Parser.pyx":1243
* if not thisline: return ( "", -1, -1 )
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+ __pyx_tuple__86 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__86);
__Pyx_GIVEREF(__pyx_tuple__86);
- /* "MACS2/IO/Parser.pyx":1244
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* chromname = chromname[ :chromname.rindex( ".fa" ) ] # <<<<<<<<<<<<<<
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+ __pyx_tuple__87 = PyTuple_Pack(1, __pyx_kp_s_fa); if (unlikely(!__pyx_tuple__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__87);
__Pyx_GIVEREF(__pyx_tuple__87);
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+ if (__Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
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if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
+ #ifdef __Pyx_Coroutine_USED
+ if (__pyx_Coroutine_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
#ifdef __Pyx_Generator_USED
if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
+ #ifdef __Pyx_StopAsyncIteration_USED
+ if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
#if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
@@ -21527,12 +22567,12 @@ PyMODINIT_FUNC PyInit_Parser(void)
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/*--- Initialize various global constants etc. ---*/
- if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
if (__pyx_module_is_main_MACS2__IO__Parser) {
- if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if PY_MAJOR_VERSION >= 3
{
@@ -21543,9 +22583,9 @@ PyMODINIT_FUNC PyInit_Parser(void)
}
#endif
/*--- Builtin init code ---*/
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+ if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
- if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
/*--- Variable export code ---*/
/*--- Function export code ---*/
@@ -21643,11 +22683,11 @@ PyMODINIT_FUNC PyInit_Parser(void)
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__pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___fw_binary_parse = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___fw_binary_parse;
__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_print = 0;
#if CYTHON_COMPILING_IN_CPYTHON
{
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+ PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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@@ -21655,8 +22695,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
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- if (PyObject_SetAttrString(__pyx_m, "BAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BAMParser = &__pyx_type_5MACS2_2IO_6Parser_BAMParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser = &__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser;
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@@ -21664,20 +22704,20 @@ PyMODINIT_FUNC PyInit_Parser(void)
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__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.__pyx___pe_binary_parse = (struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed (*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___pe_binary_parse;
__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_BAMParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_print = 0;
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+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BAMPEParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BAMPEParser = &__pyx_type_5MACS2_2IO_6Parser_BAMPEParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser = &__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser;
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__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_print = 0;
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+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BowtieParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BowtieParser = &__pyx_type_5MACS2_2IO_6Parser_BowtieParser;
/*--- Type import code ---*/
__pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
@@ -21697,6 +22737,9 @@ PyMODINIT_FUNC PyInit_Parser(void)
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
+ #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
+ if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/* "MACS2/IO/Parser.pyx":20
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__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s_unpack);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_unpack);
__Pyx_GIVEREF(__pyx_n_s_unpack);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_unpack);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_struct, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -21753,8 +22796,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
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__Pyx_GOTREF(__pyx_t_2);
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- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_findall);
__Pyx_GIVEREF(__pyx_n_s_findall);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_findall);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_re, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -21798,8 +22841,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
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__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s__94);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s__94);
__Pyx_GIVEREF(__pyx_n_s__94);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s__94);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_MACS2_Constants, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -21816,8 +22859,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s_FWTrack);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_FWTrack);
__Pyx_GIVEREF(__pyx_n_s_FWTrack);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_FWTrack);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_MACS2_IO_FixWidthTrack, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -21837,8 +22880,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s_PETrackI);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PETrackI);
__Pyx_GIVEREF(__pyx_n_s_PETrackI);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PETrackI);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_MACS2_IO_PairedEndTrack, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -21897,8 +22940,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_builtin_Exception);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_Exception);
__Pyx_GIVEREF(__pyx_builtin_Exception);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_Exception);
__pyx_t_1 = __Pyx_CalculateMetaclass(NULL, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = __Pyx_Py3MetaclassPrepare(__pyx_t_1, __pyx_t_2, __pyx_n_s_StrandFormatError, __pyx_n_s_StrandFormatError, (PyObject *) NULL, __pyx_n_s_MACS2_IO_Parser, __pyx_kp_s_Exception_about_strand_format_er); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -21944,7 +22987,7 @@ PyMODINIT_FUNC PyInit_Parser(void)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/Parser.pyx":1
- * # Time-stamp: <2016-02-15 16:02:11 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-03-09 14:18:20 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for all MACS Parser classes for input.
*/
@@ -22216,8 +23259,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject* args = PyTuple_Pack(1, arg);
- return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
+ 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
@@ -22330,10 +23377,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (value && PyExceptionInstance_Check(value)) {
instance_class = (PyObject*) Py_TYPE(value);
if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
+ 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;
}
}
}
@@ -22393,7 +23443,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (tb) {
#if CYTHON_COMPILING_IN_PYPY
PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(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);
@@ -22690,9 +23740,14 @@ static CYTHON_INLINE int __Pyx_div_int(int a, int b) {
static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
- int full_traceback) {
+ int full_traceback, CYTHON_UNUSED int nogil) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
+#ifdef WITH_THREAD
+ PyGILState_STATE state;
+ if (nogil)
+ state = PyGILState_Ensure();
+#endif
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
if (full_traceback) {
Py_XINCREF(old_exc);
@@ -22713,6 +23768,10 @@ static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
PyErr_WriteUnraisable(ctx);
Py_DECREF(ctx);
}
+#ifdef WITH_THREAD
+ if (nogil)
+ PyGILState_Release(state);
+#endif
}
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
@@ -22771,6 +23830,191 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
return 0;
}
+#if CYTHON_USE_PYLONG_INTERNALS
+ #include "longintrepr.h"
+#endif
+
+#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
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
+ if (op1 == op2) {
+ Py_RETURN_TRUE;
+ }
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_CheckExact(op1))) {
+ const long b = intval;
+ long a = PyInt_AS_LONG(op1);
+ if (a == b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ #endif
+ #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ if (likely(PyLong_CheckExact(op1))) {
+ const long b = intval;
+ long a;
+ 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;
+ }
+ case 2:
+ if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
+ a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
+ break;
+ }
+ 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;
+ }
+ 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;
+ }
+ 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;
+ }
+ 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;
+ }
+ #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15
+ default: return PyLong_Type.tp_richcompare(op1, op2, Py_EQ);
+ #else
+ default: Py_RETURN_FALSE;
+ #endif
+ }
+ }
+ if (a == b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ #endif
+ if (PyFloat_CheckExact(op1)) {
+ const long b = intval;
+ double a = PyFloat_AS_DOUBLE(op1);
+ if ((double)a == (double)b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ return PyObject_RichCompare(op1, op2, Py_EQ);
+}
+#endif
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
@@ -22779,7 +24023,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -22793,7 +24038,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -22806,8 +24052,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
return PySequence_GetItem(o, i);
#endif
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
+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);
@@ -22855,8 +24102,8 @@ static CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
return r;
}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj,
+ Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
#if CYTHON_COMPILING_IN_CPYTHON
@@ -22946,11 +24193,108 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
}
return result;
}
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
-bad:
- return NULL;
+ PyErr_Format(PyExc_TypeError,
+ "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
+bad:
+ return NULL;
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_SubtractObjC(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_subtract(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_subtract(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("subtract", return NULL)
+ result = ((double)a) - (double)b;
+ PyFPE_END_PROTECT(result)
+ return PyFloat_FromDouble(result);
+ }
+ return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2);
}
+#endif
#if !CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
@@ -23049,6 +24393,79 @@ bad:
return -1;
}
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ {
+ #if PY_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;
+}
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
@@ -23291,15 +24708,25 @@ __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
}
static int
__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
+ int result = 0;
PyObject *res = op->defaults_getter((PyObject *) op);
if (unlikely(!res))
return -1;
+ #if CYTHON_COMPILING_IN_CPYTHON
op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
Py_INCREF(op->defaults_tuple);
op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
Py_INCREF(op->defaults_kwdict);
+ #else
+ op->defaults_tuple = PySequence_ITEM(res, 0);
+ if (unlikely(!op->defaults_tuple)) result = -1;
+ else {
+ op->defaults_kwdict = PySequence_ITEM(res, 1);
+ if (unlikely(!op->defaults_kwdict)) result = -1;
+ }
+ #endif
Py_DECREF(res);
- return 0;
+ return result;
}
static int
__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) {
@@ -23547,20 +24974,20 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
#if CYTHON_COMPILING_IN_PYPY
static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
+ PyCFunction meth = f->m_ml->ml_meth;
+ PyObject *self = f->m_self;
Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ switch (f->m_ml->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) {
case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ if (likely(kw == NULL || PyDict_Size(kw) == 0))
return (*meth)(self, arg);
break;
case METH_VARARGS | METH_KEYWORDS:
return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
size = PyTuple_GET_SIZE(arg);
- if (size == 0)
+ if (likely(size == 0))
return (*meth)(self, NULL);
PyErr_Format(PyExc_TypeError,
"%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
@@ -23569,10 +24996,15 @@ static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject
}
break;
case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ if (likely(size == 1)) {
+ PyObject *result, *arg0 = PySequence_ITEM(arg, 0);
+ if (unlikely(!arg0)) return NULL;
+ result = (*meth)(self, arg0);
+ Py_DECREF(arg0);
+ return result;
+ }
PyErr_Format(PyExc_TypeError,
"%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
f->m_ml->ml_name, size);
@@ -23654,7 +25086,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0,
#endif
};
-static int __Pyx_CyFunction_init(void) {
+static int __pyx_CyFunction_init(void) {
#if !CYTHON_COMPILING_IN_PYPY
__pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
#endif
@@ -23761,7 +25193,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co
return count;
}
while (start < end) {
- mid = (start + end) / 2;
+ mid = start + (end - start) / 2;
if (code_line < entries[mid].code_line) {
end = mid;
} else if (code_line > entries[mid].code_line) {
@@ -23914,102 +25346,29 @@ bad:
Py_XDECREF(py_frame);
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0;
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
+#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;\
}
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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))) {
@@ -24026,36 +25385,125 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (long) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(long, 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
#endif
if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -24104,21 +25552,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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 long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long 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(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -24130,7 +25578,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
}
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
+ 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))) {
@@ -24147,36 +25595,125 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (int) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(int, 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
#endif
if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -24225,21 +25762,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
+ const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(int) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(int) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(int) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -24251,7 +25788,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
}
static CYTHON_INLINE short __Pyx_PyInt_As_short(PyObject *x) {
- const short neg_one = (short) -1, const_zero = 0;
+ 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))) {
@@ -24268,36 +25805,125 @@ static CYTHON_INLINE short __Pyx_PyInt_As_short(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(short, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(short, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(short) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(short, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(short, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(short, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (short) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(short, 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
#endif
if (sizeof(short) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(short, long, PyLong_AsLong(x))
- } else if (sizeof(short) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(short, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -24346,21 +25972,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value) {
- const short neg_one = (short) -1, const_zero = 0;
+ const short neg_one = (short) -1, const_zero = (short) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(short) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(short) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(short) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(short) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(short) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(short) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(short) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -24612,21 +26238,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value) {
#endif
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
- const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = 0;
+ const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = (ptrdiff_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(ptrdiff_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(ptrdiff_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(ptrdiff_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -24637,9 +26263,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
}
}
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
+ const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(enum NPY_TYPES) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+ }
+ } else {
+ if (sizeof(enum NPY_TYPES) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= 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(enum NPY_TYPES),
+ little, !is_unsigned);
+ }
+}
+
static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
- while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
- return *s1 == *s2;
+ while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
+ return *s1 == *s2;
}
static int __Pyx_check_binary_version(void) {
@@ -24776,7 +26428,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+#if 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 &&
@@ -24817,7 +26469,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_
#endif
} else
#endif
-#if !CYTHON_COMPILING_IN_PYPY
+#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);
@@ -24847,7 +26499,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
#else
if (PyLong_Check(x))
#endif
- return Py_INCREF(x), x;
+ return __Pyx_NewRef(x);
m = Py_TYPE(x)->tp_as_number;
#if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
@@ -24887,18 +26539,55 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject *x;
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
+ 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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
+ #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);
}
diff --git a/MACS2/IO/Parser.pyx b/MACS2/IO/Parser.pyx
index bd0b5f7..f86b9a3 100644
--- a/MACS2/IO/Parser.pyx
+++ b/MACS2/IO/Parser.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2016-02-15 16:02:11 Tao Liu>
+# Time-stamp: <2016-03-09 14:18:20 Tao Liu>
"""Module for all MACS Parser classes for input.
@@ -654,6 +654,7 @@ cdef class SAMParser( GenericParser ):
256 alignment is not primary
512 does not pass quality check
1024 PCR or optical duplicate
+ 2048 supplementary alignment
"""
cdef __tlen_parse_line ( self, str thisline ):
@@ -669,7 +670,7 @@ cdef class SAMParser( GenericParser ):
if thisline[ 0 ] == "@": return 0 # header line started with '@' is skipped
thisfields = thisline.split( '\t' )
bwflag = atoi( thisfields[ 1 ] )
- if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
return 0 #unmapped sequence or bad sequence or 2nd or sup alignment
if bwflag & 1:
# paired read. We should only keep sequence if the mate is mapped
@@ -698,7 +699,7 @@ cdef class SAMParser( GenericParser ):
thisref = thisfields[ 2 ]
bwflag = atoi( thisfields[ 1 ] )
CIGAR = thisfields[ 5 ]
- if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
return ( "", -1, -1 ) #unmapped sequence or bad sequence or 2nd or sup alignment
if bwflag & 1:
# paired read. We should only keep sequence if the mate is mapped
@@ -752,6 +753,7 @@ cdef class BAMParser( GenericParser ):
256 alignment is not primary
512 does not pass quality check
1024 PCR or optical duplicate
+ 2048 supplementary alignment
"""
def __init__ ( self, str filename, long buffer_size = 100000 ):
"""Open input file. Determine whether it's a gzipped file.
@@ -960,7 +962,7 @@ cdef class BAMParser( GenericParser ):
thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
(n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
- if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
return ( -1, -1, -1 ) #unmapped sequence or bad sequence or secondary or supplementary alignment
if bwflag & 1:
# paired read. We should only keep sequence if the mate is mapped
@@ -1014,6 +1016,7 @@ cdef class BAMPEParser(BAMParser):
256 alignment is not primary
512 does not pass quality check
1024 PCR or optical duplicate
+ 2048 supplementary alignment
"""
cdef public int n # total number of fragments
cdef public int d # the average length of fragments in integar
@@ -1134,7 +1137,7 @@ cdef class BAMPEParser(BAMParser):
if not data: return ret
(n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
- if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
+ if bwflag & 4 or bwflag & 512 or bwflag & 256 or bwflag & 2048:
return ret #unmapped sequence or bad sequence or 2nd or sup alignment
#if bwflag & 256 or bwflag & 2048:
# return ret # secondary or supplementary alignment
diff --git a/MACS2/PeakModel.c b/MACS2/PeakModel.c
index c2a707e..07d4335 100644
--- a/MACS2/PeakModel.c
+++ b/MACS2/PeakModel.c
@@ -1,25 +1,13 @@
-/* Generated by Cython 0.22 */
+/* Generated by Cython 0.23.4 */
#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
#error Cython requires Python 2.6+ or Python 3.2+.
#else
-#define CYTHON_ABI "0_22"
+#define CYTHON_ABI "0_23_4"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -54,6 +42,9 @@
#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_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
#define Py_OptimizeFlag 0
#endif
@@ -61,26 +52,30 @@
#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) \
+ #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) \
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#define __Pyx_DefaultClassType PyType_Type
#endif
-#if PY_MAJOR_VERSION >= 3
+#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
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
+#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)) ? \
+ #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)
@@ -99,12 +94,13 @@
#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)
- #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
#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)) ? \
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
- #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
+#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
+ #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
#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))
@@ -169,16 +165,18 @@
#else
#define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
+#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__)
@@ -191,35 +189,33 @@
#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() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
float value;
memset(&value, 0xFF, sizeof(value));
return value;
}
#endif
-#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None)
-#ifdef __cplusplus
-template<typename T>
-void __Pyx_call_destructor(T* x) {
- x->~T();
-}
-template<typename T>
-class __Pyx_FakeReference {
- public:
- __Pyx_FakeReference() : ptr(NULL) { }
- __Pyx_FakeReference(T& ref) : ptr(&ref) { }
- T *operator->() { return ptr; }
- operator T&() { return *ptr; }
- private:
- T *ptr;
-};
-#endif
#if PY_MAJOR_VERSION >= 3
@@ -238,10 +234,6 @@ class __Pyx_FakeReference {
#endif
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
#define __PYX_HAVE__MACS2__PeakModel
#define __PYX_HAVE_API__MACS2__PeakModel
#include "string.h"
@@ -249,8 +241,8 @@ class __Pyx_FakeReference {
#include "stdlib.h"
#include "numpy/arrayobject.h"
#include "numpy/ufuncobject.h"
-#include "pythread.h"
#include "stdint.h"
+#include "pythread.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */
@@ -272,6 +264,13 @@ class __Pyx_FakeReference {
# 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; char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
@@ -280,16 +279,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
#define __PYX_DEFAULT_STRING_ENCODING ""
#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
+#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))
@@ -324,8 +341,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+#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_Int(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
@@ -847,19 +865,19 @@ static struct __pyx_vtabstruct_5MACS2_9PeakModel_PeakModel *__pyx_vtabptr_5MACS2
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__); \
+ #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) \
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)\
__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
#endif
- #define __Pyx_RefNannyFinishContext() \
+ #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__)
@@ -882,13 +900,13 @@ static struct __pyx_vtabstruct_5MACS2_9PeakModel_PeakModel *__pyx_vtabptr_5MACS2
#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); \
+#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); \
+#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)
@@ -910,13 +928,34 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject
static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
+#else
+#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\
+ PyObject_RichCompare(op1, op2, Py_EQ)
+ #endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_RemainderObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
+#else
+#define __Pyx_PyInt_RemainderObjC(op1, op2, intval, inplace)\
+ (inplace ? PyNumber_InPlaceRemainder(op1, op2) : PyNumber_Remainder(op1, op2))
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
+#else
+#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\
+ (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2))
+#endif
+
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
const char* function_name);
#if CYTHON_COMPILING_IN_CPYTHON
@@ -956,20 +995,16 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
static double __Pyx__PyObject_AsDouble(PyObject* obj);
#if CYTHON_COMPILING_IN_PYPY
-#define __Pyx_PyObject_AsDouble(obj) \
-(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
- likely(PyInt_CheckExact(obj)) ? \
+#define __Pyx_PyObject_AsDouble(obj)\
+(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) :\
+ likely(PyInt_CheckExact(obj)) ?\
PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
#else
-#define __Pyx_PyObject_AsDouble(obj) \
-((likely(PyFloat_CheckExact(obj))) ? \
+#define __Pyx_PyObject_AsDouble(obj)\
+((likely(PyFloat_CheckExact(obj))) ?\
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
#endif
-#ifndef __PYX_FORCE_INIT_THREADS
- #define __PYX_FORCE_INIT_THREADS 0
-#endif
-
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
@@ -985,20 +1020,20 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
static void __Pyx_RaiseBufferFallbackError(void);
-#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) : \
+#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) : \
+#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) : \
+#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);
@@ -1019,14 +1054,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
int has_cstart, int has_cstop, int wraparound);
-static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
+static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t);
-static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */
+static CYTHON_INLINE long __Pyx_div_long(long, long);
static void __Pyx_RaiseBufferIndexError(int axis);
#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
-#if PY_MAJOR_VERSION >= 3
+#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
value = PyDict_GetItemWithError(d, key);
@@ -1047,6 +1082,13 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#endif
#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
+
+#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
@@ -1066,10 +1108,10 @@ static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name
static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x);
-#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \
+#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
+ __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\
__Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
@@ -1094,6 +1136,8 @@ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases);
@@ -1105,13 +1149,13 @@ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
#define __Pyx_CYFUNCTION_CCLASS 0x04
-#define __Pyx_CyFunction_GetClosure(f) \
+#define __Pyx_CyFunction_GetClosure(f)\
(((__pyx_CyFunctionObject *) (f))->func_closure)
-#define __Pyx_CyFunction_GetClassObj(f) \
+#define __Pyx_CyFunction_GetClassObj(f)\
(((__pyx_CyFunctionObject *) (f))->func_classobj)
-#define __Pyx_CyFunction_Defaults(type, f) \
+#define __Pyx_CyFunction_Defaults(type, f)\
((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\
((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
typedef struct {
PyCFunctionObject func;
@@ -1135,7 +1179,7 @@ typedef struct {
PyObject *func_annotations;
} __pyx_CyFunctionObject;
static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code) \
+#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\
__Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code)
static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
int flags, PyObject* qualname,
@@ -1151,7 +1195,7 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
PyObject *dict);
static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
PyObject *dict);
-static int __Pyx_CyFunction_init(void);
+static int __pyx_CyFunction_init(void);
static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname,
PyObject *mkw, PyObject *modname, PyObject *doc);
@@ -1200,8 +1244,6 @@ typedef struct {
static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
-
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
@@ -1316,7 +1358,9 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value);
-static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value);
+
+static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *);
static int __Pyx_check_binary_version(void);
@@ -1346,31 +1390,15 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel___naive_peak_pos2(struct _
/* Module declarations from 'cpython.buffer' */
-/* Module declarations from 'cpython.ref' */
-
/* Module declarations from 'libc.string' */
/* Module declarations from 'libc.stdio' */
-/* Module declarations from 'cpython.object' */
-
/* Module declarations from '__builtin__' */
/* Module declarations from 'cpython.type' */
static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
-/* Module declarations from 'libc.stdlib' */
-
-/* Module declarations from 'numpy' */
-
-/* Module declarations from 'numpy' */
-static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
-static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
-static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
-static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
-static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
-static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
-
/* Module declarations from 'cpython.version' */
/* Module declarations from 'cpython.exc' */
@@ -1439,6 +1467,22 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
+/* Module declarations from 'cpython.object' */
+
+/* Module declarations from 'cpython.ref' */
+
+/* Module declarations from 'libc.stdlib' */
+
+/* Module declarations from 'numpy' */
+
+/* Module declarations from 'numpy' */
+static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
+static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
+static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
+static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
+
/* Module declarations from 'libc.stdint' */
/* Module declarations from 'MACS2.PeakModel' */
@@ -1458,40 +1502,6 @@ static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_eval;
static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_5MACS2_9PeakModel_median(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nums); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_23NotEnoughPairsException___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_23NotEnoughPairsException_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel___init__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_opt, PyObject *__pyx_v_treatment, int __pyx_v_max_pairnum); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_2build(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_4__str__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_1d___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_1d_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_11scan_window___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_11scan_window_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_8min_tags___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_8min_tags_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_9PeakModel_2smooth(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, int __pyx_v_window_len, PyObject *__pyx_v_window); /* proto */
-static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static PyObject *__pyx_tp_new_5MACS2_9PeakModel_PeakModel(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_B[] = "B";
static char __pyx_k_H[] = "H";
static char __pyx_k_I[] = "I";
@@ -1609,7 +1619,7 @@ static char __pyx_k_2_looking_for_paired_plus_minus[] = "#2 looking for paired p
static char __pyx_k_Input_vector_needs_to_be_bigger[] = "Input vector needs to be bigger than window size.";
static char __pyx_k_Number_of_unique_tags_on_strand[] = "Number of unique tags on + strand: %d";
static char __pyx_k_Too_few_paired_peaks_d_so_I_can[] = "Too few paired peaks (%d) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.";
-static char __pyx_k_Users_taoliu_Dropbox_projects_m[] = "/Users/taoliu/Dropbox/projects/macs2/MACS/MACS2/PeakModel.pyx";
+static char __pyx_k_Users_taoliu_Dropbox_Projects_M[] = "/Users/taoliu/Dropbox/Projects/MACS2/MACS/MACS2/PeakModel.pyx";
static char __pyx_k_smooth_only_accepts_1_dimension[] = "smooth only accepts 1 dimension arrays.";
static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static char __pyx_k_Fewer_paired_peaks_d_than_d_Mode[] = "Fewer paired peaks (%d) than %d! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use %d pairs to build model!";
@@ -1650,7 +1660,7 @@ static PyObject *__pyx_n_s_RuntimeError;
static PyObject *__pyx_kp_s_Summary_of_Peak_Model_Baseline;
static PyObject *__pyx_kp_s_Too_few_paired_peaks_d_so_I_can;
static PyObject *__pyx_kp_s_Use_d_pairs_to_build_the_model;
-static PyObject *__pyx_kp_s_Users_taoliu_Dropbox_projects_m;
+static PyObject *__pyx_kp_s_Users_taoliu_Dropbox_Projects_M;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_kp_s_Window_is_on_of_flat_hanning_ham;
static PyObject *__pyx_n_s__17;
@@ -1735,6 +1745,40 @@ static PyObject *__pyx_n_s_window_len_2;
static PyObject *__pyx_n_s_x;
static PyObject *__pyx_n_s_y;
static PyObject *__pyx_n_s_zeros;
+static PyObject *__pyx_pf_5MACS2_9PeakModel_median(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_nums); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_23NotEnoughPairsException___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_23NotEnoughPairsException_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel___init__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_opt, PyObject *__pyx_v_treatment, int __pyx_v_max_pairnum); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_2build(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_4__str__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_9plus_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_10minus_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_12shifted_line_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_1d___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_1d_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_11scan_window___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_11scan_window_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_8min_tags___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_8min_tags_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_13alternative_d_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5xcorr_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr___get__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr_2__set__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5MACS2_9PeakModel_9PeakModel_5ycorr_4__del__(struct __pyx_obj_5MACS2_9PeakModel_PeakModel *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_9PeakModel_2smooth(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, int __pyx_v_window_len, PyObject *__pyx_v_window); /* proto */
+static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
+static PyObject *__pyx_tp_new_5MACS2_9PeakModel_PeakModel(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_float_0_5;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
@@ -1826,9 +1870,10 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_median(PyObject *__pyx_v_nums, CYTHON
* return (p[l/2]+p[l/2-1])/2
* else:
*/
- __pyx_t_1 = PyNumber_Remainder(__pyx_v_l, __pyx_int_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_RemainderObjC(__pyx_v_l, __pyx_int_2, 2, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_0, 0, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -1857,7 +1902,7 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_median(PyObject *__pyx_v_nums, CYTHON
}
__pyx_t_2 = __Pyx_PyNumber_Divide(__pyx_v_l, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_SubtractObjC(__pyx_t_2, __pyx_int_1, 1, 0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyObject_GetItem(__pyx_v_p, __pyx_t_6); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
@@ -1873,16 +1918,24 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_median(PyObject *__pyx_v_nums, CYTHON
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
+
+ /* "MACS2/PeakModel.pyx":37
+ * p = sorted(nums)
+ * l = len(p)
+ * if l%2 == 0: # <<<<<<<<<<<<<<
+ * return (p[l/2]+p[l/2-1])/2
+ * else:
+ */
}
- /*else*/ {
- /* "MACS2/PeakModel.pyx":40
+ /* "MACS2/PeakModel.pyx":40
* return (p[l/2]+p[l/2-1])/2
* else:
* return p[l/2] # <<<<<<<<<<<<<<
*
* class NotEnoughPairsException(Exception):
*/
+ /*else*/ {
__Pyx_XDECREF(__pyx_r);
if (unlikely(__pyx_v_p == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -2203,7 +2256,7 @@ static int __pyx_pw_5MACS2_9PeakModel_9PeakModel_1__init__(PyObject *__pyx_v_sel
if (values[2]) {
__pyx_v_max_pairnum = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_max_pairnum == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- __pyx_v_max_pairnum = ((int)500);
+ __pyx_v_max_pairnum = ((int)0x1F4);
}
}
goto __pyx_L4_argument_unpacking_done;
@@ -2496,21 +2549,15 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_6 = ((__pyx_t_5 * __pyx_v_self->lmfold) * __pyx_v_self->peaksize);
if (unlikely(__pyx_v_self->gz == 0)) {
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
- #ifdef WITH_THREAD
- PyGILState_Release(__pyx_gilstate_save);
- #endif
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = PyFloat_FromDouble(((__pyx_t_6 / __pyx_v_self->gz) / 2.0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__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_round, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -2535,21 +2582,15 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_5 = ((__pyx_t_6 * __pyx_v_self->umfold) * __pyx_v_self->peaksize);
if (unlikely(__pyx_v_self->gz == 0)) {
- #ifdef WITH_THREAD
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
- #endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
- #ifdef WITH_THREAD
- PyGILState_Release(__pyx_gilstate_save);
- #endif
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_2 = PyFloat_FromDouble(((__pyx_t_5 / __pyx_v_self->gz) / 2.0)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__pyx_t_2 = 0;
__pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_round, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -2656,6 +2697,7 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
__pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
#endif
} else {
if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
@@ -2663,6 +2705,7 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_1); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
__pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
#endif
}
} else {
@@ -2743,9 +2786,9 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
} else {
__pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = NULL;
- PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_4); __pyx_t_4 = NULL;
__Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_t_3);
__pyx_t_3 = 0;
__pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_11, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -2761,7 +2804,7 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
* self.error("Too few paired peaks (%d) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead." % (num_paired_peakpos))
* self.error("Process for pairing-model is terminated!")
*/
- __pyx_t_12 = ((__pyx_v_num_paired_peakpos < 100) != 0);
+ __pyx_t_12 = ((__pyx_v_num_paired_peakpos < 0x64) != 0);
if (__pyx_t_12) {
/* "MACS2/PeakModel.pyx":144
@@ -2794,9 +2837,9 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
} else {
__pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_11);
+ __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __pyx_t_3 = NULL;
__Pyx_GIVEREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_11);
__pyx_t_11 = 0;
__pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -2831,6 +2874,14 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "MACS2/PeakModel.pyx":143
+ *
+ * self.info("#2 number of paired peaks: %d" % (num_paired_peakpos))
+ * if num_paired_peakpos < 100: # <<<<<<<<<<<<<<
+ * self.error("Too few paired peaks (%d) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead." % (num_paired_peakpos))
+ * self.error("Process for pairing-model is terminated!")
+ */
}
/* "MACS2/PeakModel.pyx":147
@@ -2858,12 +2909,12 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_11);
__pyx_t_2 = 0;
__pyx_t_4 = 0;
__pyx_t_11 = 0;
@@ -2888,9 +2939,9 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
} else {
__pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = NULL;
- PyTuple_SET_ITEM(__pyx_t_2, 0+1, __pyx_t_11);
+ __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __pyx_t_4 = NULL;
__Pyx_GIVEREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_2, 0+1, __pyx_t_11);
__pyx_t_11 = 0;
__pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -2898,9 +2949,15 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L5;
+
+ /* "MACS2/PeakModel.pyx":147
+ * self.error("Process for pairing-model is terminated!")
+ * raise NotEnoughPairsException("No enough pairs to build model")
+ * elif num_paired_peakpos < self.max_pairnum: # <<<<<<<<<<<<<<
+ * self.warn("Fewer paired peaks (%d) than %d! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use %d pairs to build model!" % (num_paired_peakpos,self.max_pairnum,num_paired_peakpos_picked))
+ * self.debug("Use %d pairs to build the model." % (num_paired_peakpos_picked))
+ */
}
- __pyx_L5:;
/* "MACS2/PeakModel.pyx":149
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@@ -2932,9 +2989,9 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel_build(struct __pyx_obj_5MA
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- PyTuple_SET_ITEM(__pyx_t_8, 0+1, __pyx_t_2);
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__Pyx_GIVEREF(__pyx_t_2);
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@@ -5556,16 +5635,24 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel___paired_peaks(struct __py
* paired_peaks_pos[chrom] = self.__find_pair_center (plus_peaksinfo, minus_peaksinfo)
*/
goto __pyx_L3_continue;
+
+ /* "MACS2/PeakModel.pyx":346
+ * self.debug("Number of unique tags on - strand: %d" % ( minus_tags.shape[0] ) )
+ * self.debug("Number of peaks in - strand: %d" % ( len( minus_peaksinfo ) ) )
+ * if not plus_peaksinfo or not minus_peaksinfo: # <<<<<<<<<<<<<<
+ * self.debug("Chrom %s is discarded!" % (chrom) )
+ * continue
+ */
}
- /*else*/ {
- /* "MACS2/PeakModel.pyx":350
+ /* "MACS2/PeakModel.pyx":350
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* self.debug("Number of paired peaks: %d" %(len(paired_peaks_pos[chrom])))
* return paired_peaks_pos
*/
+ /*else*/ {
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+ * (mp,mn) = minuspeaks[im]
+ * if pp-self.peaksize > mp: # move minus # <<<<<<<<<<<<<<
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+ */
goto __pyx_L11;
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*/
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* if not flag_find_overlap:
*/
__pyx_v_flag_find_overlap = 0;
+
+ /* "MACS2/PeakModel.pyx":367
+ * if pp-self.peaksize > mp: # move minus
+ * im += 1
+ * elif pp+self.peaksize < mp: # move plus # <<<<<<<<<<<<<<
+ * ip += 1
+ * im = im_prev # search minus peaks from previous index
+ */
goto __pyx_L11;
}
- /*else*/ {
- /* "MACS2/PeakModel.pyx":372
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* else: # overlap!
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*/
+ /*else*/ {
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+ * else: # overlap!
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ * if pp < mp: # <<<<<<<<<<<<<<
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+ */
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int __pyx_t_2;
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+
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+ * # a peak will be called if tag number is ge min tags.
+ * if len(current_tag_list) >= self.min_tags and len(current_tag_list) <= self.max_tags: # <<<<<<<<<<<<<<
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__pyx_t_1 = 0;
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+ *
+ * if ( pos - current_tag_list[0] + 1 ) > self.peaksize: # call peak in current_tag_list when the region is long enough # <<<<<<<<<<<<<<
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@@ -6560,15 +6701,15 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel___naive_peak_pos(struct __
long __pyx_t_14;
int __pyx_t_15;
int __pyx_t_16;
- int __pyx_t_17;
+ Py_ssize_t __pyx_t_17;
int __pyx_t_18;
- int __pyx_t_19;
- int __pyx_t_20;
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int __pyx_t_22;
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const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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__pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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- __Pyx_RaiseBufferIndexError(__pyx_t_17);
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+ __pyx_t_11 = -1;
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+ if (unlikely(__pyx_t_11 != -1)) {
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
- goto __pyx_L5;
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- __pyx_L5:;
/* "MACS2/PeakModel.pyx":476
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*/
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- if (unlikely(__pyx_t_19 != -1)) {
- __Pyx_RaiseBufferIndexError(__pyx_t_19);
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+ __pyx_t_11 = -1;
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF_SET(__pyx_v_pre_p, __pyx_v_p);
- goto __pyx_L13;
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* p = es[ i_e ]
*/
__pyx_v_i_s = (__pyx_v_i_s + 1);
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goto __pyx_L12;
}
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
__Pyx_INCREF(__pyx_v_p);
__Pyx_DECREF_SET(__pyx_v_pre_p, __pyx_v_p);
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}
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* i_s += 1
*/
__pyx_v_i_e = (__pyx_v_i_e + 1);
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+ /* "MACS2/PeakModel.pyx":485
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+ * if p != pre_p:
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goto __pyx_L12;
}
- /*else*/ {
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* if ( i_e < ls ):
*/
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__pyx_t_14 = __Pyx_PyInt_As_long(__pyx_v_pre_p); if (unlikely((__pyx_t_14 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- for (__pyx_t_20 = __pyx_t_14; __pyx_t_20 < __pyx_t_12; __pyx_t_20+=1) {
- __pyx_v_i = __pyx_t_20;
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__Pyx_INCREF(__pyx_v_p);
__Pyx_DECREF_SET(__pyx_v_pre_p, __pyx_v_p);
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*/
__pyx_v_pileup = (__pyx_v_pileup - 1);
}
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__pyx_t_4 = __pyx_v_peak_length;
- for (__pyx_t_20 = 0; __pyx_t_20 < __pyx_t_4; __pyx_t_20+=1) {
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*/
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_2);
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__Pyx_GIVEREF(__pyx_t_5);
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__pyx_t_5 = 0;
__Pyx_DECREF_SET(__pyx_v_top_pos, ((PyObject*)__pyx_t_2));
__pyx_t_2 = 0;
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goto __pyx_L27;
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_16 = (((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_horizon_line.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_horizon_line.diminfo[0].strides)) == __pyx_v_top_p_num) != 0);
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__pyx_L27:;
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__Pyx_GOTREF(__pyx_t_5);
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int __pyx_t_8;
long __pyx_t_9;
- long __pyx_t_10;
- int __pyx_t_11;
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/* "MACS2/PeakModel.pyx":524
@@ -7846,7 +8017,7 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_9PeakModel___naive_peak_pos2(struct _
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__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_12);
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*/
__Pyx_Raise(__pyx_builtin_ValueError, __pyx_kp_s_smooth_only_accepts_1_dimension, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "MACS2/PeakModel.pyx":588
+ * """
+ *
+ * if x.ndim != 1: # <<<<<<<<<<<<<<
+ * raise ValueError, "smooth only accepts 1 dimension arrays."
+ *
+ */
}
/* "MACS2/PeakModel.pyx":591
@@ -8820,6 +8999,14 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_smooth(PyObject *__pyx_v_x, CYTHON_UN
*/
__Pyx_Raise(__pyx_builtin_ValueError, __pyx_kp_s_Input_vector_needs_to_be_bigger, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "MACS2/PeakModel.pyx":591
+ * raise ValueError, "smooth only accepts 1 dimension arrays."
+ *
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+ * raise ValueError, "Input vector needs to be bigger than window size."
+ *
+ */
}
/* "MACS2/PeakModel.pyx":595
@@ -8843,6 +9030,14 @@ static PyObject *__pyx_f_5MACS2_9PeakModel_smooth(PyObject *__pyx_v_x, CYTHON_UN
__Pyx_INCREF(__pyx_v_x);
__pyx_r = __pyx_v_x;
goto __pyx_L0;
+
+ /* "MACS2/PeakModel.pyx":595
+ *
+ *
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+ *
+ */
}
/* "MACS2/PeakModel.pyx":599
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "MACS2/PeakModel.pyx":599
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}
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__Pyx_GIVEREF(__pyx_t_4);
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__Pyx_GIVEREF(__pyx_v_x);
- PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_2);
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}
- PyTuple_SET_ITEM(__pyx_t_10, 0+__pyx_t_9, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_10, 0+__pyx_t_9, __pyx_t_8);
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- PyTuple_SET_ITEM(__pyx_t_10, 1+__pyx_t_9, __pyx_n_s_d);
__Pyx_GIVEREF(__pyx_n_s_d);
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_w = __pyx_t_2;
__pyx_t_2 = 0;
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+ * else:
+ */
goto __pyx_L12;
}
- /*else*/ {
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* w=eval('np.'+window+'(window_len)') # <<<<<<<<<<<<<<
*
* y=np.convolve(w/w.sum(),s,mode='valid')
*/
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__pyx_t_2 = PyNumber_Add(__pyx_kp_s_np_2, __pyx_v_window); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_10);
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__Pyx_GIVEREF(__pyx_t_2);
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__Pyx_INCREF(__pyx_v_s);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_s);
__Pyx_GIVEREF(__pyx_v_s);
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/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_9PeakModel_3smooth(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5MACS2_9PeakModel_2smooth[] = "smooth the data using a window with requested size.\n \n This method is based on the convolution of a scaled window with the signal.\n The signal is prepared by introducing reflected copies of the signal \n (with the window size) in both ends so that transient parts are minimized\n in the beginning and end part of the output signal.\n \n input:\n x: the input signal \n window_len: the dimension of the [...]
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int __pyx_v_window_len;
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* copy_shape = 0
*/
__pyx_v_copy_shape = 1;
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+ /* "numpy.pxd":208
+ * ndim = PyArray_NDIM(self)
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+ * copy_shape = 1
+ * else:
+ */
goto __pyx_L4;
}
- /*else*/ {
- /* "numpy.pxd":211
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* else:
* copy_shape = 0 # <<<<<<<<<<<<<<
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*/
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__pyx_v_copy_shape = 0;
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__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
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+ /* "numpy.pxd":213
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+ */
if (__pyx_t_1) {
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = __pyx_t_2;
__pyx_L9_bool_binop_done:;
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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ */
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+ __pyx_v_info->format = ((char *)malloc(0xFF));
/* "numpy.pxd":281
* else:
@@ -10024,7 +10307,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
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*/
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+ __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -10111,9 +10394,15 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
* stdlib.free(info.strides)
*/
free(__pyx_v_info->format);
- goto __pyx_L3;
+
+ /* "numpy.pxd":289
+ *
+ * def __releasebuffer__(ndarray self, Py_buffer* info):
+ * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<<
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+ */
}
- __pyx_L3:;
/* "numpy.pxd":291
* if PyArray_HASFIELDS(self):
@@ -10133,9 +10422,15 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
*
*/
free(__pyx_v_info->strides);
- goto __pyx_L4;
+
+ /* "numpy.pxd":291
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+ * stdlib.free(info.format)
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+ */
}
- __pyx_L4:;
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+ __Pyx_GOTREF(__pyx_t_3);
#endif
__Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3);
__pyx_t_3 = 0;
@@ -10559,6 +10855,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "numpy.pxd":798
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+ *
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}
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__pyx_t_7 = ((!(__pyx_v_little_endian != 0)) != 0);
__pyx_t_6 = __pyx_t_7;
__pyx_L7_bool_binop_done:;
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@@ -10611,6 +10923,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "numpy.pxd":801
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*/
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- /* "numpy.pxd":826
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+ * if not PyDataType_HASFIELDS(child):
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+ * if end - f < 5: # <<<<<<<<<<<<<<
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+ }
+
+ /* "numpy.pxd":826
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__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -10739,7 +11067,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -10757,14 +11085,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 104;
+ (__pyx_v_f[0]) = 0x68;
goto __pyx_L15;
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@@ -10775,7 +11103,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -10793,14 +11121,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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*/
- __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 105;
+ (__pyx_v_f[0]) = 0x69;
goto __pyx_L15;
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@@ -10811,7 +11139,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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*/
- __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -10829,14 +11157,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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*/
- __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- (__pyx_v_f[0]) = 108;
+ (__pyx_v_f[0]) = 0x6C;
goto __pyx_L15;
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@@ -10847,7 +11175,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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- __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -10865,14 +11193,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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@@ -10883,7 +11211,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_5 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -10901,14 +11229,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
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+ __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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- (__pyx_v_f[0]) = 102;
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#endif
+ #ifdef __Pyx_StopAsyncIteration_USED
+ if (__pyx_StopAsyncIteration_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
#if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
@@ -12172,12 +12649,12 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
#endif
if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
- if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
if (__pyx_module_is_main_MACS2__PeakModel) {
- if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if PY_MAJOR_VERSION >= 3
{
@@ -12188,9 +12665,9 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
}
#endif
/*--- Builtin init code ---*/
- if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitCachedBuiltins() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
- if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_InitCachedConstants() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
/*--- Variable export code ---*/
/*--- Function export code ---*/
@@ -12228,16 +12705,19 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
sizeof(PyHeapTypeObject),
#endif
0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
+ #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
+ if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
/* "MACS2/PeakModel.pyx":17
* @contact: taoliu at jimmy.harvard.edu
@@ -12281,8 +12761,8 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_n_s_array);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_array);
__Pyx_GIVEREF(__pyx_n_s_array);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_array);
__pyx_t_2 = __Pyx_Import(__pyx_n_s_array, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -12302,8 +12782,8 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s__17);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s__17);
__Pyx_GIVEREF(__pyx_n_s__17);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s__17);
__pyx_t_1 = __Pyx_Import(__pyx_n_s_MACS2_Constants, __pyx_t_2, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12320,8 +12800,8 @@ PyMODINIT_FUNC PyInit_PeakModel(void)
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_builtin_Exception);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_Exception);
__Pyx_GIVEREF(__pyx_builtin_Exception);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_Exception);
__pyx_t_2 = __Pyx_CalculateMetaclass(NULL, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_Py3MetaclassPrepare(__pyx_t_2, __pyx_t_1, __pyx_n_s_NotEnoughPairsException, __pyx_n_s_NotEnoughPairsException, (PyObject *) NULL, __pyx_n_s_MACS2_PeakModel, (PyObject *) NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -12439,6 +12919,280 @@ static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
return result;
}
+#if CYTHON_USE_PYLONG_INTERNALS
+ #include "longintrepr.h"
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
+ if (op1 == op2) {
+ Py_RETURN_TRUE;
+ }
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_CheckExact(op1))) {
+ const long b = intval;
+ long a = PyInt_AS_LONG(op1);
+ if (a == b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ #endif
+ #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ if (likely(PyLong_CheckExact(op1))) {
+ const long b = intval;
+ long a;
+ 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;
+ }
+ case 2:
+ if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
+ a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
+ break;
+ }
+ 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;
+ }
+ 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;
+ }
+ 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;
+ }
+ 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;
+ }
+ #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15
+ default: return PyLong_Type.tp_richcompare(op1, op2, Py_EQ);
+ #else
+ default: Py_RETURN_FALSE;
+ #endif
+ }
+ }
+ if (a == b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ #endif
+ if (PyFloat_CheckExact(op1)) {
+ const long b = intval;
+ double a = PyFloat_AS_DOUBLE(op1);
+ if ((double)a == (double)b) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+ }
+ return PyObject_RichCompare(op1, op2, Py_EQ);
+}
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_RemainderObjC(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 = a % b;
+ x += ((x != 0) & ((x ^ b) < 0)) * b;
+ return PyInt_FromLong(x);
+ }
+ #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_remainder(op1, op2);
+ }
+ }
+ x = a % b;
+ x += ((x != 0) & ((x ^ b) < 0)) * b;
+ return PyLong_FromLong(x);
+ long_long:
+ llx = lla % llb;
+ llx += ((llx != 0) & ((llx ^ llb) < 0)) * llb;
+ return PyLong_FromLongLong(llx);
+ }
+ #endif
+ return (inplace ? PyNumber_InPlaceRemainder : PyNumber_Remainder)(op1, op2);
+}
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx_PyInt_SubtractObjC(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_subtract(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_subtract(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("subtract", return NULL)
+ result = ((double)a) - (double)b;
+ PyFPE_END_PROTECT(result)
+ return PyFloat_FromDouble(result);
+ }
+ return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2);
+}
+#endif
+
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
@@ -12641,8 +13395,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
}
#else
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
- PyObject* args = PyTuple_Pack(1, arg);
- return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
+ 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
@@ -12664,7 +13422,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
#if CYTHON_COMPILING_IN_PYPY
- float_value = PyNumber_Float(obj);
+ float_value = PyNumber_Float(obj); if (0) goto bad;
#else
PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
if (likely(nb) && likely(nb->nb_float)) {
@@ -12822,10 +13580,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (value && PyExceptionInstance_Check(value)) {
instance_class = (PyObject*) Py_TYPE(value);
if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
+ 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;
}
}
}
@@ -12885,7 +13646,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
if (tb) {
#if CYTHON_COMPILING_IN_PYPY
PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyErr_Fetch(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);
@@ -13479,7 +14240,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
return r;
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -13493,7 +14255,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
#endif
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
+ 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)))) {
@@ -13506,8 +14269,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
return PySequence_GetItem(o, i);
#endif
}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
+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);
@@ -13605,8 +14369,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
return 0;
}
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj,
+ Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
#if CYTHON_COMPILING_IN_CPYTHON
@@ -13721,6 +14485,103 @@ static void __Pyx_RaiseBufferIndexError(int axis) {
"Out of bounds on buffer access (axis %d)", axis);
}
+#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
+
static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
PyObject *method, *result = NULL;
method = __Pyx_PyObject_GetAttrStr(obj, method_name);
@@ -13771,8 +14632,8 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb
Py_DECREF(j);
return r;
}
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck) {
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, 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) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
@@ -13979,6 +14840,79 @@ bad:
return -1;
}
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ {
+ #if PY_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;
+}
+
static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
@@ -14221,15 +15155,25 @@ __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
}
static int
__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
+ int result = 0;
PyObject *res = op->defaults_getter((PyObject *) op);
if (unlikely(!res))
return -1;
+ #if CYTHON_COMPILING_IN_CPYTHON
op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
Py_INCREF(op->defaults_tuple);
op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
Py_INCREF(op->defaults_kwdict);
+ #else
+ op->defaults_tuple = PySequence_ITEM(res, 0);
+ if (unlikely(!op->defaults_tuple)) result = -1;
+ else {
+ op->defaults_kwdict = PySequence_ITEM(res, 1);
+ if (unlikely(!op->defaults_kwdict)) result = -1;
+ }
+ #endif
Py_DECREF(res);
- return 0;
+ return result;
}
static int
__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) {
@@ -14477,20 +15421,20 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
#if CYTHON_COMPILING_IN_PYPY
static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
+ PyCFunction meth = f->m_ml->ml_meth;
+ PyObject *self = f->m_self;
Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ switch (f->m_ml->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) {
case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ if (likely(kw == NULL || PyDict_Size(kw) == 0))
return (*meth)(self, arg);
break;
case METH_VARARGS | METH_KEYWORDS:
return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
size = PyTuple_GET_SIZE(arg);
- if (size == 0)
+ if (likely(size == 0))
return (*meth)(self, NULL);
PyErr_Format(PyExc_TypeError,
"%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
@@ -14499,10 +15443,15 @@ static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject
}
break;
case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ if (likely(size == 1)) {
+ PyObject *result, *arg0 = PySequence_ITEM(arg, 0);
+ if (unlikely(!arg0)) return NULL;
+ result = (*meth)(self, arg0);
+ Py_DECREF(arg0);
+ return result;
+ }
PyErr_Format(PyExc_TypeError,
"%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
f->m_ml->ml_name, size);
@@ -14584,7 +15533,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0,
#endif
};
-static int __Pyx_CyFunction_init(void) {
+static int __pyx_CyFunction_init(void) {
#if !CYTHON_COMPILING_IN_PYPY
__pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
#endif
@@ -14691,7 +15640,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co
return count;
}
while (start < end) {
- mid = (start + end) / 2;
+ mid = start + (end - start) / 2;
if (code_line < entries[mid].code_line) {
end = mid;
} else if (code_line > entries[mid].code_line) {
@@ -14865,102 +15814,29 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) {
#endif
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0;
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
- { \
- func_type value = func_value; \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- if (is_unsigned && unlikely(value < zero)) \
- goto raise_neg_overflow; \
- else \
- goto raise_overflow; \
- } \
- } \
- return (target_type) value; \
+ #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;\
}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
+ const int 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))) {
@@ -14977,36 +15853,125 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(int, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (int) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(int, 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
#endif
if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -15055,21 +16020,21 @@ raise_neg_overflow:
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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 long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long 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(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -15081,21 +16046,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
+ const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(int) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(int) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(int) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -15107,21 +16072,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
}
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) {
- const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = 0;
+ const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(Py_intptr_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(Py_intptr_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(Py_intptr_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(Py_intptr_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(Py_intptr_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -15133,7 +16098,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) {
}
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
+ 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))) {
@@ -15150,36 +16115,125 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
+ 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
#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(long, unsigned long, PyLong_AsUnsignedLong(x))
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ __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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
+#if CYTHON_USE_PYLONG_INTERNALS
+ const digit* digits = ((PyLongObject*)x)->ob_digit;
switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
- case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ case 0: return (long) 0;
+ case -1: __PYX_VERIFY_RETURN_INT(long, 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
#endif
if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
+ __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))
}
}
{
@@ -15249,7 +16303,7 @@ static PyObject* __Pyx_Globals(void) {
goto bad;
for (i = PyList_GET_SIZE(names)-1; i >= 0; i--) {
#if CYTHON_COMPILING_IN_PYPY
- PyObject* name = PySequence_GetItem(names, i);
+ PyObject* name = PySequence_ITEM(names, i);
if (!name)
goto bad;
#else
@@ -15524,21 +16578,21 @@ bad:
#endif
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
- const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = 0;
+ const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = (ptrdiff_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
if (sizeof(ptrdiff_t) < sizeof(long)) {
return PyInt_FromLong((long) value);
} else if (sizeof(ptrdiff_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
}
} else {
if (sizeof(ptrdiff_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
- } else if (sizeof(ptrdiff_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
}
}
{
@@ -15549,9 +16603,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
}
}
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
+ const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(enum NPY_TYPES) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+ }
+ } else {
+ if (sizeof(enum NPY_TYPES) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(enum NPY_TYPES) <= 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(enum NPY_TYPES),
+ little, !is_unsigned);
+ }
+}
+
static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
- while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
- return *s1 == *s2;
+ while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
+ return *s1 == *s2;
}
static int __Pyx_check_binary_version(void) {
@@ -15688,7 +16768,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
return __Pyx_PyObject_AsStringAndSize(o, &ignore);
}
static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+#if 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 &&
@@ -15729,7 +16809,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_
#endif
} else
#endif
-#if !CYTHON_COMPILING_IN_PYPY
+#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);
@@ -15759,7 +16839,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
#else
if (PyLong_Check(x))
#endif
- return Py_INCREF(x), x;
+ return __Pyx_NewRef(x);
m = Py_TYPE(x)->tp_as_number;
#if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
@@ -15799,18 +16879,55 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject *x;
#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
+ 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_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
+ #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);
}
diff --git a/MACS2/PeakModel.pyx b/MACS2/PeakModel.pyx
index 054165b..4186ca5 100644
--- a/MACS2/PeakModel.pyx
+++ b/MACS2/PeakModel.pyx
@@ -559,7 +559,7 @@ cpdef smooth(x, int window_len=11, str window='hanning'):
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by introducing reflected copies of the signal
(with the window size) in both ends so that transient parts are minimized
- in the begining and end part of the output signal.
+ in the beginning and end part of the output signal.
input:
x: the input signal
diff --git a/PKG-INFO b/PKG-INFO
index cf74d85..a5c58f7 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.1.20160226
+Version: 2.1.1.20160309
Summary: Model Based Analysis for ChIP-Seq data
Home-page: http://github.com/taoliu/MACS/
Author: Tao Liu
diff --git a/bin/macs2 b/bin/macs2
index d11db9e..68118ab 100644
--- a/bin/macs2
+++ b/bin/macs2
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2016-02-15 14:56:39 Tao Liu>
+# Time-stamp: <2016-03-09 14:34:14 Tao Liu>
"""Description: MACS v2 main executable.
@@ -190,7 +190,7 @@ def add_callpeak_parser( subparsers ):
group_input.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs" )
group_input.add_argument( "--keep-dup", dest = "keepduplicates", type = str, default = "1",
- help = "It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The 'auto' option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. The default is to keep one tag at the same location. Default: 1" )
+ help = "It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The 'auto' option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. Note, if you've used samtools or picard to flag reads as 'PC [...]
group_input.add_argument( "--buffer-size", dest = "buffer_size", type = int, default = "100000",
help = "Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHR [...]
@@ -213,7 +213,7 @@ def add_callpeak_parser( subparsers ):
# group for bimodal
group_bimodal = argparser_callpeak.add_argument_group( "Shifting model arguments" )
group_bimodal.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
+ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
group_bimodal.add_argument( "--bw", dest = "bw", type = int, default = 300,
help = "Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300")
group_bimodal.add_argument( "-m", "--mfold", dest = "mfold", type = int, default = [5,50], nargs = 2,
@@ -354,11 +354,11 @@ def add_filterdup_parser( subparsers ):
argparser_filterdup.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), DEFAULT:hs" )
argparser_filterdup.add_argument( "-s", "--tsize", dest = "tsize", type = int,
- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set" )
+ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set" )
argparser_filterdup.add_argument( "-p", "--pvalue", dest = "pvalue", type = float,
help = "Pvalue cutoff for binomial distribution test. DEFAULT:1e-5" )
argparser_filterdup.add_argument( "--keep-dup", dest = "keepduplicates", type = str, default = "auto",
- help = "It controls the '%(prog)s' behavior towards duplicate tags/pairs at the exact same location -- the same coordination and the same strand. The 'auto' option makes '%(prog)s' calculate the maximum tags at the exact same location based on binomal distribution using given -p as pvalue cutoff; and the 'all' option keeps every tags (useful if you only want to convert formats). If an integer is given, at most this number of tags will be kept at the [...]
+ help = "It controls the '%(prog)s' behavior towards duplicate tags/pairs at the exact same location -- the same coordination and the same strand. The 'auto' option makes '%(prog)s' calculate the maximum tags at the exact same location based on binomal distribution using given -p as pvalue cutoff; and the 'all' option keeps every tags (useful if you only want to convert formats). If an integer is given, at most this number of tags will be kept at the [...]
argparser_filterdup.add_argument( "--verbose", dest = "verbose", type = int, default = 2,
help = "Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. DEFAULT:2" )
add_outdir_option( argparser_filterdup )
@@ -373,7 +373,7 @@ def add_bdgpeakcall_parser( subparsers ):
"""Add function 'peak calling on bedGraph' argument parsers.
"""
argparser_bdgpeakcall = subparsers.add_parser( "bdgpeakcall",
- help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_bdgpeakcall.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
help = "MACS score in bedGraph. REQUIRED" )
argparser_bdgpeakcall.add_argument( "-c", "--cutoff" , dest = "cutoff", type = float,
@@ -398,7 +398,7 @@ def add_bdgbroadcall_parser( subparsers ):
"""Add function 'broad peak calling on bedGraph' argument parsers.
"""
argparser_bdgbroadcall = subparsers.add_parser( "bdgbroadcall",
- help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_bdgbroadcall.add_argument( "-i", "--ifile", dest = "ifile" , type = str, required = True,
help = "MACS score in bedGraph. REQUIRED" )
argparser_bdgbroadcall.add_argument( "-c", "--cutoff-peak", dest = "cutoffpeak", type = float,
@@ -421,7 +421,7 @@ def add_bdgcmp_parser( subparsers ):
"""Add function 'peak calling on bedGraph' argument parsers.
"""
argparser_bdgcmp = subparsers.add_parser( "bdgcmp",
- help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_bdgcmp.add_argument( "-t", "--tfile", dest = "tfile", type = str, required = True,
help = "Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED")
argparser_bdgcmp.add_argument( "-c", "--cfile", dest = "cfile", type = str, required = True,
@@ -447,7 +447,7 @@ def add_bdgopt_parser( subparsers ):
"""Add function 'operations on score column of bedGraph' argument parsers.
"""
argparser_bdgopt = subparsers.add_parser( "bdgopt",
- help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_bdgopt.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
help = "MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED" )
argparser_bdgopt.add_argument( "-m", "--method", dest = "method", type = str,
@@ -464,7 +464,7 @@ def add_cmbreps_parser( subparsers ):
"""Add function 'combine replicates' argument parsers.
"""
argparser_cmbreps = subparsers.add_parser( "cmbreps",
- help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_cmbreps.add_argument( "-i", dest = "ifile", type = str, required = True, nargs = "+",
help = "MACS score in bedGraph for each replicate. Require exactly two files such as '-i A B'. REQUIRED" )
# argparser_cmbreps.add_argument( "-w", dest = "weights", type = float, nargs = "*",
@@ -495,7 +495,7 @@ def add_randsample_parser( subparsers ):
default = None)
add_outdir_option( argparser_randsample )
argparser_randsample.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
+ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
argparser_randsample.add_argument( "-f", "--format", dest = "format", type = str,
choices=("AUTO","BAM","SAM","BED","ELAND","ELANDMULTI","ELANDEXPORT","BOWTIE"),
help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\". The default AUTO option will %(prog)s decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\"",
@@ -506,7 +506,7 @@ def add_randsample_parser( subparsers ):
def add_bdgdiff_parser( subparsers ):
argparser_bdgdiff = subparsers.add_parser( "bdgdiff",
- help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+ help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
argparser_bdgdiff.add_argument( "--t1", dest = "t1bdg", type = str, required = True,
help = "MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED" )
argparser_bdgdiff.add_argument( "--t2", dest="t2bdg", type = str, required = True,
@@ -575,7 +575,7 @@ def add_predictd_parser( subparsers ):
argparser_predictd.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs" )
argparser_predictd.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
+ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
argparser_predictd.add_argument( "--bw", dest = "bw", type = int, default = 300,
help = "Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300")
argparser_predictd.add_argument( "-m", "--mfold", dest = "mfold", type = int, default = [5,50], nargs = 2,
diff --git a/setup.py b/setup.py
index f1da836..dadfbaf 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2016-02-26 10:41:57 Tao Liu>
+# Time-stamp: <2016-03-09 13:35:48 Tao Liu>
"""Description
@@ -58,7 +58,7 @@ def main():
]
setup(name="MACS2",
- version="2.1.1.20160226",
+ version="2.1.1.20160309",
description="Model Based Analysis for ChIP-Seq data",
author='Tao Liu',
author_email='vladimir.liu at gmail.com',
diff --git a/setup_w_cython.py b/setup_w_cython.py
index 5154664..c722a6d 100644
--- a/setup_w_cython.py
+++ b/setup_w_cython.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2016-02-26 10:42:04 Tao Liu>
+# Time-stamp: <2016-03-09 13:36:00 Tao Liu>
"""Description:
@@ -83,7 +83,7 @@ def main():
]
setup(name="MACS2",
- version="2.1.1.20160226",
+ version="2.1.1.20160309",
description="Model Based Analysis for ChIP-Seq data",
author='Tao Liu',
author_email='vladimir.liu at gmail.com',
--
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