-/* Generated by Cython 0.16 on Thu Nov 22 15:20:54 2012 */
+/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
#else
+
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#define PY_LONG_LONG LONG_LONG
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-#ifndef Py_HUGE_VAL
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-#ifdef PYPY_VERSION
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-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
#endif
#if PY_VERSION_HEX < 0x02050000
#define PyNumber_Index(o) PyNumber_Int(o)
#define PyIndex_Check(o) PyNumber_Check(o)
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
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- #define __PYX_BUILD_PY_SSIZE_T "n"
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#if PY_VERSION_HEX < 0x02060000
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#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) \
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#define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
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-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
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#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
#define __Pyx_DOCSTR(n) (n)
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-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
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- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
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#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
"complex.pxd",
};
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds);
+
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+
/*--- Type declarations ---*/
+struct __pyx_Generator_object;
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
struct __pyx_obj_9csamtools_IteratorRow;
struct __pyx_obj_9csamtools_IteratorRowAllRefs;
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+struct __pyx_Generator_object {
PyObject_HEAD
+ __pyx_generator_body_t body;
+ int is_running;
+ int resume_label;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+};
+
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+ struct __pyx_Generator_object __pyx_base;
PyObject *__pyx_v_x;
PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
*
*/
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
- PyObject_HEAD
+ struct __pyx_Generator_object __pyx_base;
PyObject *__pyx_v_x;
PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
+
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+ #define __Pyx_RefNannySetupContext(name)
#define __Pyx_RefNannyFinishContext()
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#define __Pyx_DECREF(r) Py_DECREF(r)
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
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-#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
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static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#ifndef CYTHON_PROFILE
#define CYTHON_PROFILE 1
#endif
+
#ifndef CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_PROFILE_REUSE_FRAME 0
#endif
+
#if CYTHON_PROFILE
+
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
+
#if CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_FRAME_MODIFIER static
#define CYTHON_FRAME_DEL
#define CYTHON_FRAME_MODIFIER
#define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame)
#endif
+
#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
int __Pyx_use_tracing = 0;
+
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
__Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
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+
#define __Pyx_TraceException() \
if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyObject *exc_info = __Pyx_GetExceptionTuple(); \
Py_DECREF(exc_info); \
} \
}
+
#define __Pyx_TraceReturn(result) \
if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyThreadState_GET()->c_profilefunc( \
PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
CYTHON_FRAME_DEL; \
}
+
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
+
#else
+
#define __Pyx_TraceDeclarations
#define __Pyx_TraceCall(funcname, srcfile, firstlineno)
#define __Pyx_TraceException()
#define __Pyx_TraceReturn(result)
+
#endif /* CYTHON_PROFILE */
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
+ const char* function_name, int kw_allowed); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
Py_DECREF(j);
return r;
}
+
+
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
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+
+
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
- if (PyList_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- else if (likely(i >= 0)) {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- return m->sq_item(o, i);
- }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
}
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ else {
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static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
}
static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
Py_INCREF(value);
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if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
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value = PyDict_GetItem(d, key);
if (unlikely(!value)) {
value = default_value;
m = __Pyx_GetAttrString(d, "get");
if (!m) return NULL;
value = PyObject_CallFunctionObjArgs(m, key,
- (default_value == Py_None) ? NULL : default_value, NULL);
+ (default_value == Py_None) ? NULL : default_value, NULL);
Py_DECREF(m);
}
#endif
#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
__Pyx_DelItem_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
int r;
if (!j) return -1;
Py_DECREF(j);
return r;
}
+
static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) {
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- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- return m->sq_ass_item(o, i, (PyObject *)NULL);
- }
+ if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0))
+ return PySequence_DelItem(o, i);
+ else {
+ PyObject *j = PyInt_FromSsize_t(i);
+ return __Pyx_DelItem_Generic(o, j);
}
- return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
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static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
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-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
- ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
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typedef struct {
PyCFunctionObject func;
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- PyObject *func_dict;
- PyObject *func_weakreflist;
- PyObject *func_name;
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-static int __Pyx_CyFunction_init(void);
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+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
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+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
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+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
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static void __Pyx_WriteUnraisable(const char *name, int clineno,
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static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
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-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
/* Module declarations from 'cpython.version' */
/* Module declarations from 'cpython.ref' */
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_Generator = 0;
static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0;
static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0;
static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_UnicodeDecodeError;
-static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other); /* proto */
-static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "\t";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
-static char __pyx_k__a[] = "a";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
static char __pyx_k_250[] = "MIDNSHP=X";
static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)";
static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_256[] = "/ifs/devel/pysam/pysam/csamtools.pyx";
-static char __pyx_k_257[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
-static char __pyx_k_266[] = "\n stderr is captured.\n ";
-static char __pyx_k_273[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_290[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_254[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
+static char __pyx_k_255[] = "\n stderr is captured.\n ";
+static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__PI[] = "PI";
static char __pyx_k__PL[] = "PL";
static char __pyx_k__PN[] = "PN";
+static char __pyx_k__PP[] = "PP";
static char __pyx_k__PU[] = "PU";
static char __pyx_k__RG[] = "RG";
static char __pyx_k__SM[] = "SM";
static char __pyx_k__chr[] = "chr";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
-static char __pyx_k__inf[] = "inf";
static char __pyx_k__map[] = "map";
static char __pyx_k__max[] = "max";
static char __pyx_k__min[] = "min";
-static char __pyx_k__ofd[] = "ofd";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__raw[] = "raw";
static char __pyx_k___open[] = "_open";
static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
-static char __pyx_k__retval[] = "retval";
static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__samtools[] = "samtools";
-static char __pyx_k__stderr_f[] = "stderr_f";
-static char __pyx_k__stderr_h[] = "stderr_h";
-static char __pyx_k__stdout_f[] = "stdout_f";
-static char __pyx_k__stdout_h[] = "stdout_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
static char __pyx_k__truncate[] = "truncate";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__out_stderr[] = "out_stderr";
-static char __pyx_k__out_stdout[] = "out_stdout";
static char __pyx_k__references[] = "references";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__AlignedRead[] = "AlignedRead";
static char __pyx_k__defaultdict[] = "defaultdict";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__snp_quality[] = "snp_quality";
-static char __pyx_k__stdout_save[] = "stdout_save";
static char __pyx_k__IndexedReads[] = "IndexedReads";
static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___parseRegion[] = "_parseRegion";
static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_n_s_249;
static PyObject *__pyx_kp_s_251;
+static PyObject *__pyx_kp_s_254;
+static PyObject *__pyx_kp_s_255;
static PyObject *__pyx_kp_s_256;
-static PyObject *__pyx_kp_s_257;
-static PyObject *__pyx_kp_s_266;
-static PyObject *__pyx_kp_s_273;
+static PyObject *__pyx_kp_s_262;
static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_290;
static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_n_s__PI;
static PyObject *__pyx_n_s__PL;
static PyObject *__pyx_n_s__PN;
+static PyObject *__pyx_n_s__PP;
static PyObject *__pyx_n_s__PU;
static PyObject *__pyx_n_s__PileupColumn;
static PyObject *__pyx_n_s__PileupProxy;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
static PyObject *__pyx_n_s___samtools_dispatch;
-static PyObject *__pyx_n_s__a;
static PyObject *__pyx_n_s__add_sq_text;
static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__calcsize;
static PyObject *__pyx_n_s__callback;
-static PyObject *__pyx_n_s__cargs;
static PyObject *__pyx_n_s__catch_stdout;
static PyObject *__pyx_n_s__check_header;
static PyObject *__pyx_n_s__check_sq;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
static PyObject *__pyx_n_s__index;
-static PyObject *__pyx_n_s__inf;
static PyObject *__pyx_n_s__is_del;
static PyObject *__pyx_n_s__is_head;
static PyObject *__pyx_n_s__is_tail;
static PyObject *__pyx_n_s__nextiter;
static PyObject *__pyx_n_s__nreferences;
static PyObject *__pyx_n_s__object;
-static PyObject *__pyx_n_s__ofd;
static PyObject *__pyx_n_s__offset;
static PyObject *__pyx_n_s__open;
static PyObject *__pyx_n_s__ord;
static PyObject *__pyx_n_s__os;
-static PyObject *__pyx_n_s__out_stderr;
-static PyObject *__pyx_n_s__out_stdout;
static PyObject *__pyx_n_s__pack_into;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__pileups;
static PyObject *__pyx_n_s__remove;
static PyObject *__pyx_n_s__reopen;
static PyObject *__pyx_n_s__restore;
-static PyObject *__pyx_n_s__retval;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__rname;
static PyObject *__pyx_n_s__s;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__stderr;
-static PyObject *__pyx_n_s__stderr_f;
-static PyObject *__pyx_n_s__stderr_h;
static PyObject *__pyx_n_s__stdout;
-static PyObject *__pyx_n_s__stdout_f;
-static PyObject *__pyx_n_s__stdout_h;
-static PyObject *__pyx_n_s__stdout_save;
static PyObject *__pyx_n_s__stepper;
static PyObject *__pyx_n_s__streams;
static PyObject *__pyx_n_s__strip;
static PyObject *__pyx_k_tuple_183;
static PyObject *__pyx_k_tuple_184;
static PyObject *__pyx_k_tuple_252;
-static PyObject *__pyx_k_tuple_254;
+static PyObject *__pyx_k_tuple_257;
static PyObject *__pyx_k_tuple_258;
+static PyObject *__pyx_k_tuple_259;
static PyObject *__pyx_k_tuple_260;
-static PyObject *__pyx_k_tuple_262;
-static PyObject *__pyx_k_tuple_264;
-static PyObject *__pyx_k_tuple_267;
-static PyObject *__pyx_k_tuple_269;
-static PyObject *__pyx_k_tuple_271;
-static PyObject *__pyx_k_tuple_274;
-static PyObject *__pyx_k_tuple_275;
-static PyObject *__pyx_k_tuple_276;
-static PyObject *__pyx_k_tuple_277;
-static PyObject *__pyx_k_tuple_278;
-static PyObject *__pyx_k_tuple_279;
-static PyObject *__pyx_k_tuple_281;
-static PyObject *__pyx_k_tuple_282;
-static PyObject *__pyx_k_tuple_284;
-static PyObject *__pyx_k_tuple_286;
-static PyObject *__pyx_k_tuple_288;
-static PyObject *__pyx_k_tuple_291;
-static PyObject *__pyx_k_codeobj_255;
-static PyObject *__pyx_k_codeobj_259;
-static PyObject *__pyx_k_codeobj_261;
-static PyObject *__pyx_k_codeobj_263;
-static PyObject *__pyx_k_codeobj_265;
-static PyObject *__pyx_k_codeobj_268;
-static PyObject *__pyx_k_codeobj_270;
-static PyObject *__pyx_k_codeobj_272;
-static PyObject *__pyx_k_codeobj_280;
-static PyObject *__pyx_k_codeobj_283;
-static PyObject *__pyx_k_codeobj_285;
-static PyObject *__pyx_k_codeobj_287;
-static PyObject *__pyx_k_codeobj_289;
-static PyObject *__pyx_k_codeobj_292;
-static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_k_tuple_261;
+static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
/* "csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
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if (__pyx_t_11) {
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- if (__pyx_pw_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
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Py_DECREF(o); o = 0;
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PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_9Fastafile_11__dealloc__(o);
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PyErr_Restore(etype, eval, etb);
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static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_9Fastafile_8filename_1__get__(o);
+ return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
}
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- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_2_isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6_open)},
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+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
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{0, 0, 0, 0}
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static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pw_9csamtools_9Fastafile_5__len__, /*sq_length*/
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0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pw_9csamtools_9Fastafile_5__len__, /*mp_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(o);
+ __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5query_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
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PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
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else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
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else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
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PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
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static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
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static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_10overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_12opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_14fancy_str)},
+ {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)},
+ {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)},
+ {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)},
+ {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)},
{0, 0, 0, 0}
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&__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
&__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pw_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
+ __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_11AlignedRead_5__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_11AlignedRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_Samfile *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
- if (__pyx_pw_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_7Samfile_31__dealloc__(o);
+ __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_8filename_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_10references_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_7lengths_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_6mapped_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_4text_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_6header_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_20fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_22mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_24count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_26pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_28close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_32write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_34__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_36__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_38_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_42__next__)},
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
{0, 0, 0, 0}
};
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_7Samfile_41__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_7Samfile_43__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
__pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
__pyx_getsets_9csamtools_Samfile, /*tp_getset*/
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_1n_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
}
static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(o, v);
+ return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
&__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_11PileupProxy_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_11PileupProxy_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_5indel_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_5level_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
&__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_10PileupRead_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_10PileupRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(o);
+ __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
{0, 0, 0, 0}
};
__pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
- if (__pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_4__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
{0, 0, 0, 0}
};
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
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+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
{0, 0, 0, 0}
};
__pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(o);
+ __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
{0, 0, 0, 0}
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__pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+ return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_4addReference)},
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+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
{0, 0, 0, 0}
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__pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
0, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
- if (__pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
{0, 0, 0, 0}
};
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
{0, 0, 0, 0}
};
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(o);
+ __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
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- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_4find)},
+ {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)},
+ {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)},
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};
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_12IndexedReads_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
&__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_7SNPCall_1__str__, /*tp_str*/
+ __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
#endif
};
+static PyObject *__pyx_tp_new_9csamtools___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_Generator_object *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_Generator_object *)o);
+ p->exc_type = 0;
+ p->exc_value = 0;
+ p->exc_traceback = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ Py_XDECREF(p->exc_type);
+ Py_XDECREF(p->exc_value);
+ Py_XDECREF(p->exc_traceback);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools___pyx_Generator(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ if (p->exc_type) {
+ e = (*v)(p->exc_type, a); if (e) return e;
+ }
+ if (p->exc_value) {
+ e = (*v)(p->exc_value, a); if (e) return e;
+ }
+ if (p->exc_traceback) {
+ e = (*v)(p->exc_traceback, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->exc_type);
+ p->exc_type = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_value);
+ p->exc_value = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_traceback);
+ p->exc_traceback = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools___pyx_Generator[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
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+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
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+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
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+ 0, /*nb_hex*/
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+ 0, /*nb_inplace_add*/
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+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
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+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
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+ 0, /*nb_inplace_and*/
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+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
* bam_fetch(self.samfile.x.bam,
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
* self.index,
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_79));
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* if callback:
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_82));
PyTuple_SET_ITEM(__pyx_k_tuple_83, 0, ((PyObject *)__pyx_kp_s_82));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_82));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
*
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
*
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PyTuple_SET_ITEM(__pyx_k_tuple_88, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* for x from 0 <= x < self.samfile.header.n_targets:
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* for x from 0 <= x < self.samfile.header.n_targets:
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
*
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* cdef int tid
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_94, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* cdef uint32_t total = 0
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_95));
PyTuple_SET_ITEM(__pyx_k_tuple_96, 0, ((PyObject *)__pyx_kp_s_95));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_95));
*
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- __Pyx_GOTREF(__pyx_k_tuple_97);
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
* result = {}
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
* record = fields[0]
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- __Pyx_GOTREF(__pyx_k_tuple_101);
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_100));
PyTuple_SET_ITEM(__pyx_k_tuple_101, 0, ((PyObject *)__pyx_kp_s_100));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_100));
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PyTuple_SET_ITEM(__pyx_k_tuple_118, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
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__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
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__Pyx_INCREF(((PyObject *)__pyx_kp_s_179));
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__Pyx_GIVEREF(Py_None);
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PyErr_SetObject(type, value);
+
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
Py_XDECREF(tmp_tb);
}
}
+
bad:
return;
}
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
#else
- if (unlikely(!PyUnicode_Check(key)))
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
goto invalid_keyword_type;
}
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
+
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
#else
- if (unlikely(!PyUnicode_Check(key))) {
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
#endif
goto invalid_keyword_type;
} else {
if (*name) {
values[name-argnames] = value;
} else {
+ /* unexpected keyword found */
for (name=argnames; name != first_kw_arg; name++) {
if (**name == key) goto arg_passed_twice;
#if PY_MAJOR_VERSION >= 3
{
Py_ssize_t num_expected;
const char *more_or_less;
+
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
Py_XINCREF(*value);
Py_XINCREF(*tb);
}
+
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
goto bad;
#if PY_VERSION_HEX >= 0x02050000
{
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
- 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);
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- 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);
- }
+ 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
if (level>0) {
PyObject *modname) {
PyObject *result;
PyObject *metaclass;
+
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+
/* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
return result;
}
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- }
- if (op->func_doc == 0) {
- Py_INCREF(Py_None);
- return Py_None;
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- op->func_doc = Py_None; /* Mark as deleted */
- else
- op->func_doc = value;
- Py_INCREF(op->func_doc);
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (op->func_name == NULL) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (value == NULL || !PyUnicode_Check(value)) {
-#else
- if (value == NULL || !PyString_Check(value)) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (op->func_dict == NULL) {
- op->func_dict = PyDict_New();
- if (op->func_dict == NULL)
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (value == NULL) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- PyObject* dict = PyModule_GetDict(__pyx_m);
- Py_XINCREF(dict);
- return dict;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
-{
- if (op->defaults_tuple) {
- Py_INCREF(op->defaults_tuple);
- return op->defaults_tuple;
- }
- if (op->defaults_getter) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (res) {
- Py_INCREF(res);
- op->defaults_tuple = res;
- }
- return res;
- }
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
- PyObject *closure, PyObject *module, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
+ __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
if (op == NULL)
return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
+ Py_XINCREF(self);
+ op->func.m_self = self;
Py_XINCREF(module);
op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_getter = NULL;
PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
+ return (PyObject *)op;
}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
+
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
PyObject_GC_Del(m);
}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
+
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
if (obj == Py_None)
- obj = NULL;
+ obj = NULL;
return PyMethod_New(func, obj, type);
}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
- PyObject *func_name = __Pyx_CyFunction_get_name(op);
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- func_name, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
-#endif
-}
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static int __Pyx_CyFunction_init(void)
-{
- if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+
+static int __pyx_binding_PyCFunctionType_init(void) {
+ __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
return -1;
- __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
+ }
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
return 0;
-}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, sizeof(size));
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
+
}
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
return (equals == Py_EQ);
} else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
}
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
return (equals == Py_EQ);
} else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
return (equals == Py_NE);
} else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
+ if (equals == Py_EQ)
+ return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]);
+ else
+ return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]);
} else {
int result = PyUnicode_Compare(s1, s2);
if ((result == -1) && unlikely(PyErr_Occurred()))
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
+
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
+
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
+
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
{
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
+ Py_XDECREF(self->exc_type);
+ Py_XDECREF(self->exc_value);
+ Py_XDECREF(self->exc_traceback);
+
self->exc_type = NULL;
self->exc_value = NULL;
self->exc_traceback = NULL;
- Py_XDECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_traceback);
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+
+static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
{
PyObject *retval;
- if (unlikely(self->is_running)) {
+
+ if (self->is_running) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
return NULL;
}
- if (unlikely(self->resume_label == 0)) {
- if (unlikely(value && value != Py_None)) {
+
+ if (self->resume_label == 0) {
+ if (value && value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"can't send non-None value to a "
"just-started generator");
return NULL;
}
}
- if (unlikely(self->resume_label == -1)) {
+
+ if (self->resume_label == -1) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
+
+
if (value)
__Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
else
__Pyx_Generator_ExceptionClear(self);
+
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
+
if (retval)
__Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
else
__Pyx_Generator_ExceptionClear(self);
+
return retval;
}
+
static PyObject *__Pyx_Generator_Next(PyObject *self)
{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
}
+
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
}
+
static PyObject *__Pyx_Generator_Close(PyObject *self)
{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
PyErr_SetNone(PyExc_StopIteration);
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
+
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
__Pyx_Raise(typ, val, tb, NULL);
return __Pyx_Generator_SendEx(generator, NULL);
}
-static int
-__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
-{
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_VISIT(gen->closure);
- Py_VISIT(gen->classobj);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static void
-__Pyx_Generator_dealloc(PyObject *self)
-{
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- PyObject_ClearWeakRefs(self);
- PyObject_GC_Track(self);
- if (gen->resume_label > 0) {
- Py_TYPE(gen)->tp_del(self);
- if (self->ob_refcnt > 0)
- return; /* resurrected. :( */
- }
- PyObject_GC_UnTrack(self);
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- PyObject_GC_Del(gen);
-}
-static void
-__Pyx_Generator_del(PyObject *self)
-{
- PyObject *res;
- PyObject *error_type, *error_value, *error_traceback;
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- if (gen->resume_label <= 0)
- return ;
- assert(self->ob_refcnt == 0);
- self->ob_refcnt = 1;
- __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
- res = __Pyx_Generator_Close(self);
- if (res == NULL)
- PyErr_WriteUnraisable(self);
- else
- Py_DECREF(res);
- __Pyx_ErrRestore(error_type, error_value, error_traceback);
- /* Undo the temporary resurrection; can't use DECREF here, it would
- * cause a recursive call.
- */
- assert(self->ob_refcnt > 0);
- if (--self->ob_refcnt == 0)
- return; /* this is the normal path out */
- /* close() resurrected it! Make it look like the original Py_DECREF
- * never happened.
- */
- {
- Py_ssize_t refcnt = self->ob_refcnt;
- _Py_NewReference(self);
- self->ob_refcnt = refcnt;
- }
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --self->ob_type->tp_frees;
- --self->ob_type->tp_allocs;
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
- T_INT,
- offsetof(__pyx_GeneratorObject, is_running),
- READONLY,
- NULL},
- {0, 0, 0, 0, 0}
-};
-static PyMethodDef __pyx_Generator_methods[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
- {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
- {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
- {0, 0, 0, 0}
-};
-static PyTypeObject __pyx_GeneratorType = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("generator"), /*tp_name*/
- sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- PyObject_GenericGetAttr, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- PyObject_SelfIter, /*tp_iter*/
- (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_Generator_methods, /*tp_methods*/
- __pyx_Generator_memberlist, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- __Pyx_Generator_del, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static
-__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure)
-{
- __pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
- if (gen == NULL)
- return NULL;
- gen->body = body;
- gen->closure = closure;
- Py_XINCREF(closure);
- gen->is_running = 0;
- gen->resume_label = 0;
- gen->classobj = NULL;
- gen->exc_type = NULL;
- gen->exc_value = NULL;
- gen->exc_traceback = NULL;
- gen->gi_weakreflist = NULL;
- PyObject_GC_Track(gen);
- return gen;
-}
-static int __pyx_Generator_init(void)
-{
- return PyType_Ready(&__pyx_GeneratorType);
-}
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename) {
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
static PyObject *__Pyx_ImportModule(const char *name) {
PyObject *py_name = 0;
PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
if (!py_name)
goto bad;
py_module = PyImport_Import(py_name);
}
#endif
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
+
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
+ py_srcfile = PyString_FromString(__pyx_filename);
#else
- py_srcfile = PyUnicode_FromString(filename);
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
#endif
if (!py_srcfile) goto bad;
- if (c_line) {
+ if (__pyx_clineno) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#endif
}
else {
#endif
}
if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = PyCode_New(
0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
+ #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
+ __pyx_lineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
+ if (!py_code) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
+ py_frame->f_lineno = __pyx_lineno;
PyTraceBack_Here(py_frame);
bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
return 0;
}
-
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
projects / python-pysam.git / commitdiff