From 856d7b78b3462d3c615e837047407db1a1627424 Mon Sep 17 00:00:00 2001 From: Fabio Zanini Date: Wed, 26 Jul 2017 11:47:51 -0700 Subject: [PATCH] Version bump 0.9.1 --- VERSION | 2 +- python2/HTSeq/_version.py | 2 +- python2/src/_HTSeq.c | 6034 ++++++++++++++++++++++++++++++++---- python3/HTSeq/_version.py | 2 +- python3/src/_HTSeq.c | 6125 +++++++++++++++++++++++++++++++++---- 5 files changed, 11071 insertions(+), 1094 deletions(-) diff --git a/VERSION b/VERSION index ac39a10..f374f66 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.0 +0.9.1 diff --git a/python2/HTSeq/_version.py b/python2/HTSeq/_version.py index acb984f..7ffab00 100644 --- a/python2/HTSeq/_version.py +++ b/python2/HTSeq/_version.py @@ -1 +1 @@ -__version__ = "0.9.0" \ No newline at end of file +__version__ = "0.9.1" \ No newline at end of file diff --git a/python2/src/_HTSeq.c b/python2/src/_HTSeq.c index 7887c69..b5aa357 100644 --- a/python2/src/_HTSeq.c +++ b/python2/src/_HTSeq.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.25.2 */ +/* Generated by Cython 0.26 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -7,7 +7,7 @@ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_25_2" +#define CYTHON_ABI "0_26" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -29,6 +29,7 @@ #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif +#define __PYX_COMMA , #ifndef HAVE_LONG_LONG #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) #define HAVE_LONG_LONG @@ -181,16 +182,20 @@ #ifndef Py_TPFLAGS_HAVE_FINALIZE #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); +#if PY_VERSION_HEX < 0x030700A0 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject **args, + Py_ssize_t nargs, PyObject *kwnames); #else #define __Pyx_PyCFunctionFast _PyCFunctionFast + #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords #endif #if CYTHON_FAST_PYCCALL #define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))))) #else #define __Pyx_PyFastCFunction_Check(func) 0 #endif @@ -317,6 +322,12 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif #if CYTHON_USE_ASYNC_SLOTS #if PY_VERSION_HEX >= 0x030500B1 #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods @@ -371,6 +382,35 @@ # endif #endif #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include +#endif +#ifndef CYTHON_FALLTHROUGH + #ifdef __cplusplus + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) || (defined(__GNUC__) && defined(__attribute__)) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif #ifndef CYTHON_INLINE #if defined(__clang__) @@ -478,8 +518,8 @@ typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* enc #else #define __Pyx_sst_abs(value) ((value<0) ? -value : value) #endif -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) #define __Pyx_PyBytes_FromString PyBytes_FromString @@ -492,8 +532,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize #endif -#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) @@ -615,10 +658,12 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m; static PyObject *__pyx_d; static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -653,6 +698,7 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { "python2/src/HTSeq/_HTSeq.pyx", "python2/src/HTSeq/_HTSeq.pxd", + "stringsource", "__init__.pxd", "type.pxd", }; @@ -1684,6 +1730,12 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + /* PyObjectCallMethod0.proto */ static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); @@ -1768,7 +1820,7 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); // PROTO + __Pyx_TypeInfo* type); /* BufferIndexError.proto */ static void __Pyx_RaiseBufferIndexError(int axis); @@ -1778,6 +1830,9 @@ static void __Pyx_RaiseBufferIndexError(int axis); /* BufferFallbackError.proto */ static void __Pyx_RaiseBufferFallbackError(void); +/* GetAttr3.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); + /* None.proto */ static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t, Py_ssize_t); @@ -1834,6 +1889,9 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /* bytes_index.proto */ static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds); +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + /* CallNextTpTraverse.proto */ static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); @@ -1843,6 +1901,9 @@ static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); /* SetVTable.proto */ static int __Pyx_SetVtable(PyObject *dict, void *vtable); +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); + /* GetNameInClass.proto */ static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name); @@ -1850,6 +1911,9 @@ static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name); #include "descrobject.h" static PyObject* __Pyx_Method_ClassMethod(PyObject *method); +/* CLineInTraceback.proto */ +static int __Pyx_CLineForTraceback(int c_line); + /* CodeObjectCache.proto */ typedef struct { PyCodeObject* code_object; @@ -1869,6 +1933,9 @@ 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); +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + /* BufferStructDeclare.proto */ typedef struct { Py_ssize_t shape, strides, suboffsets; @@ -1899,9 +1966,6 @@ static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - /* None.proto */ static CYTHON_INLINE long __Pyx_pow_long(long, long); @@ -2010,10 +2074,10 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); /* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); /* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *); @@ -2111,6 +2175,11 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_parse_cigar(PyObject *, int __pyx_skip_d static PyObject *__pyx_f_5HTSeq_6_HTSeq_build_cigar_list(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_build_cigar_list *__pyx_optional_args); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq__parse_SAM_optional_field_value(PyObject *); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq_quotesafe_split(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_quotesafe_split *__pyx_optional_args); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_Alignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_AlignmentWithSequenceReversal__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_BowtieAlignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_CigarOperation__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_SAM_Alignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *, PyObject *); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 }; #define __Pyx_MODULE_NAME "HTSeq._HTSeq" int __pyx_module_is_main_HTSeq___HTSeq = 0; @@ -2181,6 +2250,7 @@ static const char __pyx_k_chr[] = "chr"; static const char __pyx_k_csv[] = "csv"; static const char __pyx_k_end[] = "end"; static const char __pyx_k_int[] = "int"; +static const char __pyx_k_new[] = "__new__"; static const char __pyx_k_nmm[] = ".nmm"; static const char __pyx_k_pos[] = "pos"; static const char __pyx_k_qto[] = "qto"; @@ -2197,6 +2267,7 @@ static const char __pyx_k_Read[] = "Read"; static const char __pyx_k_aend[] = "aend"; static const char __pyx_k_auto[] = "auto"; static const char __pyx_k_copy[] = "copy"; +static const char __pyx_k_dict[] = "__dict__"; static const char __pyx_k_flag[] = "flag"; static const char __pyx_k_gzip[] = "gzip"; static const char __pyx_k_iadd[] = "__iadd__"; @@ -2265,14 +2336,17 @@ static const char __pyx_k_memmap[] = "memmap"; static const char __pyx_k_name_2[] = "name"; static const char __pyx_k_offset[] = "offset"; static const char __pyx_k_padded[] = "padded"; +static const char __pyx_k_pickle[] = "pickle"; static const char __pyx_k_reduce[] = "__reduce__"; static const char __pyx_k_ref_iv[] = "ref_iv"; +static const char __pyx_k_result[] = "result"; static const char __pyx_k_rstrip[] = "rstrip"; static const char __pyx_k_second[] = "second"; static const char __pyx_k_solexa[] = "solexa"; static const char __pyx_k_stderr[] = "stderr"; static const char __pyx_k_strand[] = "strand"; static const char __pyx_k_type_2[] = "type"; +static const char __pyx_k_update[] = "update"; static const char __pyx_k_values[] = "values"; static const char __pyx_k_xrange[] = "xrange"; static const char __pyx_k_aligned[] = "aligned"; @@ -2303,6 +2377,7 @@ static const char __pyx_k_inserted[] = "inserted"; static const char __pyx_k_is_read1[] = "is_read1"; static const char __pyx_k_is_read2[] = "is_read2"; static const char __pyx_k_overlaps[] = "overlaps"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; static const char __pyx_k_ref_left[] = "ref_left"; static const char __pyx_k_stranded[] = "stranded"; static const char __pyx_k_typecode[] = "typecode"; @@ -2315,6 +2390,7 @@ static const char __pyx_k_enumerate[] = "enumerate"; static const char __pyx_k_is_paired[] = "is_paired"; static const char __pyx_k_is_qcfail[] = "is_qcfail"; static const char __pyx_k_itertools[] = "itertools"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; static const char __pyx_k_qualscale[] = "qualscale"; static const char __pyx_k_storage_2[] = "_storage"; static const char __pyx_k_translate[] = "translate"; @@ -2332,6 +2408,7 @@ static const char __pyx_k_s_object_s[] = "<%s object '%s'>"; static const char __pyx_k_solexa_old[] = "solexa-old"; static const char __pyx_k_AlignedRead[] = "AlignedRead"; static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_PickleError[] = "PickleError"; static const char __pyx_k_bowtie_line[] = "bowtie_line"; static const char __pyx_k_cigar_pairs[] = "cigar_pairs"; static const char __pyx_k_cigartuples[] = "cigartuples"; @@ -2347,12 +2424,15 @@ static const char __pyx_k_hard_clipped[] = "hard-clipped"; static const char __pyx_k_is_duplicate[] = "is_duplicate"; static const char __pyx_k_is_secondary[] = "is_secondary"; static const char __pyx_k_mate_aligned[] = "mate_aligned"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; static const char __pyx_k_reference_id[] = "reference_id"; static const char __pyx_k_s_object_s_s[] = "<%s object, %s, %s>"; static const char __pyx_k_soft_clipped[] = "soft-clipped"; +static const char __pyx_k_stringsource[] = "stringsource"; static const char __pyx_k_chrom_vectors[] = "chrom_vectors"; static const char __pyx_k_from_SAM_line[] = "from_SAM_line"; static const char __pyx_k_mismatch_prop[] = "mismatch_prop"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; static const char __pyx_k_reference_end[] = "reference_end"; static const char __pyx_k_track_options[] = "track_options"; static const char __pyx_k_trim_left_end[] = "trim_left_end"; @@ -2373,6 +2453,7 @@ static const char __pyx_k_mate_is_reverse[] = "mate_is_reverse"; static const char __pyx_k_query_qualities[] = "query_qualities"; static const char __pyx_k_read_as_aligned[] = "read_as_aligned"; static const char __pyx_k_reference_start[] = "reference_start"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; static const char __pyx_k_start_too_small[] = "start too small"; static const char __pyx_k_template_length[] = "template_length"; static const char __pyx_k_unmatched_quote[] = "unmatched quote"; @@ -2388,6 +2469,7 @@ static const char __pyx_k_is_vector_of_sets[] = "is_vector_of_sets"; static const char __pyx_k_next_reference_id[] = "next_reference_id"; static const char __pyx_k_GenomicArray_steps[] = "GenomicArray_steps"; static const char __pyx_k_Illegal_index_type[] = "Illegal index type"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; static const char __pyx_k_characters_per_line[] = "characters_per_line"; static const char __pyx_k_raw_optional_fields[] = "raw_optional_fields"; @@ -2410,6 +2492,7 @@ static const char __pyx_k_Illegal_CIGAR_string_s[] = "Illegal CIGAR string '%s'" static const char __pyx_k_Quality_string_missing[] = "Quality string missing."; static const char __pyx_k_from_pysam_AlignedRead[] = "from_pysam_AlignedRead"; static const char __pyx_k_get_reverse_complement[] = "get_reverse_complement"; +static const char __pyx_k_pyx_unpickle_Alignment[] = "__pyx_unpickle_Alignment"; static const char __pyx_k_quote_must_be_length_1[] = "'quote' must be length 1"; static const char __pyx_k_split_must_be_length_1[] = "'split' must be length 1"; static const char __pyx_k_GenomicInterval_xranged[] = "GenomicInterval_xranged"; @@ -2426,9 +2509,14 @@ static const char __pyx_k_cigar_operation_code_dict[] = "cigar_operation_code_di static const char __pyx_k_from_pysam_AlignedSegment[] = "from_pysam_AlignedSegment"; static const char __pyx_k_s_object_s_s_aligned_to_s[] = "<%s object: %s '%s' aligned to %s>"; static const char __pyx_k_trim_right_end_with_quals[] = "trim_right_end_with_quals"; +static const char __pyx_k_pyx_unpickle_SAM_Alignment[] = "__pyx_unpickle_SAM_Alignment"; static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_pyx_unpickle_CigarOperation[] = "__pyx_unpickle_CigarOperation"; static const char __pyx_k_Inconsistent_CIGAR_operation[] = "Inconsistent CIGAR operation."; +static const char __pyx_k_python2_src_HTSeq__HTSeq_pyx[] = "python2/src/HTSeq/_HTSeq.pyx"; +static const char __pyx_k_pyx_unpickle_BowtieAlignment[] = "__pyx_unpickle_BowtieAlignment"; static const char __pyx_k_only_be_used_with_storage_type[] = " only be used with storage type 'StepVector'."; +static const char __pyx_k_pyx_unpickle_AlignmentWithSequ[] = "__pyx_unpickle_AlignmentWithSequenceReversal"; static const char __pyx_k_s_d_base_s_s_on_ref_iv_s_query[] = "< %s: %d base(s) %s on ref iv %s, query iv [%d,%d) >"; static const char __pyx_k_Automatic_adding_of_chromosomes[] = "Automatic adding of chromosomes can "; static const char __pyx_k_Illegal_base_letter_encountered[] = "Illegal base letter encountered."; @@ -2439,7 +2527,6 @@ static const char __pyx_k_assignment_to_qual_with_illegal[] = "assignment to qua static const char __pyx_k_chroms_must_be_a_list_or_a_dict[] = "'chroms' must be a list or a dict or 'auto'."; static const char __pyx_k_count_array_has_too_few_columns[] = "'count_array' has too few columns."; static const char __pyx_k_count_array_too_small_for_seque[] = "'count_array' too small for sequence."; -static const char __pyx_k_home_fabio_university_postdoc_h[] = "/home/fabio/university/postdoc/htseq/htseq/python2/src/HTSeq/_HTSeq.pyx"; static const char __pyx_k_make_translation_table_for_comp[] = "_make_translation_table_for_complementation"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_seq_and_qualstr_do_not_have_the[] = "'seq' and 'qualstr' do not have the same length."; @@ -2449,6 +2536,11 @@ static const char __pyx_k_Cannot_extend_an_interval_to_inc[] = "Cannot extend an static const char __pyx_k_Cannot_subset_to_zero_length_int[] = "Cannot subset to zero-length interval."; static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static const char __pyx_k_GenomicInterval_from_directional[] = "GenomicInterval_from_directional"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x1b[] = "Incompatible checksums (%s vs 0x1b7eeff = (_read, _read_as_sequenced, iv, read_as_aligned))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x48[] = "Incompatible checksums (%s vs 0x482c176 = (_read, _read_as_sequenced, iv, read_as_aligned, reserved, substitutions))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x77[] = "Incompatible checksums (%s vs 0x77bfdf2 = (_read, iv))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xb5[] = "Incompatible checksums (%s vs 0xb5bd29c = (query_from, query_to, ref_iv, size, type))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xf6[] = "Incompatible checksums (%s vs 0xf6933f3 = (_flag, _read, _read_as_sequenced, aQual, cigar, failed_platform_qc, inferred_insert_size, iv, mate_start, not_primary_alignment, optional_fields, original_sam_line, pcr_or_optical_duplicate, pe_which, proper_pair, read_as_aligned, supplementary))"; static const char __pyx_k_Indefinite_length_chromosomes_ca[] = "Indefinite-length chromosomes can "; static const char __pyx_k_Malformed_SAM_line_MRNM_although[] = "Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared"; static const char __pyx_k_Malformed_SAM_line_RNAME_althoug[] = "Malformed SAM line: RNAME == '*' although flag bit &0x0004 cleared"; @@ -2506,6 +2598,11 @@ static PyObject *__pyx_kp_s_Illegal_index_type_2; static PyObject *__pyx_kp_s_Illegal_quality_scale_s; static PyObject *__pyx_kp_s_Illegal_storage_mode; static PyObject *__pyx_n_s_ImportError; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x1b; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x48; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x77; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xb5; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xf6; static PyObject *__pyx_kp_s_Inconsistent_CIGAR_operation; static PyObject *__pyx_kp_s_Indefinite_length_chromosomes_ca; static PyObject *__pyx_n_s_IndexError; @@ -2523,6 +2620,7 @@ static PyObject *__pyx_n_s_NotImplementedError; static PyObject *__pyx_n_s_O; static PyObject *__pyx_n_s_P; static PyObject *__pyx_kp_s_Paired_end_read; +static PyObject *__pyx_n_s_PickleError; static PyObject *__pyx_kp_s_Please_Install_PySam_to_use_this; static PyObject *__pyx_kp_s_Quality_string_has_not_the_same; static PyObject *__pyx_kp_s_Quality_string_missing; @@ -2597,6 +2695,7 @@ static PyObject *__pyx_n_s_cigar_pairs; static PyObject *__pyx_n_s_cigar_string; static PyObject *__pyx_n_s_cigartuples; static PyObject *__pyx_n_s_class; +static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_n_s_close; static PyObject *__pyx_n_s_collections; static PyObject *__pyx_n_s_compile; @@ -2613,6 +2712,7 @@ static PyObject *__pyx_n_s_cv; static PyObject *__pyx_n_s_d; static PyObject *__pyx_n_s_deleted; static PyObject *__pyx_n_s_descr; +static PyObject *__pyx_n_s_dict; static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_empty; static PyObject *__pyx_n_s_end; @@ -2637,7 +2737,6 @@ static PyObject *__pyx_n_s_gettid; static PyObject *__pyx_n_s_getvalue; static PyObject *__pyx_n_s_gzip; static PyObject *__pyx_kp_s_hard_clipped; -static PyObject *__pyx_kp_s_home_fabio_university_postdoc_h; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_iadd; static PyObject *__pyx_n_s_iadd___locals_addval; @@ -2688,6 +2787,7 @@ static PyObject *__pyx_n_s_name_2; static PyObject *__pyx_n_s_ndarray; static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_new; static PyObject *__pyx_n_s_next_reference_id; static PyObject *__pyx_n_s_next_reference_start; static PyObject *__pyx_kp_s_nmm; @@ -2708,8 +2808,18 @@ static PyObject *__pyx_kp_s_part; static PyObject *__pyx_n_s_path; static PyObject *__pyx_n_s_pattern; static PyObject *__pyx_n_s_phred; +static PyObject *__pyx_n_s_pickle; static PyObject *__pyx_n_s_pos; static PyObject *__pyx_n_s_pysam; +static PyObject *__pyx_kp_s_python2_src_HTSeq__HTSeq_pyx; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_Alignment; +static PyObject *__pyx_n_s_pyx_unpickle_AlignmentWithSequ; +static PyObject *__pyx_n_s_pyx_unpickle_BowtieAlignment; +static PyObject *__pyx_n_s_pyx_unpickle_CigarOperation; +static PyObject *__pyx_n_s_pyx_unpickle_SAM_Alignment; static PyObject *__pyx_n_s_pyx_vtable; static PyObject *__pyx_n_s_qfrom; static PyObject *__pyx_n_s_qname; @@ -2730,11 +2840,13 @@ static PyObject *__pyx_n_s_re_cigar_codes; static PyObject *__pyx_n_s_read; static PyObject *__pyx_n_s_read_as_aligned; static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; static PyObject *__pyx_n_s_ref_iv; static PyObject *__pyx_n_s_ref_left; static PyObject *__pyx_n_s_reference_end; static PyObject *__pyx_n_s_reference_id; static PyObject *__pyx_n_s_reference_start; +static PyObject *__pyx_n_s_result; static PyObject *__pyx_n_s_revcomp_of; static PyObject *__pyx_n_s_rfrom; static PyObject *__pyx_n_s_rstrip; @@ -2762,6 +2874,7 @@ static PyObject *__pyx_n_s_seq; static PyObject *__pyx_kp_s_seq_and_qualstr_do_not_have_the; static PyObject *__pyx_kp_s_sequence_matched; static PyObject *__pyx_kp_s_sequence_mismatched; +static PyObject *__pyx_n_s_setstate_cython; static PyObject *__pyx_n_s_shape; static PyObject *__pyx_n_s_size; static PyObject *__pyx_n_s_skipped; @@ -2784,6 +2897,7 @@ static PyObject *__pyx_n_s_storage; static PyObject *__pyx_n_s_storage_2; static PyObject *__pyx_n_s_strand; static PyObject *__pyx_n_s_stranded; +static PyObject *__pyx_kp_s_stringsource; static PyObject *__pyx_n_s_sys; static PyObject *__pyx_n_s_t; static PyObject *__pyx_n_s_tags; @@ -2805,6 +2919,7 @@ static PyObject *__pyx_n_s_unknown; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_kp_s_unmatched_quote; static PyObject *__pyx_n_s_unnamed; +static PyObject *__pyx_n_s_update; static PyObject *__pyx_n_s_upper; static PyObject *__pyx_n_s_values; static PyObject *__pyx_n_s_vec; @@ -2953,6 +3068,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_5_read_4__del__(struct __pyx_obj_5 static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_4__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_6__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal___init__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_read_as_aligned, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4read___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ @@ -2961,6 +3078,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_ali static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_2__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment___init__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_bowtie_line); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ @@ -2968,6 +3087,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_4__del__(struct _ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_2__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_4__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation___init__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_type_, int __pyx_v_size, int __pyx_v_rfrom, int __pyx_v_rto, int __pyx_v_qfrom, int __pyx_v_qto, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand, int __pyx_v_check); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_2__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4check(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ @@ -2983,6 +3104,8 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from___get__(s static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_6__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_10parse_cigar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_string, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12build_cigar_list(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_pairs, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_sf); /* proto */ @@ -3024,7 +3147,14 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_17original_sam_line___g static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_16__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_18__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14quotesafe_split(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_s, PyObject *__pyx_v_split, PyObject *__pyx_v_quote); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_16__pyx_unpickle_Alignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_18__pyx_unpickle_AlignmentWithSequenceReversal(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_20__pyx_unpickle_BowtieAlignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_22__pyx_unpickle_CigarOperation(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_24__pyx_unpickle_SAM_Alignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicInterval(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ @@ -3048,6 +3178,11 @@ static PyObject *__pyx_int_10; static PyObject *__pyx_int_11; static PyObject *__pyx_int_16; static PyObject *__pyx_int_70; +static PyObject *__pyx_int_28831487; +static PyObject *__pyx_int_75678070; +static PyObject *__pyx_int_125566450; +static PyObject *__pyx_int_190567068; +static PyObject *__pyx_int_258552819; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_k_; static PyObject *__pyx_k__7; @@ -3085,11 +3220,21 @@ static PyObject *__pyx_tuple__49; static PyObject *__pyx_tuple__51; static PyObject *__pyx_tuple__53; static PyObject *__pyx_tuple__55; +static PyObject *__pyx_tuple__56; +static PyObject *__pyx_tuple__58; +static PyObject *__pyx_tuple__60; +static PyObject *__pyx_tuple__62; +static PyObject *__pyx_tuple__64; static PyObject *__pyx_codeobj__6; static PyObject *__pyx_codeobj__48; static PyObject *__pyx_codeobj__50; static PyObject *__pyx_codeobj__52; static PyObject *__pyx_codeobj__54; +static PyObject *__pyx_codeobj__57; +static PyObject *__pyx_codeobj__59; +static PyObject *__pyx_codeobj__61; +static PyObject *__pyx_codeobj__63; +static PyObject *__pyx_codeobj__65; /* "HTSeq/_HTSeq.pyx":53 * """ @@ -3122,9 +3267,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -3133,16 +3282,19 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 1); __PYX_ERR(0, 53, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_end)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 2); __PYX_ERR(0, 53, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -3155,6 +3307,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -6052,6 +6205,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_21xrange(PyObject *__ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6069,6 +6223,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_21xrange(PyObject *__ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6218,6 +6373,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_23xrange_d(PyObject * const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6235,6 +6391,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_23xrange_d(PyObject * } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7049,9 +7206,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7060,16 +7221,19 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start_d)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("GenomicInterval_from_directional", 0, 3, 4, 1); __PYX_ERR(0, 250, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_length)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("GenomicInterval_from_directional", 0, 3, 4, 2); __PYX_ERR(0, 250, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -7082,6 +7246,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -7278,8 +7443,11 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7288,11 +7456,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pos)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 2, 3, 1); __PYX_ERR(0, 276, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -7305,6 +7475,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; @@ -8066,9 +8237,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -8077,16 +8252,19 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("create", 0, 3, 4, 1); __PYX_ERR(0, 324, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("create", 0, 3, 4, 2); __PYX_ERR(0, 324, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_memmap_dir); @@ -8099,6 +8277,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -8575,7 +8754,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_3_create_view(PyObject *_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -8584,6 +8765,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_3_create_view(PyObject *_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_vec)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else { @@ -11792,10 +11974,15 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_3_ChromVector_unpickle(PyObject *__pyx_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -11804,21 +11991,25 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_3_ChromVector_unpickle(PyObject *__pyx_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_array)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 1); __PYX_ERR(0, 474, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_offset)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 2); __PYX_ERR(0, 474, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_is_vector_of_sets)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 3); __PYX_ERR(0, 474, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage_2)) != 0)) kw_args--; else { @@ -12006,10 +12197,15 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -12018,21 +12214,25 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chroms)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stranded); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode); if (value) { values[2] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage); if (value) { values[3] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 4: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_memmap_dir); @@ -12045,9 +12245,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -13541,8 +13745,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -13551,11 +13758,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_length); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start_index); @@ -13568,7 +13777,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -14172,8 +14383,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -14182,11 +14396,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_file_or_filename)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_track_options); @@ -14199,7 +14415,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -14344,7 +14562,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10write_bedgraph_file(st * f = file_or_filename * else: */ - __pyx_t_1 = PyObject_HasAttr(__pyx_v_file_or_filename, __pyx_n_s_write); if (unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 589, __pyx_L1_error) + __pyx_t_1 = __Pyx_HasAttr(__pyx_v_file_or_filename, __pyx_n_s_write); if (unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 589, __pyx_L1_error) __pyx_t_4 = (__pyx_t_1 != 0); if (__pyx_t_4) { @@ -14825,7 +15043,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10write_bedgraph_file(st * f.close() * */ - __pyx_t_4 = PyObject_HasAttr(__pyx_v_file_or_filename, __pyx_n_s_write); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(0, 603, __pyx_L1_error) + __pyx_t_4 = __Pyx_HasAttr(__pyx_v_file_or_filename, __pyx_n_s_write); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(0, 603, __pyx_L1_error) __pyx_t_1 = ((!(__pyx_t_4 != 0)) != 0); if (__pyx_t_1) { @@ -15373,8 +15591,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_5_GenomicArray_unpickle(PyObject *__pyx const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -15383,11 +15604,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_5_GenomicArray_unpickle(PyObject *__pyx case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stranded)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_GenomicArray_unpickle", 1, 3, 3, 1); __PYX_ERR(0, 610, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom_vectors)) != 0)) kw_args--; else { @@ -15842,7 +16065,9 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -15851,6 +16076,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_seq)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_name_2); @@ -15863,6 +16089,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -16775,7 +17002,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -16784,6 +17013,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_fasta_file)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_characters_per_line); @@ -16796,6 +17026,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -17436,7 +17667,7 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_8Sequence_add_bases_to_count_array(struc * for i in xrange(seq_length): * b = seq_cstr[i] */ - __pyx_t_8 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_8; /* "HTSeq/_HTSeq.pyx":722 @@ -17966,7 +18197,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 747, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 747, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":748 @@ -17976,7 +18207,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 748, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 748, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":749 @@ -18144,7 +18375,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -18153,6 +18386,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_mismatch_prop); @@ -18165,6 +18399,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -18413,7 +18648,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 771, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 771, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":772 @@ -18423,7 +18658,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 772, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 772, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":773 @@ -18591,7 +18826,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -18600,6 +18837,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_mismatch_prop); @@ -18612,6 +18850,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -19016,9 +19255,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -19027,16 +19270,19 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_seq)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_name_2)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 1); __PYX_ERR(0, 794, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_qualstr)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 2); __PYX_ERR(0, 794, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_qualscale); @@ -19049,6 +19295,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -19527,7 +19774,7 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities__fill_qual_arr(s * if self._qualscale == "phred": * for i in xrange(seq_len): */ - __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 822, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 822, __pyx_L1_error) __pyx_v_qualstr = __pyx_t_12; /* "HTSeq/_HTSeq.pyx":823 @@ -20430,7 +20677,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_7qualstr___get_ * cdef int i * cdef numpy.ndarray[numpy.int_t, ndim = 1] qual_array */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 871, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 871, __pyx_L1_error) __pyx_v_qualstr_phred_cstr = __pyx_t_1; /* "HTSeq/_HTSeq.pyx":874 @@ -20553,7 +20800,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_7qualstr___get_ * if self._qualarr is None: * self._fill_qual_arr() */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 882, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 882, __pyx_L1_error) __pyx_v_qualstr_phred_cstr = __pyx_t_1; /* "HTSeq/_HTSeq.pyx":883 @@ -20741,7 +20988,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_6write_to_fastq * fastq_file.write("@%s %s\n" % (self.name, self.descr)) * else: */ - __pyx_t_2 = PyObject_HasAttr(((PyObject *)__pyx_v_self), __pyx_n_s_descr); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 891, __pyx_L1_error) + __pyx_t_2 = __Pyx_HasAttr(((PyObject *)__pyx_v_self), __pyx_n_s_descr); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 891, __pyx_L1_error) __pyx_t_3 = (__pyx_t_2 != 0); if (__pyx_t_3) { } else { @@ -21077,6 +21324,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_9get_fastq_str( const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -21094,6 +21342,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_9get_fastq_str( } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22101,7 +22350,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 948, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 948, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":949 @@ -22111,7 +22360,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 949, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 949, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":950 @@ -22351,7 +22600,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22360,6 +22611,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_max_mm_qual); @@ -22372,6 +22624,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -22630,7 +22883,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 976, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 976, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":977 @@ -22640,7 +22893,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 977, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 977, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":978 @@ -22880,7 +23133,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22889,6 +23144,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_max_mm_qual); @@ -22901,6 +23157,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -23131,7 +23388,9 @@ static int __pyx_pw_5HTSeq_6_HTSeq_9Alignment_1__init__(PyObject *__pyx_v_self, const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -23140,6 +23399,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_9Alignment_1__init__(PyObject *__pyx_v_self, case 0: if 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PyDict_GetItem(__pyx_kwds, __pyx_n_s_ref_left); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom); if (value) { values[2] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -26732,8 +28302,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11parse_cigar(PyObject *__pyx_self, PyO } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -27653,9 +29226,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_13build_cigar_list(PyObject *__pyx_self const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -27664,16 +29241,19 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_13build_cigar_list(PyObject *__pyx_self case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_cigar_pairs)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_ref_left); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom); if (value) { values[2] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -27686,8 +29266,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_13build_cigar_list(PyObject *__pyx_self } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -28359,7 +29942,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L10_try_end; + goto __pyx_L8_try_end; __pyx_L3_error:; __Pyx_PyThreadState_assign __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -28429,7 +30012,7 @@ static PyObject 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-28817,7 +30400,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment * a.cigartuples = [(cigar_operation_code_dict[c.type], c.size) * for c in self.cigar] */ - goto __pyx_L17; + goto __pyx_L15; } /* "HTSeq/_HTSeq.pyx":1266 @@ -28839,7 +30422,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment */ if (__Pyx_PyObject_SetAttrStr(__pyx_v_a, __pyx_n_s_reference_id, __pyx_int_neg_1) < 0) __PYX_ERR(0, 1267, __pyx_L1_error) } - __pyx_L17:; + __pyx_L15:; /* "HTSeq/_HTSeq.pyx":1268 * a.reference_start = -1 @@ -28928,7 +30511,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment * a.next_reference_id = sf.gettid(self.mate_start.chrom) * a.next_reference_start = self.mate_start.start */ - goto __pyx_L20; + goto __pyx_L18; } /* "HTSeq/_HTSeq.pyx":1272 @@ -28950,7 +30533,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment */ if (__Pyx_PyObject_SetAttrStr(__pyx_v_a, 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self.cigar] */ - goto __pyx_L13; + goto __pyx_L11; } /* "HTSeq/_HTSeq.pyx":1298 @@ -29455,7 +31038,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_2to_pysam_AlignedRead(s */ if (__Pyx_PyObject_SetAttrStr(__pyx_v_a, __pyx_n_s_tid, __pyx_int_neg_1) < 0) __PYX_ERR(0, 1299, __pyx_L1_error) } - __pyx_L13:; + __pyx_L11:; /* "HTSeq/_HTSeq.pyx":1300 * a.pos = -1 @@ -29544,7 +31127,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_2to_pysam_AlignedRead(s * a.mrnm = sf.gettid(self.mate_start.chrom) * a.mpos = self.mate_start.start */ - goto __pyx_L16; + goto __pyx_L14; } /* "HTSeq/_HTSeq.pyx":1304 @@ -29566,7 +31149,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_2to_pysam_AlignedRead(s */ if (__Pyx_PyObject_SetAttrStr(__pyx_v_a, __pyx_n_s_mpos, __pyx_int_neg_1) < 0) __PYX_ERR(0, 1305, __pyx_L1_error) } - __pyx_L16:; + __pyx_L14:; /* "HTSeq/_HTSeq.pyx":1306 * a.mrnm = -1 @@ -29630,7 +31213,9 @@ static PyObject 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PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -30693,6 +32281,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_7from_pysam_AlignedSegm case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_read)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_samfile)) != 0)) kw_args--; else { @@ -35241,6 +36830,429 @@ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_4__del__(st return __pyx_r; } +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * cdef bint use_setstate + * state = (self._flag, self._read, self._read_as_sequenced, self.aQual, self.cigar, self.failed_platform_qc, self.inferred_insert_size, self.iv, self.mate_start, self.not_primary_alignment, self.optional_fields, self.original_sam_line, self.pcr_or_optical_duplicate, self.pe_which, self.proper_pair, 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self.mate_start, self.not_primary_alignment, self.optional_fields, self.original_sam_line, self.pcr_or_optical_duplicate, self.pe_which, self.proper_pair, self.read_as_aligned, self.supplementary) + * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< + * if _dict is not None: + * state += _dict, + */ + __pyx_t_9 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_9)) __PYX_ERR(2, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __pyx_v__dict = __pyx_t_9; + __pyx_t_9 = 0; + + /* "(tree fragment)":5 + * state = (self._flag, self._read, self._read_as_sequenced, self.aQual, self.cigar, self.failed_platform_qc, self.inferred_insert_size, self.iv, self.mate_start, self.not_primary_alignment, self.optional_fields, self.original_sam_line, self.pcr_or_optical_duplicate, self.pe_which, self.proper_pair, self.read_as_aligned, self.supplementary) + * _dict = getattr(self, '__dict__', None) + * if _dict is not None: # <<<<<<<<<<<<<< + * state += _dict, 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__PYX_ERR(2, 994, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(3, 994, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); @@ -38044,11 +42700,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { * * cdef inline int import_ufunc() except -1: */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 995, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(3, 995, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 995, __pyx_L5_except_error) + __PYX_ERR(3, 995, __pyx_L5_except_error) } goto __pyx_L5_except_error; __pyx_L5_except_error:; @@ -38066,7 +42722,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); goto __pyx_L1_error; - __pyx_L10_try_end:; + __pyx_L8_try_end:; } /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 @@ -38136,7 +42792,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { * except Exception: * raise ImportError("numpy.core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(2, 999, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(3, 999, __pyx_L3_error) /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * @@ -38149,7 +42805,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L10_try_end; + goto __pyx_L8_try_end; __pyx_L3_error:; __Pyx_PyThreadState_assign @@ -38162,7 +42818,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1000, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(3, 1000, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); @@ -38172,11 +42828,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__46, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1001, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__46, NULL); if 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(!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38562,7 +43218,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_Sequence(PyTypeObject *t, CYTHON_UN static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Sequence(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38731,7 +43387,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_SequenceWithQualities(PyTypeObject static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SequenceWithQualities(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38935,7 +43591,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_Alignment(PyTypeObject *t, CYTHON_U static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38949,10 +43605,10 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment(PyObject *o, visitproc v, int e; struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; if (p->_read) { - e = (*v)(((PyObject*)p->_read), a); if (e) return e; + e = (*v)(((PyObject *)p->_read), a); if (e) return e; } if (p->iv) { - e = (*v)(((PyObject*)p->iv), a); if (e) return e; + e = (*v)(((PyObject *)p->iv), a); if (e) return e; } return 0; } @@ -39008,6 +43664,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_9Alignment_iv(PyObject *o, PyObject *v, } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_Alignment[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_7__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39091,7 +43749,7 @@ static PyObject 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*)p->read_as_aligned), a); if (e) return e; } if (p->_read_as_sequenced) { - e = (*v)(((PyObject*)p->_read_as_sequenced), a); if (e) return e; + e = (*v)(((PyObject *)p->_read_as_sequenced), a); if (e) return e; } return 0; } @@ -39159,6 +43817,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_3__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_5__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39247,7 +43907,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_SAM_Alignment(PyTypeObject *t, PyOb static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39269,7 +43929,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o, visitproc e = (*v)(p->cigar, a); if (e) return e; } if (p->mate_start) { - e = (*v)(((PyObject*)p->mate_start), a); if (e) return e; + e = (*v)(((PyObject *)p->mate_start), a); if (e) return e; } if (p->optional_fields) { e = (*v)(p->optional_fields, a); if (e) return e; @@ -39478,6 +44138,8 @@ static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_SAM_Alignment[] = { {"get_sam_line", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_11get_sam_line, METH_NOARGS, 0}, {"optional_field", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_13optional_field, METH_O, 0}, {"raw_optional_fields", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15raw_optional_fields, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_17__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_19__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39585,7 +44247,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_ChromVector(PyTypeObject *t, CYTHON static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_ChromVector(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p = (struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39603,7 +44265,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_ChromVector(PyObject *o, visitproc v e = (*v)(p->array, a); if (e) return e; } if (p->iv) { - e = (*v)(((PyObject*)p->iv), a); if (e) return e; + e = (*v)(((PyObject *)p->iv), a); if (e) return e; } return 0; } @@ -39728,7 +44390,7 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ @@ -39744,7 +44406,7 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_coerce*/ #endif 0, /*nb_int*/ @@ -39754,16 +44416,16 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*reserved*/ #endif 0, /*nb_float*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_oct*/ #endif - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_hex*/ #endif __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_9__iadd__, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ @@ -39883,7 +44545,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicArray(PyTypeObject *t, CYTHO static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicArray(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40082,7 +44744,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_BowtieAlignment(PyTypeObject *t, Py static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_BowtieAlignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40120,6 +44782,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions(PyObject } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_BowtieAlignment[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_3__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_5__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -40209,7 +44873,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_CigarOperation(PyTypeObject *t, CYT static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_CigarOperation(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40223,7 +44887,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_CigarOperation(PyObject *o, visitpro int e; struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; if (p->ref_iv) { - e = (*v)(((PyObject*)p->ref_iv), a); if (e) return e; + e = (*v)(((PyObject *)p->ref_iv), a); if (e) return e; } return 0; } @@ -40307,6 +44971,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_to(PyObject *o, P static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_CigarOperation[] = { {"check", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_5check, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_7__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_9__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -40542,6 +45208,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Illegal_quality_scale_s, __pyx_k_Illegal_quality_scale_s, sizeof(__pyx_k_Illegal_quality_scale_s), 0, 0, 1, 0}, {&__pyx_kp_s_Illegal_storage_mode, __pyx_k_Illegal_storage_mode, sizeof(__pyx_k_Illegal_storage_mode), 0, 0, 1, 0}, {&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x1b, __pyx_k_Incompatible_checksums_s_vs_0x1b, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x1b), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x48, __pyx_k_Incompatible_checksums_s_vs_0x48, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x48), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x77, __pyx_k_Incompatible_checksums_s_vs_0x77, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x77), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0xb5, __pyx_k_Incompatible_checksums_s_vs_0xb5, sizeof(__pyx_k_Incompatible_checksums_s_vs_0xb5), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0xf6, __pyx_k_Incompatible_checksums_s_vs_0xf6, sizeof(__pyx_k_Incompatible_checksums_s_vs_0xf6), 0, 0, 1, 0}, {&__pyx_kp_s_Inconsistent_CIGAR_operation, __pyx_k_Inconsistent_CIGAR_operation, sizeof(__pyx_k_Inconsistent_CIGAR_operation), 0, 0, 1, 0}, {&__pyx_kp_s_Indefinite_length_chromosomes_ca, __pyx_k_Indefinite_length_chromosomes_ca, sizeof(__pyx_k_Indefinite_length_chromosomes_ca), 0, 0, 1, 0}, {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, @@ -40559,6 +45230,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_O, __pyx_k_O, sizeof(__pyx_k_O), 0, 0, 1, 1}, {&__pyx_n_s_P, __pyx_k_P, sizeof(__pyx_k_P), 0, 0, 1, 1}, {&__pyx_kp_s_Paired_end_read, __pyx_k_Paired_end_read, sizeof(__pyx_k_Paired_end_read), 0, 0, 1, 0}, + {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1}, {&__pyx_kp_s_Please_Install_PySam_to_use_this, __pyx_k_Please_Install_PySam_to_use_this, sizeof(__pyx_k_Please_Install_PySam_to_use_this), 0, 0, 1, 0}, {&__pyx_kp_s_Quality_string_has_not_the_same, __pyx_k_Quality_string_has_not_the_same, sizeof(__pyx_k_Quality_string_has_not_the_same), 0, 0, 1, 0}, {&__pyx_kp_s_Quality_string_missing, __pyx_k_Quality_string_missing, sizeof(__pyx_k_Quality_string_missing), 0, 0, 1, 0}, @@ -40633,6 +45305,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_cigar_string, __pyx_k_cigar_string, sizeof(__pyx_k_cigar_string), 0, 0, 1, 1}, {&__pyx_n_s_cigartuples, __pyx_k_cigartuples, sizeof(__pyx_k_cigartuples), 0, 0, 1, 1}, {&__pyx_n_s_class, __pyx_k_class, sizeof(__pyx_k_class), 0, 0, 1, 1}, + {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, {&__pyx_n_s_collections, __pyx_k_collections, sizeof(__pyx_k_collections), 0, 0, 1, 1}, {&__pyx_n_s_compile, __pyx_k_compile, sizeof(__pyx_k_compile), 0, 0, 1, 1}, @@ -40649,6 +45322,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_d, __pyx_k_d, sizeof(__pyx_k_d), 0, 0, 1, 1}, {&__pyx_n_s_deleted, __pyx_k_deleted, sizeof(__pyx_k_deleted), 0, 0, 1, 1}, {&__pyx_n_s_descr, __pyx_k_descr, sizeof(__pyx_k_descr), 0, 0, 1, 1}, + {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, @@ -40673,7 +45347,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_getvalue, __pyx_k_getvalue, sizeof(__pyx_k_getvalue), 0, 0, 1, 1}, {&__pyx_n_s_gzip, __pyx_k_gzip, sizeof(__pyx_k_gzip), 0, 0, 1, 1}, {&__pyx_kp_s_hard_clipped, __pyx_k_hard_clipped, sizeof(__pyx_k_hard_clipped), 0, 0, 1, 0}, - {&__pyx_kp_s_home_fabio_university_postdoc_h, __pyx_k_home_fabio_university_postdoc_h, sizeof(__pyx_k_home_fabio_university_postdoc_h), 0, 0, 1, 0}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, {&__pyx_n_s_iadd, __pyx_k_iadd, sizeof(__pyx_k_iadd), 0, 0, 1, 1}, {&__pyx_n_s_iadd___locals_addval, __pyx_k_iadd___locals_addval, sizeof(__pyx_k_iadd___locals_addval), 0, 0, 1, 1}, @@ -40724,6 +45397,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_ndarray, __pyx_k_ndarray, sizeof(__pyx_k_ndarray), 0, 0, 1, 1}, {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0}, + {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1}, {&__pyx_n_s_next_reference_id, __pyx_k_next_reference_id, sizeof(__pyx_k_next_reference_id), 0, 0, 1, 1}, {&__pyx_n_s_next_reference_start, __pyx_k_next_reference_start, sizeof(__pyx_k_next_reference_start), 0, 0, 1, 1}, {&__pyx_kp_s_nmm, __pyx_k_nmm, sizeof(__pyx_k_nmm), 0, 0, 1, 0}, @@ -40744,8 +45418,18 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1}, {&__pyx_n_s_pattern, __pyx_k_pattern, sizeof(__pyx_k_pattern), 0, 0, 1, 1}, {&__pyx_n_s_phred, __pyx_k_phred, sizeof(__pyx_k_phred), 0, 0, 1, 1}, + {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1}, {&__pyx_n_s_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 0, 1, 1}, {&__pyx_n_s_pysam, __pyx_k_pysam, sizeof(__pyx_k_pysam), 0, 0, 1, 1}, + {&__pyx_kp_s_python2_src_HTSeq__HTSeq_pyx, __pyx_k_python2_src_HTSeq__HTSeq_pyx, sizeof(__pyx_k_python2_src_HTSeq__HTSeq_pyx), 0, 0, 1, 0}, + {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_Alignment, __pyx_k_pyx_unpickle_Alignment, sizeof(__pyx_k_pyx_unpickle_Alignment), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_AlignmentWithSequ, __pyx_k_pyx_unpickle_AlignmentWithSequ, sizeof(__pyx_k_pyx_unpickle_AlignmentWithSequ), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_BowtieAlignment, __pyx_k_pyx_unpickle_BowtieAlignment, sizeof(__pyx_k_pyx_unpickle_BowtieAlignment), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_CigarOperation, __pyx_k_pyx_unpickle_CigarOperation, sizeof(__pyx_k_pyx_unpickle_CigarOperation), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_SAM_Alignment, __pyx_k_pyx_unpickle_SAM_Alignment, sizeof(__pyx_k_pyx_unpickle_SAM_Alignment), 0, 0, 1, 1}, {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1}, {&__pyx_n_s_qfrom, __pyx_k_qfrom, sizeof(__pyx_k_qfrom), 0, 0, 1, 1}, {&__pyx_n_s_qname, __pyx_k_qname, sizeof(__pyx_k_qname), 0, 0, 1, 1}, @@ -40766,11 +45450,13 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1}, {&__pyx_n_s_read_as_aligned, __pyx_k_read_as_aligned, sizeof(__pyx_k_read_as_aligned), 0, 0, 1, 1}, {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1}, {&__pyx_n_s_ref_iv, __pyx_k_ref_iv, sizeof(__pyx_k_ref_iv), 0, 0, 1, 1}, {&__pyx_n_s_ref_left, __pyx_k_ref_left, sizeof(__pyx_k_ref_left), 0, 0, 1, 1}, {&__pyx_n_s_reference_end, __pyx_k_reference_end, sizeof(__pyx_k_reference_end), 0, 0, 1, 1}, {&__pyx_n_s_reference_id, __pyx_k_reference_id, sizeof(__pyx_k_reference_id), 0, 0, 1, 1}, {&__pyx_n_s_reference_start, __pyx_k_reference_start, sizeof(__pyx_k_reference_start), 0, 0, 1, 1}, + {&__pyx_n_s_result, __pyx_k_result, sizeof(__pyx_k_result), 0, 0, 1, 1}, {&__pyx_n_s_revcomp_of, __pyx_k_revcomp_of, sizeof(__pyx_k_revcomp_of), 0, 0, 1, 1}, {&__pyx_n_s_rfrom, __pyx_k_rfrom, sizeof(__pyx_k_rfrom), 0, 0, 1, 1}, {&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1}, @@ -40798,6 +45484,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_seq_and_qualstr_do_not_have_the, __pyx_k_seq_and_qualstr_do_not_have_the, sizeof(__pyx_k_seq_and_qualstr_do_not_have_the), 0, 0, 1, 0}, {&__pyx_kp_s_sequence_matched, __pyx_k_sequence_matched, sizeof(__pyx_k_sequence_matched), 0, 0, 1, 0}, {&__pyx_kp_s_sequence_mismatched, __pyx_k_sequence_mismatched, sizeof(__pyx_k_sequence_mismatched), 0, 0, 1, 0}, + {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, {&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1}, {&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1}, {&__pyx_n_s_skipped, __pyx_k_skipped, sizeof(__pyx_k_skipped), 0, 0, 1, 1}, @@ -40820,6 +45507,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_storage_2, __pyx_k_storage_2, sizeof(__pyx_k_storage_2), 0, 0, 1, 1}, {&__pyx_n_s_strand, __pyx_k_strand, sizeof(__pyx_k_strand), 0, 0, 1, 1}, {&__pyx_n_s_stranded, __pyx_k_stranded, sizeof(__pyx_k_stranded), 0, 0, 1, 1}, + {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0}, {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1}, {&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1}, 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__pyx_L1_error:; @@ -41344,6 +46064,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error) Py_INCREF(__pyx_d); __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_cython_runtime = PyImport_AddModule((char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error) #if CYTHON_COMPILING_IN_PYPY Py_INCREF(__pyx_b); #endif @@ -41441,16 +46162,19 @@ PyMODINIT_FUNC PyInit__HTSeq(void) if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_Alignment) < 0) __PYX_ERR(0, 1000, __pyx_L1_error) __pyx_type_5HTSeq_6_HTSeq_Alignment.tp_print = 0; if (PyObject_SetAttrString(__pyx_m, "Alignment", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_Alignment) < 0) __PYX_ERR(0, 1000, __pyx_L1_error) + if (__Pyx_setup_reduce((PyObject*)&__pyx_type_5HTSeq_6_HTSeq_Alignment) < 0) __PYX_ERR(0, 1000, __pyx_L1_error) __pyx_ptype_5HTSeq_6_HTSeq_Alignment = 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< 0) __PYX_ERR(0, 1073, __pyx_L1_error) __pyx_ptype_5HTSeq_6_HTSeq_BowtieAlignment = &__pyx_type_5HTSeq_6_HTSeq_BowtieAlignment; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_CigarOperation) < 0) __PYX_ERR(0, 1109, __pyx_L1_error) __pyx_type_5HTSeq_6_HTSeq_CigarOperation.tp_print = 0; if (PyObject_SetAttrString(__pyx_m, "CigarOperation", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_CigarOperation) < 0) __PYX_ERR(0, 1109, __pyx_L1_error) + if (__Pyx_setup_reduce((PyObject*)&__pyx_type_5HTSeq_6_HTSeq_CigarOperation) < 0) __PYX_ERR(0, 1109, __pyx_L1_error) __pyx_ptype_5HTSeq_6_HTSeq_CigarOperation = &__pyx_type_5HTSeq_6_HTSeq_CigarOperation; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq___pyx_scope_struct____iadd__) < 0) __PYX_ERR(0, 439, __pyx_L1_error) __pyx_type_5HTSeq_6_HTSeq___pyx_scope_struct____iadd__.tp_print = 0; @@ -41479,12 +46205,12 @@ PyMODINIT_FUNC PyInit__HTSeq(void) #else sizeof(PyHeapTypeObject), #endif - 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) __PYX_ERR(3, 9, 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__Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) __PYX_ERR(3, 155, __pyx_L1_error) + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) __PYX_ERR(3, 168, __pyx_L1_error) + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) __PYX_ERR(3, 172, __pyx_L1_error) + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) __PYX_ERR(3, 181, __pyx_L1_error) + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) __PYX_ERR(3, 861, __pyx_L1_error) /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ @@ -42110,6 +46836,60 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; PyType_Modified(__pyx_ptype_5HTSeq_6_HTSeq_SAM_Alignment); + /* "(tree fragment)":1 + * def __pyx_unpickle_Alignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0x77bfdf2: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_17__pyx_unpickle_Alignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_Alignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":9 + * __pyx_unpickle_Alignment__set_state( result, __pyx_state) + * return result + * cdef __pyx_unpickle_Alignment__set_state(Alignment result, tuple __pyx_state): # <<<<<<<<<<<<<< + * result._read = __pyx_state[0]; result.iv = __pyx_state[1] + * if hasattr(result, '__dict__'): + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_19__pyx_unpickle_AlignmentWithSequenceReversal, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_AlignmentWithSequ, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":1 + * def __pyx_unpickle_BowtieAlignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0x482c176: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_21__pyx_unpickle_BowtieAlignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_BowtieAlignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":9 + * __pyx_unpickle_BowtieAlignment__set_state( result, __pyx_state) + * return result + * cdef __pyx_unpickle_BowtieAlignment__set_state(BowtieAlignment result, tuple __pyx_state): # <<<<<<<<<<<<<< + * result._read = __pyx_state[0]; result._read_as_sequenced = __pyx_state[1]; result.iv = __pyx_state[2]; result.read_as_aligned = __pyx_state[3]; result.reserved = __pyx_state[4]; result.substitutions = __pyx_state[5] + * if hasattr(result, '__dict__'): + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_23__pyx_unpickle_CigarOperation, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_CigarOperation, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":1 + * def __pyx_unpickle_SAM_Alignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0xf6933f3: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_25__pyx_unpickle_SAM_Alignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_SAM_Alignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + /* "HTSeq/_HTSeq.pyx":1 * import sys # <<<<<<<<<<<<<< * import os @@ -42140,7 +46920,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_XDECREF(__pyx_t_8); if (__pyx_m) { if (__pyx_d) { - __Pyx_AddTraceback("init HTSeq._HTSeq", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init HTSeq._HTSeq", 0, __pyx_lineno, __pyx_filename); } Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { @@ -42564,17 +47344,22 @@ static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, P PyCFunctionObject *func = (PyCFunctionObject*)func_obj; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))); assert(nargs >= 0); assert(nargs == 0 || args != NULL); /* _PyCFunction_FastCallDict() must not be called with an exception set, because it may clear it (directly or indirectly) and so the caller loses its exception */ assert(!PyErr_Occurred()); - return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs); + } } -#endif // CYTHON_FAST_PYCCALL +#endif /* PyFunctionFastCall */ #if CYTHON_FAST_PYCALL @@ -42693,8 +47478,8 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_LeaveRecursiveCall(); return result; } -#endif // CPython < 3.6 -#endif // CYTHON_FAST_PYCALL +#endif +#endif /* PyObjectCall */ #if CYTHON_COMPILING_IN_CPYTHON @@ -42754,11 +47539,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec return __Pyx_PyFunction_FastCall(func, &arg, 1); } #endif -#ifdef __Pyx_CyFunction_USED - if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { -#else if (likely(PyCFunction_Check(func))) { -#endif if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { return __Pyx_PyObject_CallMethO(func, arg); #if CYTHON_FAST_PYCCALL @@ -42781,7 +47562,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec #endif /* PyObjectCallNoArg */ - #if CYTHON_COMPILING_IN_CPYTHON + #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { #if CYTHON_FAST_PYCALL if (PyFunction_Check(func)) { @@ -42802,20 +47583,20 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { #endif /* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } /* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", index, (index == 1) ? "" : "s"); } /* IterFinish */ - static CYTHON_INLINE int __Pyx_IterFinish(void) { + static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_FAST_THREAD_STATE PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; @@ -42850,7 +47631,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* UnpackItemEndCheck */ - static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); @@ -42862,7 +47643,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* GetModuleGlobalName */ - static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { PyObject *result; #if !CYTHON_AVOID_BORROWED_REFS result = PyDict_GetItem(__pyx_d, name); @@ -42880,7 +47661,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* BytesEquals */ - static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else @@ -42898,7 +47679,16 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } else if (length == 1) { return (equals == Py_EQ); } else { - int result = memcmp(ps1, ps2, (size_t)length); + int result; +#if CYTHON_USE_UNICODE_INTERNALS + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { @@ -42918,7 +47708,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* UnicodeEquals */ - static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { + static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else @@ -42958,6 +47748,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { goto return_ne; } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif kind = __Pyx_PyUnicode_KIND(s1); if (kind != __Pyx_PyUnicode_KIND(s2)) { goto return_ne; @@ -43002,7 +47807,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* SliceObject */ - static CYTHON_INLINE int __Pyx_PyObject_SetSlice(PyObject* obj, PyObject* value, + static CYTHON_INLINE int __Pyx_PyObject_SetSlice(PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { @@ -43100,7 +47905,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { if (op1 == op2) { Py_RETURN_TRUE; @@ -43185,7 +47990,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED #endif /* GetItemInt */ - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; r = PyObject_GetItem(o, j); @@ -43196,9 +48001,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, i); + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); Py_INCREF(r); return r; } @@ -43211,9 +48019,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, i); + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); Py_INCREF(r); return r; } @@ -43266,7 +48077,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); return 0; @@ -43279,17 +48090,17 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } /* None */ - static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { + static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } /* SliceObject */ - static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, + static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { @@ -43386,7 +48197,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* FetchCommonType */ - static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { PyObject* fake_module; PyTypeObject* cached_type = NULL; fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); @@ -43425,7 +48236,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* CythonFunction */ - static PyObject * + static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { @@ -44007,8 +48818,39 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py Py_INCREF(dict); } +/* GetAttr */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_COMPILING_IN_CPYTHON +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +/* HasAttr */ + static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { + PyObject *r; + if (unlikely(!__Pyx_PyBaseString_Check(n))) { + PyErr_SetString(PyExc_TypeError, + "hasattr(): attribute name must be string"); + return -1; + } + r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + /* PyObjectCallMethod0 */ - static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { + static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { PyObject *method, *result = NULL; method = __Pyx_PyObject_GetAttrStr(obj, method_name); if (unlikely(!method)) goto bad; @@ -44030,12 +48872,12 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } /* UnpackTupleError */ - static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { + static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { @@ -44046,7 +48888,7 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* UnpackTuple2 */ - static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, + static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int is_tuple, int has_known_size, int decref_tuple) { Py_ssize_t index; PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; @@ -44093,17 +48935,32 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* dict_iter */ - static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, + static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_source_is_dict) { is_dict = is_dict || likely(PyDict_CheckExact(iterable)); *p_source_is_dict = is_dict; -#if !CYTHON_COMPILING_IN_PYPY if (is_dict) { +#if !CYTHON_COMPILING_IN_PYPY *p_orig_length = PyDict_Size(iterable); Py_INCREF(iterable); return iterable; - } +#elif PY_MAJOR_VERSION >= 3 + static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; + const char *name = PyUnicode_AsUTF8(method_name); + PyObject **pp = NULL; + if (strcmp(name, "iteritems") == 0) pp = &py_items; + else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; + else if (strcmp(name, "itervalues") == 0) pp = &py_values; + if (pp) { + if (!*pp) { + *pp = PyUnicode_FromString(name + 4); + if (!*pp) + return NULL; + } + method_name = *pp; + } #endif + } *p_orig_length = 0; if (method_name) { PyObject* iter; @@ -44189,7 +49046,7 @@ static CYTHON_INLINE int __Pyx_dict_iter_next( } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { @@ -44305,7 +49162,7 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U #endif /* SetItemInt */ - static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { + static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { int r; if (!j) return -1; r = PyObject_SetItem(o, j, v); @@ -44353,14 +49210,14 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje } /* StringJoin */ - #if !CYTHON_COMPILING_IN_CPYTHON + #if !CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL); } #endif /* bytes_tailmatch */ - static int __Pyx_PyBytes_SingleTailmatch(PyObject* self, PyObject* arg, + static int __Pyx_PyBytes_SingleTailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, Py_ssize_t end, int direction) { const char* self_ptr = PyBytes_AS_STRING(self); Py_ssize_t self_len = PyBytes_GET_SIZE(self); @@ -44431,7 +49288,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, } /* unicode_tailmatch */ - static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr, + static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr, Py_ssize_t start, Py_ssize_t end, int direction) { if (unlikely(PyTuple_Check(substr))) { Py_ssize_t i, count = PyTuple_GET_SIZE(substr); @@ -44456,7 +49313,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, } /* str_tailmatch */ - static CYTHON_INLINE int __Pyx_PyStr_Tailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, + static CYTHON_INLINE int __Pyx_PyStr_Tailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, Py_ssize_t end, int direction) { if (PY_MAJOR_VERSION < 3) @@ -44466,7 +49323,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { @@ -44582,7 +49439,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED #endif /* BufferFormatCheck */ - static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } @@ -45132,26 +49989,41 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { } /* BufferIndexError */ - static void __Pyx_RaiseBufferIndexError(int axis) { + static void __Pyx_RaiseBufferIndexError(int axis) { PyErr_Format(PyExc_IndexError, "Out of bounds on buffer access (axis %d)", axis); } /* BufferFallbackError */ - static void __Pyx_RaiseBufferFallbackError(void) { + static void __Pyx_RaiseBufferFallbackError(void) { PyErr_SetString(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } +/* GetAttr3 */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) + goto bad; + PyErr_Clear(); + r = d; + Py_INCREF(d); + } + return r; +bad: + return NULL; +} + /* None */ - static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } /* None */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); @@ -45159,7 +50031,7 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { } /* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { *type = tstate->exc_type; *value = tstate->exc_value; @@ -45183,7 +50055,7 @@ static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject #endif /* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { PyObject *exc_type = tstate->curexc_type; if (exc_type == err) return 1; @@ -45193,7 +50065,7 @@ static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tsta #endif /* GetException */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { #else static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { @@ -45254,7 +50126,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; @@ -45328,7 +50200,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* bytes_index */ - static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds) { + static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds) { if (check_bounds) { Py_ssize_t size = PyBytes_GET_SIZE(bytes); if (unlikely(index >= size) | ((index < 0) & unlikely(index < -size))) { @@ -45341,8 +50213,22 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return PyBytes_AS_STRING(bytes)[index]; } +/* ImportFrom */ + static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + /* CallNextTpTraverse */ - static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { + static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_traverse != current_tp_traverse) type = type->tp_base; @@ -45354,7 +50240,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* CallNextTpClear */ - static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { + static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_clear != current_tp_clear) type = type->tp_base; @@ -45365,7 +50251,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { + static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 PyObject *ob = PyCapsule_New(vtable, 0, 0); #else @@ -45382,8 +50268,73 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return -1; } +/* SetupReduce */ + #define __Pyx_setup_reduce_GET_ATTR_OR_BAD(res, obj, name) res = PyObject_GetAttrString(obj, name); if (res == NULL) goto BAD; +static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = PyObject_GetAttrString(meth, "__name__"); + if (name_attr) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (ret < 0) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject* builtin_object = NULL; + static PyObject *object_reduce = NULL; + static PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; + if (PyObject_HasAttrString(type_obj, "__getstate__")) goto GOOD; + if (object_reduce_ex == NULL) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(builtin_object, __pyx_b, "object"); + __Pyx_setup_reduce_GET_ATTR_OR_BAD(object_reduce, builtin_object, "__reduce__"); + __Pyx_setup_reduce_GET_ATTR_OR_BAD(object_reduce_ex, builtin_object, "__reduce_ex__"); + } + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce_ex, type_obj, "__reduce_ex__"); + if (reduce_ex == object_reduce_ex) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce, type_obj, "__reduce__"); + if (object_reduce == reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce_cython, type_obj, "__reduce_cython__"); + ret = PyDict_SetItemString(((PyTypeObject*)type_obj)->tp_dict, "__reduce__", reduce_cython); if (ret < 0) goto BAD; + ret = PyDict_DelItemString(((PyTypeObject*)type_obj)->tp_dict, "__reduce_cython__"); if (ret < 0) goto BAD; + setstate = PyObject_GetAttrString(type_obj, "__setstate__"); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(setstate_cython, type_obj, "__setstate_cython__"); + ret = PyDict_SetItemString(((PyTypeObject*)type_obj)->tp_dict, "__setstate__", setstate_cython); if (ret < 0) goto BAD; + ret = PyDict_DelItemString(((PyTypeObject*)type_obj)->tp_dict, "__setstate_cython__"); if (ret < 0) goto BAD; + } + PyType_Modified((PyTypeObject*)type_obj); + } + } + goto GOOD; +BAD: + if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); + ret = -1; +GOOD: + Py_XDECREF(builtin_object); + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; +} + /* GetNameInClass */ - static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name) { + static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name) { PyObject *result; result = __Pyx_PyObject_GetAttrStr(nmspace, name); if (!result) @@ -45392,7 +50343,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* ClassMethod */ - static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { + static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { #if CYTHON_COMPILING_IN_PYPY if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { return PyClassMethod_New(method); @@ -45436,8 +50387,42 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return NULL; } +/* CLineInTraceback */ + static int __Pyx_CLineForTraceback(int c_line) { +#ifdef CYTHON_CLINE_IN_TRACEBACK + return ((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0; +#else + PyObject **cython_runtime_dict; + PyObject *use_cline; + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (unlikely(!cython_runtime_dict)) { + PyObject *ptype, *pvalue, *ptraceback; + PyObject *use_cline_obj; + PyErr_Fetch(&ptype, &pvalue, &ptraceback); + use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + use_cline = NULL; + } + PyErr_Restore(ptype, pvalue, ptraceback); + } else { + use_cline = PyDict_GetItem(*_PyObject_GetDictPtr(__pyx_cython_runtime), __pyx_n_s_cline_in_traceback); + } + if (!use_cline) { + c_line = 0; + PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (PyObject_Not(use_cline) != 0) { + c_line = 0; + } + return c_line; +#endif +} + /* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + 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; @@ -45517,7 +50502,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { } /* AddTraceback */ - #include "compile.h" + #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( @@ -45576,12 +50561,15 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (c_line) { + c_line = __Pyx_CLineForTraceback(c_line); + } + 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); + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); } py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ @@ -45597,29 +50585,39 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, Py_XDECREF(py_frame); } -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); } - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } - Py_DECREF(obj); - view->obj = NULL; } -#endif - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) @@ -45640,8 +50638,29 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return (target_type) value;\ } -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + /* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -45671,39 +50690,8 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } } -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - /* None */ - static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { + static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { long t = b; switch (e) { case 3: @@ -45728,7 +50716,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -45759,7 +50747,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* Declarations */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); @@ -45779,7 +50767,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Arithmetic */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); @@ -45914,7 +50902,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Declarations */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); @@ -45934,7 +50922,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Arithmetic */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); @@ -46069,7 +51057,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -46100,19 +51088,19 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (long) val; + return (int) val; } } else #endif @@ -46121,32 +51109,32 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; @@ -46160,86 +51148,86 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (long) -1; + return (int) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; } #endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } @@ -46248,7 +51236,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - long val; + int val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -46268,40 +51256,40 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return val; } #endif - return (long) -1; + return (int) -1; } } else { - long val; + int val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; + "value too large to convert to int"); + return (int) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; + "can't convert negative value to int"); + return (int) -1; } /* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (int) val; + return (long) val; } } else #endif @@ -46310,32 +51298,32 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; @@ -46349,86 +51337,86 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (int) -1; + return (long) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; } #endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } @@ -46437,7 +51425,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - int val; + long val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -46457,28 +51445,28 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return val; } #endif - return (int) -1; + return (long) -1; } } else { - int val; + long val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; + "value too large to convert to long"); + return (long) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + "can't convert negative value to long"); + return (long) -1; } /* CIntFromPy */ - static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { + static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -46667,7 +51655,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *x) { + static CYTHON_INLINE npy_long __Pyx_PyInt_As_npy_long(PyObject *x) { const npy_long neg_one = (npy_long) -1, const_zero = (npy_long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -46856,7 +51844,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { const char neg_one = (char) -1, const_zero = (char) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -47045,7 +52033,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { + static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); @@ -47061,7 +52049,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* ModuleImport */ - #ifndef __PYX_HAVE_RT_ImportModule + #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; @@ -47079,7 +52067,7 @@ static PyObject *__Pyx_ImportModule(const char *name) { #endif /* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType + #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) @@ -47144,7 +52132,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif /* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { @@ -47169,6 +52157,8 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif if (!*t->p) return -1; + if (PyObject_Hash(*t->p) == -1) + PyErr_Clear(); ++t; } return 0; @@ -47177,11 +52167,11 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); } -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { Py_ssize_t ignore; return __Pyx_PyObject_AsStringAndSize(o, &ignore); } -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { #if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if ( #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII diff --git a/python3/HTSeq/_version.py b/python3/HTSeq/_version.py index acb984f..7ffab00 100644 --- a/python3/HTSeq/_version.py +++ b/python3/HTSeq/_version.py @@ -1 +1 @@ -__version__ = "0.9.0" \ No newline at end of file +__version__ = "0.9.1" \ No newline at end of file diff --git a/python3/src/_HTSeq.c b/python3/src/_HTSeq.c index 2dce43c..1a9e880 100644 --- a/python3/src/_HTSeq.c +++ b/python3/src/_HTSeq.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.25.2 */ +/* Generated by Cython 0.26 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -7,7 +7,7 @@ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_25_2" +#define CYTHON_ABI "0_26" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -29,6 +29,7 @@ #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif +#define __PYX_COMMA , #ifndef HAVE_LONG_LONG #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) #define HAVE_LONG_LONG @@ -181,16 +182,20 @@ #ifndef Py_TPFLAGS_HAVE_FINALIZE #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); +#if PY_VERSION_HEX < 0x030700A0 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject **args, + Py_ssize_t nargs, PyObject *kwnames); #else #define __Pyx_PyCFunctionFast _PyCFunctionFast + #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords #endif #if CYTHON_FAST_PYCCALL #define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))))) #else #define __Pyx_PyFastCFunction_Check(func) 0 #endif @@ -317,6 +322,12 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif #if CYTHON_USE_ASYNC_SLOTS #if PY_VERSION_HEX >= 0x030500B1 #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods @@ -371,6 +382,35 @@ # endif #endif #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include +#endif +#ifndef CYTHON_FALLTHROUGH + #ifdef __cplusplus + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) || (defined(__GNUC__) && defined(__attribute__)) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif #ifndef CYTHON_INLINE #if defined(__clang__) @@ -478,8 +518,8 @@ typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* enc #else #define __Pyx_sst_abs(value) ((value<0) ? -value : value) #endif -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) #define __Pyx_PyBytes_FromString PyBytes_FromString @@ -492,8 +532,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize #endif -#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) @@ -615,10 +658,12 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } static PyObject *__pyx_m; static PyObject *__pyx_d; static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static PyObject *__pyx_empty_unicode; @@ -653,6 +698,7 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { "python3/src/HTSeq/_HTSeq.pyx", "python3/src/HTSeq/_HTSeq.pxd", + "stringsource", "__init__.pxd", "type.pxd", }; @@ -1677,6 +1723,12 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + /* PyObjectCallMethod0.proto */ static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); @@ -1704,6 +1756,20 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long int (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) #endif +/* decode_c_string_utf16.proto */ +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 0; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = -1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} + /* decode_c_bytes.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, @@ -1739,7 +1805,7 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts); static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, - __Pyx_TypeInfo* type); // PROTO + __Pyx_TypeInfo* type); /* BufferIndexError.proto */ static void __Pyx_RaiseBufferIndexError(int axis); @@ -1749,6 +1815,9 @@ static void __Pyx_RaiseBufferIndexError(int axis); /* BufferFallbackError.proto */ static void __Pyx_RaiseBufferFallbackError(void); +/* GetAttr3.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); + /* None.proto */ static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t, Py_ssize_t); @@ -1817,6 +1886,9 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /* bytes_index.proto */ static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds); +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + /* CallNextTpTraverse.proto */ static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); @@ -1826,8 +1898,8 @@ static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); /* SetVTable.proto */ static int __Pyx_SetVtable(PyObject *dict, void *vtable); -/* ImportFrom.proto */ -static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); /* GetNameInClass.proto */ static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name); @@ -1836,6 +1908,9 @@ static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name); #include "descrobject.h" static PyObject* __Pyx_Method_ClassMethod(PyObject *method); +/* CLineInTraceback.proto */ +static int __Pyx_CLineForTraceback(int c_line); + /* CodeObjectCache.proto */ typedef struct { PyCodeObject* code_object; @@ -1855,6 +1930,9 @@ 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); +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + /* BufferStructDeclare.proto */ typedef struct { Py_ssize_t shape, strides, suboffsets; @@ -1885,9 +1963,6 @@ static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - /* None.proto */ static CYTHON_INLINE long __Pyx_pow_long(long, long); @@ -1996,10 +2071,10 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); /* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); /* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *); @@ -2097,6 +2172,11 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_parse_cigar(PyObject *, int __pyx_skip_d static PyObject *__pyx_f_5HTSeq_6_HTSeq_build_cigar_list(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_build_cigar_list *__pyx_optional_args); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq__parse_SAM_optional_field_value(PyObject *); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq_quotesafe_split(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_quotesafe_split *__pyx_optional_args); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_Alignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_AlignmentWithSequenceReversal__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_BowtieAlignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_CigarOperation__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *, PyObject *); /*proto*/ +static PyObject *__pyx_f_5HTSeq_6_HTSeq___pyx_unpickle_SAM_Alignment__set_state(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *, PyObject *); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_uint8_t = { "uint8_t", NULL, sizeof(__pyx_t_5numpy_uint8_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_uint8_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_uint8_t), 0 }; #define __Pyx_MODULE_NAME "HTSeq._HTSeq" @@ -2158,6 +2238,7 @@ static const char __pyx_k__34[] = "\""; static const char __pyx_k_add[] = "add"; static const char __pyx_k_csv[] = "csv"; static const char __pyx_k_end[] = "end"; +static const char __pyx_k_new[] = "__new__"; static const char __pyx_k_nmm[] = ".nmm"; static const char __pyx_k_pos[] = "pos"; static const char __pyx_k_qto[] = "qto"; @@ -2174,6 +2255,7 @@ static const char __pyx_k_Read[] = "Read"; static const char __pyx_k_aend[] = "aend"; static const char __pyx_k_auto[] = "auto"; static const char __pyx_k_copy[] = "copy"; +static const char __pyx_k_dict[] = "__dict__"; static const char __pyx_k_flag[] = "flag"; static const char __pyx_k_gzip[] = "gzip"; static const char __pyx_k_iadd[] = "__iadd__"; @@ -2244,14 +2326,17 @@ static const char __pyx_k_memmap[] = "memmap"; static const char __pyx_k_name_2[] = "name"; static const char __pyx_k_offset[] = "offset"; static const char __pyx_k_padded[] = "padded"; +static const char __pyx_k_pickle[] = "pickle"; static const char __pyx_k_reduce[] = "__reduce__"; static const char __pyx_k_ref_iv[] = "ref_iv"; +static const char __pyx_k_result[] = "result"; static const char __pyx_k_rstrip[] = "rstrip"; static const char __pyx_k_second[] = "second"; static const char __pyx_k_solexa[] = "solexa"; static const char __pyx_k_stderr[] = "stderr"; static const char __pyx_k_strand[] = "strand"; static const char __pyx_k_type_2[] = "type"; +static const char __pyx_k_update[] = "update"; static const char __pyx_k_values[] = "values"; static const char __pyx_k_aligned[] = "aligned"; static const char __pyx_k_compile[] = "compile"; @@ -2284,6 +2369,7 @@ static const char __pyx_k_inserted[] = "inserted"; static const char __pyx_k_is_read1[] = "is_read1"; static const char __pyx_k_is_read2[] = "is_read2"; static const char __pyx_k_overlaps[] = "overlaps"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; static const char __pyx_k_ref_left[] = "ref_left"; static const char __pyx_k_stranded[] = "stranded"; static const char __pyx_k_typecode[] = "typecode"; @@ -2297,6 +2383,7 @@ static const char __pyx_k_is_paired[] = "is_paired"; static const char __pyx_k_is_qcfail[] = "is_qcfail"; static const char __pyx_k_itertools[] = "itertools"; static const char __pyx_k_maketrans[] = "maketrans"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; static const char __pyx_k_qualscale[] = "qualscale"; static const char __pyx_k_storage_2[] = "_storage"; static const char __pyx_k_translate[] = "translate"; @@ -2314,6 +2401,7 @@ static const char __pyx_k_s_object_s[] = "<%s object '%s'>"; static const char __pyx_k_solexa_old[] = "solexa-old"; static const char __pyx_k_AlignedRead[] = "AlignedRead"; static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_PickleError[] = "PickleError"; static const char __pyx_k_bowtie_line[] = "bowtie_line"; static const char __pyx_k_cigar_pairs[] = "cigar_pairs"; static const char __pyx_k_cigartuples[] = "cigartuples"; @@ -2329,12 +2417,15 @@ static const char __pyx_k_hard_clipped[] = "hard-clipped"; static const char __pyx_k_is_duplicate[] = "is_duplicate"; static const char __pyx_k_is_secondary[] = "is_secondary"; static const char __pyx_k_mate_aligned[] = "mate_aligned"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; static const char __pyx_k_reference_id[] = "reference_id"; static const char __pyx_k_s_object_s_s[] = "<%s object, %s, %s>"; static const char __pyx_k_soft_clipped[] = "soft-clipped"; +static const char __pyx_k_stringsource[] = "stringsource"; static const char __pyx_k_chrom_vectors[] = "chrom_vectors"; static const char __pyx_k_from_SAM_line[] = "from_SAM_line"; static const char __pyx_k_mismatch_prop[] = "mismatch_prop"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; static const char __pyx_k_reference_end[] = "reference_end"; static const char __pyx_k_track_options[] = "track_options"; static const char __pyx_k_trim_left_end[] = "trim_left_end"; @@ -2355,6 +2446,7 @@ static const char __pyx_k_mate_is_reverse[] = "mate_is_reverse"; static const char __pyx_k_query_qualities[] = "query_qualities"; static const char __pyx_k_read_as_aligned[] = "read_as_aligned"; static const char __pyx_k_reference_start[] = "reference_start"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; static const char __pyx_k_start_too_small[] = "start too small"; static const char __pyx_k_template_length[] = "template_length"; static const char __pyx_k_unmatched_quote[] = "unmatched quote"; @@ -2370,6 +2462,7 @@ static const char __pyx_k_is_vector_of_sets[] = "is_vector_of_sets"; static const char __pyx_k_next_reference_id[] = "next_reference_id"; static const char __pyx_k_GenomicArray_steps[] = "GenomicArray_steps"; static const char __pyx_k_Illegal_index_type[] = "Illegal index type"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; static const char __pyx_k_characters_per_line[] = "characters_per_line"; static const char __pyx_k_raw_optional_fields[] = "raw_optional_fields"; @@ -2393,6 +2486,7 @@ static const char __pyx_k_Illegal_CIGAR_string_s[] = "Illegal CIGAR string '%s'" static const char __pyx_k_Quality_string_missing[] = "Quality string missing."; static const char __pyx_k_from_pysam_AlignedRead[] = "from_pysam_AlignedRead"; static const char __pyx_k_get_reverse_complement[] = "get_reverse_complement"; +static const char __pyx_k_pyx_unpickle_Alignment[] = "__pyx_unpickle_Alignment"; static const char __pyx_k_quote_must_be_length_1[] = "'quote' must be length 1"; static const char __pyx_k_split_must_be_length_1[] = "'split' must be length 1"; static const char __pyx_k_Illegal_quality_scale_s[] = "Illegal quality scale '%s'."; @@ -2408,8 +2502,13 @@ static const char __pyx_k_cigar_operation_code_dict[] = "cigar_operation_code_di static const char __pyx_k_from_pysam_AlignedSegment[] = "from_pysam_AlignedSegment"; static const char __pyx_k_s_object_s_s_aligned_to_s[] = "<%s object: %s '%s' aligned to %s>"; static const char __pyx_k_trim_right_end_with_quals[] = "trim_right_end_with_quals"; +static const char __pyx_k_pyx_unpickle_SAM_Alignment[] = "__pyx_unpickle_SAM_Alignment"; static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_pyx_unpickle_CigarOperation[] = "__pyx_unpickle_CigarOperation"; static const char __pyx_k_Inconsistent_CIGAR_operation[] = "Inconsistent CIGAR operation."; +static const char __pyx_k_python3_src_HTSeq__HTSeq_pyx[] = "python3/src/HTSeq/_HTSeq.pyx"; +static const char __pyx_k_pyx_unpickle_BowtieAlignment[] = "__pyx_unpickle_BowtieAlignment"; +static const char __pyx_k_pyx_unpickle_AlignmentWithSequ[] = "__pyx_unpickle_AlignmentWithSequenceReversal"; static const char __pyx_k_s_d_base_s_s_on_ref_iv_s_query[] = "< %s: %d base(s) %s on ref iv %s, query iv [%d,%d) >"; static const char __pyx_k_Automatic_adding_of_chromosomes[] = "Automatic adding of chromosomes can only be used with storage type 'StepVector'."; static const char __pyx_k_Illegal_base_letter_encountered[] = "Illegal base letter encountered."; @@ -2420,7 +2519,6 @@ static const char __pyx_k_assignment_to_qual_with_illegal[] = "assignment to qua static const char __pyx_k_chroms_must_be_a_list_or_a_dict[] = "'chroms' must be a list or a dict or 'auto'."; static const char __pyx_k_count_array_has_too_few_columns[] = "'count_array' has too few columns."; static const char __pyx_k_count_array_too_small_for_seque[] = "'count_array' too small for sequence."; -static const char __pyx_k_home_fabio_university_postdoc_h[] = "/home/fabio/university/postdoc/htseq/htseq/python3/src/HTSeq/_HTSeq.pyx"; static const char __pyx_k_make_translation_table_for_comp[] = "_make_translation_table_for_complementation"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_seq_and_qualstr_do_not_have_the[] = "'seq' and 'qualstr' do not have the same length."; @@ -2430,6 +2528,11 @@ static const char __pyx_k_Cannot_extend_an_interval_to_inc[] = "Cannot extend an static const char __pyx_k_Cannot_subset_to_zero_length_int[] = "Cannot subset to zero-length interval."; static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static const char __pyx_k_GenomicInterval_from_directional[] = "GenomicInterval_from_directional"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x1b[] = "Incompatible checksums (%s vs 0x1b7eeff = (_read, _read_as_sequenced, iv, read_as_aligned))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x48[] = "Incompatible checksums (%s vs 0x482c176 = (_read, _read_as_sequenced, iv, read_as_aligned, reserved, substitutions))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0x77[] = "Incompatible checksums (%s vs 0x77bfdf2 = (_read, iv))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xb5[] = "Incompatible checksums (%s vs 0xb5bd29c = (query_from, query_to, ref_iv, size, type))"; +static const char __pyx_k_Incompatible_checksums_s_vs_0xf6[] = "Incompatible checksums (%s vs 0xf6933f3 = (_flag, _read, _read_as_sequenced, aQual, cigar, failed_platform_qc, inferred_insert_size, iv, mate_start, not_primary_alignment, optional_fields, original_sam_line, pcr_or_optical_duplicate, pe_which, proper_pair, read_as_aligned, supplementary))"; static const char __pyx_k_Indefinite_length_chromosomes_ca[] = "Indefinite-length chromosomes can only be used with storage type 'StepVector'."; static const char __pyx_k_Malformed_SAM_line_MRNM_although[] = "Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared"; static const char __pyx_k_Malformed_SAM_line_RNAME_althoug[] = "Malformed SAM line: RNAME == '*' although flag bit &0x0004 cleared"; @@ -2488,6 +2591,11 @@ static PyObject *__pyx_kp_u_Illegal_index_type_2; static PyObject *__pyx_kp_u_Illegal_quality_scale_s; static PyObject *__pyx_kp_u_Illegal_storage_mode; static PyObject *__pyx_n_s_ImportError; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x1b; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x48; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0x77; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xb5; +static PyObject *__pyx_kp_s_Incompatible_checksums_s_vs_0xf6; static PyObject *__pyx_kp_u_Inconsistent_CIGAR_operation; static PyObject *__pyx_kp_u_Indefinite_length_chromosomes_ca; static PyObject *__pyx_n_s_IndexError; @@ -2505,6 +2613,7 @@ static PyObject *__pyx_n_s_NotImplementedError; static PyObject *__pyx_n_u_O; static PyObject *__pyx_n_u_P; static PyObject *__pyx_kp_u_Paired_end_read; +static PyObject *__pyx_n_s_PickleError; static PyObject *__pyx_kp_u_Please_Install_PySam_to_use_this; static PyObject *__pyx_kp_u_Quality_string_has_not_the_same; static PyObject *__pyx_kp_u_Quality_string_missing; @@ -2578,6 +2687,7 @@ static PyObject *__pyx_n_s_cigar_pairs; static PyObject *__pyx_n_s_cigar_string; static PyObject *__pyx_n_s_cigartuples; static PyObject *__pyx_n_s_class; +static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_n_s_close; static PyObject *__pyx_n_s_collections; static PyObject *__pyx_n_s_compile; @@ -2594,6 +2704,7 @@ static PyObject *__pyx_n_u_d; static PyObject *__pyx_n_s_decode; static PyObject *__pyx_n_u_deleted; static PyObject *__pyx_n_u_descr; +static PyObject *__pyx_n_s_dict; static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_empty; static PyObject *__pyx_n_s_encode; @@ -2617,7 +2728,6 @@ static PyObject *__pyx_n_s_gettid; static PyObject *__pyx_n_s_getvalue; static PyObject *__pyx_n_s_gzip; static PyObject *__pyx_kp_u_hard_clipped; -static PyObject *__pyx_kp_s_home_fabio_university_postdoc_h; static PyObject *__pyx_n_u_i; static PyObject *__pyx_n_s_iadd; static PyObject *__pyx_n_s_iadd___locals_addval; @@ -2670,6 +2780,7 @@ static PyObject *__pyx_n_u_name_2; static PyObject *__pyx_n_u_ndarray; static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_new; static PyObject *__pyx_n_s_next_reference_id; static PyObject *__pyx_n_s_next_reference_start; static PyObject *__pyx_kp_u_nmm; @@ -2689,8 +2800,18 @@ static PyObject *__pyx_kp_u_part; static PyObject *__pyx_n_s_path; static PyObject *__pyx_n_s_pattern; static PyObject *__pyx_n_u_phred; +static PyObject *__pyx_n_s_pickle; static PyObject *__pyx_n_s_pos; static PyObject *__pyx_n_s_pysam; +static PyObject *__pyx_kp_s_python3_src_HTSeq__HTSeq_pyx; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_Alignment; +static PyObject *__pyx_n_s_pyx_unpickle_AlignmentWithSequ; +static PyObject *__pyx_n_s_pyx_unpickle_BowtieAlignment; +static PyObject *__pyx_n_s_pyx_unpickle_CigarOperation; +static PyObject *__pyx_n_s_pyx_unpickle_SAM_Alignment; static PyObject *__pyx_n_s_pyx_vtable; static PyObject *__pyx_n_s_qfrom; static PyObject *__pyx_n_s_qname; @@ -2711,11 +2832,13 @@ static PyObject *__pyx_n_s_re_cigar_codes; static PyObject *__pyx_n_s_read; static PyObject *__pyx_n_s_read_as_aligned; static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; static PyObject *__pyx_n_s_ref_iv; static PyObject *__pyx_n_s_ref_left; static PyObject *__pyx_n_s_reference_end; static PyObject *__pyx_n_s_reference_id; static PyObject *__pyx_n_s_reference_start; +static PyObject *__pyx_n_s_result; static PyObject *__pyx_n_u_revcomp_of; static PyObject *__pyx_n_s_rfrom; static PyObject *__pyx_n_s_rstrip; @@ -2744,6 +2867,7 @@ static PyObject *__pyx_n_u_seq; static PyObject *__pyx_kp_u_seq_and_qualstr_do_not_have_the; static PyObject *__pyx_kp_u_sequence_matched; static PyObject *__pyx_kp_u_sequence_mismatched; +static PyObject *__pyx_n_s_setstate_cython; static PyObject *__pyx_n_s_shape; static PyObject *__pyx_n_s_size; static PyObject *__pyx_n_u_skipped; @@ -2767,6 +2891,7 @@ static PyObject *__pyx_n_s_storage; static PyObject *__pyx_n_s_storage_2; static PyObject *__pyx_n_s_strand; static PyObject *__pyx_n_s_stranded; +static PyObject *__pyx_kp_s_stringsource; static PyObject *__pyx_n_s_sys; static PyObject *__pyx_n_s_tags; static PyObject *__pyx_n_s_template_length; @@ -2788,6 +2913,7 @@ static PyObject *__pyx_n_u_unknown; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_kp_u_unmatched_quote; static PyObject *__pyx_n_u_unnamed; +static PyObject *__pyx_n_s_update; static PyObject *__pyx_n_s_upper; static PyObject *__pyx_n_s_values; static PyObject *__pyx_n_s_vec; @@ -2936,6 +3062,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_5_read_4__del__(struct __pyx_obj_5 static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_4__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_6__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal___init__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_read_as_aligned, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4read___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ @@ -2944,6 +3072,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_ali static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_2__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment___init__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_bowtie_line); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ @@ -2951,6 +3081,8 @@ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_4__del__(struct _ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_2__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_4__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation___init__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_type_, int __pyx_v_size, int __pyx_v_rfrom, int __pyx_v_rto, int __pyx_v_qfrom, int __pyx_v_qto, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand, int __pyx_v_check); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_2__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4check(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ @@ -2966,6 +3098,8 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from___get__(s static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_6__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_10parse_cigar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_string, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12build_cigar_list(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_pairs, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedSegment(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_sf); /* proto */ @@ -3007,7 +3141,14 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_17original_sam_line___g static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_16__reduce_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_18__setstate_cython__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14quotesafe_split(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_s, PyObject *__pyx_v_split, PyObject *__pyx_v_quote); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_16__pyx_unpickle_Alignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_18__pyx_unpickle_AlignmentWithSequenceReversal(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_20__pyx_unpickle_BowtieAlignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_22__pyx_unpickle_CigarOperation(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5HTSeq_6_HTSeq_24__pyx_unpickle_SAM_Alignment(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicInterval(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ @@ -3031,6 +3172,11 @@ static PyObject *__pyx_int_10; static PyObject *__pyx_int_11; static PyObject *__pyx_int_16; static PyObject *__pyx_int_70; +static PyObject *__pyx_int_28831487; +static PyObject *__pyx_int_75678070; +static PyObject *__pyx_int_125566450; +static PyObject *__pyx_int_190567068; +static PyObject *__pyx_int_258552819; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_k_; static PyObject *__pyx_k__7; @@ -3064,11 +3210,21 @@ static PyObject *__pyx_tuple__44; static PyObject *__pyx_tuple__46; static PyObject *__pyx_tuple__48; static PyObject *__pyx_tuple__51; +static PyObject *__pyx_tuple__52; +static PyObject *__pyx_tuple__54; +static PyObject *__pyx_tuple__56; +static PyObject *__pyx_tuple__58; +static PyObject *__pyx_tuple__60; static PyObject *__pyx_codeobj__6; static PyObject *__pyx_codeobj__45; static PyObject *__pyx_codeobj__47; static PyObject *__pyx_codeobj__49; static PyObject *__pyx_codeobj__50; +static PyObject *__pyx_codeobj__53; +static PyObject *__pyx_codeobj__55; +static PyObject *__pyx_codeobj__57; +static PyObject *__pyx_codeobj__59; +static PyObject *__pyx_codeobj__61; /* "HTSeq/_HTSeq.pyx":56 * """ @@ -3101,9 +3257,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -3112,16 +3272,19 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 1); __PYX_ERR(0, 56, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_end)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 2); __PYX_ERR(0, 56, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -3134,6 +3297,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -6031,6 +6195,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_21range(PyObject *__p const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6048,6 +6213,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_21range(PyObject *__p } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6197,6 +6363,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_23range_d(PyObject *_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -6214,6 +6381,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_23range_d(PyObject *_ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7028,9 +7196,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7039,16 +7211,19 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start_d)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("GenomicInterval_from_directional", 0, 3, 4, 1); __PYX_ERR(0, 253, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_length)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("GenomicInterval_from_directional", 0, 3, 4, 2); __PYX_ERR(0, 253, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -7061,6 +7236,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_1GenomicInterval_from_directional(PyObj } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -7257,8 +7433,11 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -7267,11 +7446,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pos)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 2, 3, 1); __PYX_ERR(0, 279, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -7284,6 +7465,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; @@ -8045,9 +8227,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -8056,16 +8242,19 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("create", 0, 3, 4, 1); __PYX_ERR(0, 327, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("create", 0, 3, 4, 2); __PYX_ERR(0, 327, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_memmap_dir); @@ -8078,6 +8267,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create(PyObject *__pyx_v } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -8554,7 +8744,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_3_create_view(PyObject *_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -8563,6 +8755,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_3_create_view(PyObject *_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_vec)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else { @@ -11771,10 +11964,15 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_3_ChromVector_unpickle(PyObject *__pyx_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -11783,21 +11981,25 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_3_ChromVector_unpickle(PyObject *__pyx_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_array)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 1); __PYX_ERR(0, 477, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_offset)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 2); __PYX_ERR(0, 477, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_is_vector_of_sets)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_ChromVector_unpickle", 1, 5, 5, 3); __PYX_ERR(0, 477, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage_2)) != 0)) kw_args--; else { @@ -11985,10 +12187,15 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -11997,21 +12204,25 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chroms)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stranded); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode); if (value) { values[2] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_storage); if (value) { values[3] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 4: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_memmap_dir); @@ -12024,9 +12235,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__(PyObject *__pyx_v_se } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -13521,8 +13736,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -13531,11 +13749,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_length); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start_index); @@ -13548,7 +13768,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom(PyObject *__p } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -14152,8 +14374,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -14162,11 +14387,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_file_or_filename)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_track_options); @@ -14179,7 +14406,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file(Py } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -14324,7 +14553,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10write_bedgraph_file(st * f = file_or_filename * else: */ - __pyx_t_1 = PyObject_HasAttr(__pyx_v_file_or_filename, __pyx_n_u_write); if (unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 592, __pyx_L1_error) + __pyx_t_1 = __Pyx_HasAttr(__pyx_v_file_or_filename, __pyx_n_u_write); if (unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 592, __pyx_L1_error) __pyx_t_4 = (__pyx_t_1 != 0); if (__pyx_t_4) { @@ -14805,7 +15034,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10write_bedgraph_file(st * f.close() * */ - __pyx_t_4 = PyObject_HasAttr(__pyx_v_file_or_filename, __pyx_n_u_write); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(0, 606, __pyx_L1_error) + __pyx_t_4 = __Pyx_HasAttr(__pyx_v_file_or_filename, __pyx_n_u_write); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(0, 606, __pyx_L1_error) __pyx_t_1 = ((!(__pyx_t_4 != 0)) != 0); if (__pyx_t_1) { @@ -15353,8 +15582,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_5_GenomicArray_unpickle(PyObject *__pyx const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -15363,11 +15595,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_5_GenomicArray_unpickle(PyObject *__pyx case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stranded)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_typecode)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_GenomicArray_unpickle", 1, 3, 3, 1); __PYX_ERR(0, 613, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom_vectors)) != 0)) kw_args--; else { @@ -15720,7 +15954,9 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -15729,6 +15965,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_seq)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_name_2); @@ -15741,6 +15978,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__(PyObject *__pyx_v_self, P } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -16664,7 +16902,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -16673,6 +16913,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_fasta_file)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_characters_per_line); @@ -16685,6 +16926,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19write_to_fasta_file(PyObjec } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -17332,7 +17574,7 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_8Sequence_add_bases_to_count_array(struc * for i in range(seq_length): * b = seq_cstr[i] */ - __pyx_t_8 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 715, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 715, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_8; /* "HTSeq/_HTSeq.pyx":716 @@ -17862,7 +18104,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 741, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 741, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":742 @@ -17872,7 +18114,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 742, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 742, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":743 @@ -18040,7 +18282,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -18049,6 +18293,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_mismatch_prop); @@ -18061,6 +18306,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_23trim_left_end(PyObject *__p } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -18309,7 +18555,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 765, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 765, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":766 @@ -18319,7 +18565,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_f_5HTSeq_6_HTSeq_8Sequenc * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 766, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 766, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":767 @@ -18487,7 +18733,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -18496,6 +18744,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_mismatch_prop); @@ -18508,6 +18757,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_8Sequence_25trim_right_end(PyObject *__ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -18912,9 +19162,13 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -18923,16 +19177,19 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_seq)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_name_2)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 1); __PYX_ERR(0, 788, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_qualstr)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 4, 2); __PYX_ERR(0, 788, __pyx_L3_error) } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_qualscale); @@ -18945,6 +19202,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__(PyObject *_ } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -19423,7 +19681,7 @@ static PyObject *__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities__fill_qual_arr(s * if self._qualscale == "phred": * for i in range(seq_len): */ - __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 816, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 816, __pyx_L1_error) __pyx_v_qualstr = __pyx_t_12; /* "HTSeq/_HTSeq.pyx":817 @@ -20326,7 +20584,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_7qualstr___get_ * cdef int i * cdef numpy.ndarray[numpy.uint8_t, ndim = 1] qual_array */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 865, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 865, __pyx_L1_error) __pyx_v_qualstr_phred_cstr = __pyx_t_1; /* "HTSeq/_HTSeq.pyx":868 @@ -20449,7 +20707,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_7qualstr___get_ * if self._qualarr is None: * self._fill_qual_arr() */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 877, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->_qualstr_phred); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 877, __pyx_L1_error) __pyx_v_qualstr_phred_cstr = __pyx_t_1; /* "HTSeq/_HTSeq.pyx":878 @@ -20637,7 +20895,7 @@ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_6write_to_fastq * fastq_file.write("@%s %s\n" % (self.name, self.descr)) * else: */ - __pyx_t_2 = PyObject_HasAttr(((PyObject *)__pyx_v_self), __pyx_n_u_descr); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 886, __pyx_L1_error) + __pyx_t_2 = __Pyx_HasAttr(((PyObject *)__pyx_v_self), __pyx_n_u_descr); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 886, __pyx_L1_error) __pyx_t_3 = (__pyx_t_2 != 0); if (__pyx_t_3) { } else { @@ -21001,6 +21259,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_9get_fastq_str( const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -21018,6 +21277,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_9get_fastq_str( } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22025,7 +22285,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 943, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 943, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":944 @@ -22035,7 +22295,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 944, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 944, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":945 @@ -22275,7 +22535,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22284,6 +22546,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_max_mm_qual); @@ -22296,6 +22559,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15trim_left_end } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -22554,7 +22818,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef char * pat_cstr = pattern.seq * cdef int match = 0 */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 971, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 971, __pyx_L1_error) __pyx_v_seq_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":972 @@ -22564,7 +22828,7 @@ static struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_f_5HTSeq_6_H * cdef int match = 0 * cdef int i, j */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 972, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_AsWritableString(__pyx_v_pattern->seq); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) __PYX_ERR(0, 972, __pyx_L1_error) __pyx_v_pat_cstr = __pyx_t_10; /* "HTSeq/_HTSeq.pyx":973 @@ -22804,7 +23068,9 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -22813,6 +23079,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_pattern)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_max_mm_qual); @@ -22825,6 +23092,7 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_right_en } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -23055,7 +23323,9 @@ static int __pyx_pw_5HTSeq_6_HTSeq_9Alignment_1__init__(PyObject *__pyx_v_self, const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; case 0: break; default: goto __pyx_L5_argtuple_error; } @@ -23064,6 +23334,7 @@ static int __pyx_pw_5HTSeq_6_HTSeq_9Alignment_1__init__(PyObject *__pyx_v_self, case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_read)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_iv)) != 0)) kw_args--; else { @@ -23773,6 +24044,307 @@ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_4__del__(struct __pyx_obj_5HTS return __pyx_r; } +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * cdef bint use_setstate + * state = (self._read, self.iv) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_5HTSeq_6_HTSeq_9Alignment_4__reduce_cython__(((struct 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PyDict_GetItem(__pyx_kwds, __pyx_n_s_ref_left); if (value) { values[1] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 2: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chrom); if (value) { values[2] = value; kw_args--; } } + CYTHON_FALLTHROUGH; case 3: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_strand); @@ -26660,8 +28241,11 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_11parse_cigar(PyObject *__pyx_self, PyO } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); break; default: goto __pyx_L5_argtuple_error; @@ -27581,9 +29165,13 @@ static PyObject *__pyx_pw_5HTSeq_6_HTSeq_13build_cigar_list(PyObject *__pyx_self const Py_ssize_t pos_args = 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__Pyx_AddTraceback("numpy.import_array", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 988, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(3, 988, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); @@ -38089,11 +42756,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { * * cdef inline int import_umath() except -1: */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 989, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(3, 989, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 989, __pyx_L5_except_error) + __PYX_ERR(3, 989, __pyx_L5_except_error) } goto __pyx_L5_except_error; __pyx_L5_except_error:; @@ -38111,7 +42778,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); goto __pyx_L1_error; - __pyx_L10_try_end:; + __pyx_L8_try_end:; } /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":985 @@ -38181,7 +42848,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { * except Exception: * raise ImportError("numpy.core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(2, 993, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(3, 993, __pyx_L3_error) /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":992 * @@ -38194,7 +42861,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L10_try_end; + goto __pyx_L8_try_end; __pyx_L3_error:; __Pyx_PyThreadState_assign @@ -38208,7 +42875,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_umath", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 994, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(3, 994, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); @@ -38220,11 +42887,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { * * cdef inline int import_ufunc() except -1: */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__42, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 995, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__42, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(3, 995, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 995, __pyx_L5_except_error) + __PYX_ERR(3, 995, __pyx_L5_except_error) } goto __pyx_L5_except_error; __pyx_L5_except_error:; @@ -38242,7 +42909,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); goto __pyx_L1_error; - __pyx_L10_try_end:; + __pyx_L8_try_end:; } /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":991 @@ -38312,7 +42979,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { * except Exception: * raise ImportError("numpy.core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(2, 999, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(3, 999, __pyx_L3_error) /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":998 * @@ -38325,7 +42992,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L10_try_end; + goto __pyx_L8_try_end; __pyx_L3_error:; __Pyx_PyThreadState_assign @@ -38338,7 +43005,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1000, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(3, 1000, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); @@ -38348,11 +43015,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< */ - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__43, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1001, __pyx_L5_except_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__43, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(3, 1001, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 1001, __pyx_L5_except_error) + __PYX_ERR(3, 1001, __pyx_L5_except_error) } goto __pyx_L5_except_error; __pyx_L5_except_error:; @@ -38370,7 +43037,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); goto __pyx_L1_error; - __pyx_L10_try_end:; + __pyx_L8_try_end:; } /* "../../../../../../usr/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":997 @@ -38416,7 +43083,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicInterval(PyTypeObject *t, CY static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicInterval(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38738,7 +43405,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_Sequence(PyTypeObject *t, CYTHON_UN static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Sequence(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -38907,7 +43574,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_SequenceWithQualities(PyTypeObject static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SequenceWithQualities(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39111,7 +43778,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_Alignment(PyTypeObject *t, CYTHON_U static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39125,10 +43792,10 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment(PyObject *o, visitproc v, int e; struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; if (p->_read) { - e = (*v)(((PyObject*)p->_read), a); if (e) return e; + e = (*v)(((PyObject *)p->_read), a); if (e) return e; } if (p->iv) { - e = (*v)(((PyObject*)p->iv), a); if (e) return e; + e = (*v)(((PyObject *)p->iv), a); if (e) return e; } return 0; } @@ -39184,6 +43851,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_9Alignment_iv(PyObject *o, PyObject *v, } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_Alignment[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_7__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39267,7 +43936,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyTyp static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p = (struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39283,10 +43952,10 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyObje struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p = (struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o; e = __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment(o, v, a); if (e) return e; if (p->read_as_aligned) { - e = (*v)(((PyObject*)p->read_as_aligned), a); if (e) return e; + e = (*v)(((PyObject *)p->read_as_aligned), a); if (e) return e; } if (p->_read_as_sequenced) { - e = (*v)(((PyObject*)p->_read_as_sequenced), a); if (e) return e; + e = (*v)(((PyObject *)p->_read_as_sequenced), a); if (e) return e; } return 0; } @@ -39335,6 +44004,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_3__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_5__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39423,7 +44094,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_SAM_Alignment(PyTypeObject *t, PyOb static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39445,7 +44116,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o, visitproc e = (*v)(p->cigar, a); if (e) return e; } if (p->mate_start) { - e = (*v)(((PyObject*)p->mate_start), a); if (e) return e; + e = (*v)(((PyObject *)p->mate_start), a); if (e) return e; } if (p->optional_fields) { e = (*v)(p->optional_fields, a); if (e) return e; @@ -39654,6 +44325,8 @@ static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_SAM_Alignment[] = { {"get_sam_line", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_11get_sam_line, METH_NOARGS, 0}, {"optional_field", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_13optional_field, METH_O, 0}, {"raw_optional_fields", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15raw_optional_fields, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_17__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_19__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -39761,7 +44434,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_ChromVector(PyTypeObject *t, CYTHON static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_ChromVector(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p = (struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -39779,7 +44452,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_ChromVector(PyObject *o, visitproc v e = (*v)(p->array, a); if (e) return e; } if (p->iv) { - e = (*v)(((PyObject*)p->iv), a); if (e) return e; + e = (*v)(((PyObject *)p->iv), a); if (e) return e; } return 0; } @@ -39904,7 +44577,7 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ @@ -39920,7 +44593,7 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_coerce*/ #endif 0, /*nb_int*/ @@ -39930,16 +44603,16 @@ static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*reserved*/ #endif 0, /*nb_float*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_oct*/ #endif - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_hex*/ #endif __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_9__iadd__, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ - #if PY_MAJOR_VERSION < 3 || CYTHON_COMPILING_IN_PYPY + #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ @@ -40059,7 +44732,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicArray(PyTypeObject *t, CYTHO static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicArray(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40258,7 +44931,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_BowtieAlignment(PyTypeObject *t, Py static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_BowtieAlignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40296,6 +44969,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions(PyObject } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_BowtieAlignment[] = { + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_3__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_5__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -40385,7 +45060,7 @@ static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_CigarOperation(PyTypeObject *t, CYT static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_CigarOperation(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; #if PY_VERSION_HEX >= 0x030400a1 - if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { if (PyObject_CallFinalizerFromDealloc(o)) return; } #endif @@ -40399,7 +45074,7 @@ static int __pyx_tp_traverse_5HTSeq_6_HTSeq_CigarOperation(PyObject *o, visitpro int e; struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; if (p->ref_iv) { - e = (*v)(((PyObject*)p->ref_iv), a); if (e) return e; + e = (*v)(((PyObject *)p->ref_iv), a); if (e) return e; } return 0; } @@ -40483,6 +45158,8 @@ static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_to(PyObject *o, P static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_CigarOperation[] = { {"check", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_5check, METH_NOARGS, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_7__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_9__setstate_cython__, METH_O, 0}, {0, 0, 0, 0} }; @@ -40719,6 +45396,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_Illegal_quality_scale_s, __pyx_k_Illegal_quality_scale_s, sizeof(__pyx_k_Illegal_quality_scale_s), 0, 1, 0, 0}, {&__pyx_kp_u_Illegal_storage_mode, __pyx_k_Illegal_storage_mode, sizeof(__pyx_k_Illegal_storage_mode), 0, 1, 0, 0}, {&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x1b, __pyx_k_Incompatible_checksums_s_vs_0x1b, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x1b), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x48, __pyx_k_Incompatible_checksums_s_vs_0x48, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x48), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0x77, __pyx_k_Incompatible_checksums_s_vs_0x77, sizeof(__pyx_k_Incompatible_checksums_s_vs_0x77), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0xb5, __pyx_k_Incompatible_checksums_s_vs_0xb5, sizeof(__pyx_k_Incompatible_checksums_s_vs_0xb5), 0, 0, 1, 0}, + {&__pyx_kp_s_Incompatible_checksums_s_vs_0xf6, __pyx_k_Incompatible_checksums_s_vs_0xf6, sizeof(__pyx_k_Incompatible_checksums_s_vs_0xf6), 0, 0, 1, 0}, {&__pyx_kp_u_Inconsistent_CIGAR_operation, __pyx_k_Inconsistent_CIGAR_operation, sizeof(__pyx_k_Inconsistent_CIGAR_operation), 0, 1, 0, 0}, {&__pyx_kp_u_Indefinite_length_chromosomes_ca, __pyx_k_Indefinite_length_chromosomes_ca, sizeof(__pyx_k_Indefinite_length_chromosomes_ca), 0, 1, 0, 0}, {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, @@ -40736,6 +45418,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_u_O, __pyx_k_O, sizeof(__pyx_k_O), 0, 1, 0, 1}, {&__pyx_n_u_P, __pyx_k_P, sizeof(__pyx_k_P), 0, 1, 0, 1}, {&__pyx_kp_u_Paired_end_read, __pyx_k_Paired_end_read, sizeof(__pyx_k_Paired_end_read), 0, 1, 0, 0}, + {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1}, {&__pyx_kp_u_Please_Install_PySam_to_use_this, __pyx_k_Please_Install_PySam_to_use_this, sizeof(__pyx_k_Please_Install_PySam_to_use_this), 0, 1, 0, 0}, {&__pyx_kp_u_Quality_string_has_not_the_same, __pyx_k_Quality_string_has_not_the_same, sizeof(__pyx_k_Quality_string_has_not_the_same), 0, 1, 0, 0}, {&__pyx_kp_u_Quality_string_missing, __pyx_k_Quality_string_missing, sizeof(__pyx_k_Quality_string_missing), 0, 1, 0, 0}, @@ -40809,6 +45492,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_cigar_string, __pyx_k_cigar_string, sizeof(__pyx_k_cigar_string), 0, 0, 1, 1}, {&__pyx_n_s_cigartuples, __pyx_k_cigartuples, sizeof(__pyx_k_cigartuples), 0, 0, 1, 1}, {&__pyx_n_s_class, __pyx_k_class, sizeof(__pyx_k_class), 0, 0, 1, 1}, + {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, {&__pyx_n_s_collections, __pyx_k_collections, sizeof(__pyx_k_collections), 0, 0, 1, 1}, {&__pyx_n_s_compile, __pyx_k_compile, sizeof(__pyx_k_compile), 0, 0, 1, 1}, @@ -40825,6 +45509,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_decode, __pyx_k_decode, sizeof(__pyx_k_decode), 0, 0, 1, 1}, {&__pyx_n_u_deleted, __pyx_k_deleted, sizeof(__pyx_k_deleted), 0, 1, 0, 1}, {&__pyx_n_u_descr, __pyx_k_descr, sizeof(__pyx_k_descr), 0, 1, 0, 1}, + {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, @@ -40848,7 +45533,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_getvalue, __pyx_k_getvalue, sizeof(__pyx_k_getvalue), 0, 0, 1, 1}, {&__pyx_n_s_gzip, __pyx_k_gzip, sizeof(__pyx_k_gzip), 0, 0, 1, 1}, {&__pyx_kp_u_hard_clipped, __pyx_k_hard_clipped, sizeof(__pyx_k_hard_clipped), 0, 1, 0, 0}, - {&__pyx_kp_s_home_fabio_university_postdoc_h, __pyx_k_home_fabio_university_postdoc_h, sizeof(__pyx_k_home_fabio_university_postdoc_h), 0, 0, 1, 0}, {&__pyx_n_u_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 1, 0, 1}, {&__pyx_n_s_iadd, __pyx_k_iadd, sizeof(__pyx_k_iadd), 0, 0, 1, 1}, {&__pyx_n_s_iadd___locals_addval, __pyx_k_iadd___locals_addval, sizeof(__pyx_k_iadd___locals_addval), 0, 0, 1, 1}, @@ -40901,6 +45585,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_u_ndarray, __pyx_k_ndarray, sizeof(__pyx_k_ndarray), 0, 1, 0, 1}, {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, {&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0}, + {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1}, {&__pyx_n_s_next_reference_id, __pyx_k_next_reference_id, sizeof(__pyx_k_next_reference_id), 0, 0, 1, 1}, {&__pyx_n_s_next_reference_start, __pyx_k_next_reference_start, sizeof(__pyx_k_next_reference_start), 0, 0, 1, 1}, {&__pyx_kp_u_nmm, __pyx_k_nmm, sizeof(__pyx_k_nmm), 0, 1, 0, 0}, @@ -40920,8 +45605,18 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1}, {&__pyx_n_s_pattern, __pyx_k_pattern, sizeof(__pyx_k_pattern), 0, 0, 1, 1}, {&__pyx_n_u_phred, __pyx_k_phred, sizeof(__pyx_k_phred), 0, 1, 0, 1}, + {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1}, {&__pyx_n_s_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 0, 1, 1}, {&__pyx_n_s_pysam, __pyx_k_pysam, sizeof(__pyx_k_pysam), 0, 0, 1, 1}, + {&__pyx_kp_s_python3_src_HTSeq__HTSeq_pyx, __pyx_k_python3_src_HTSeq__HTSeq_pyx, sizeof(__pyx_k_python3_src_HTSeq__HTSeq_pyx), 0, 0, 1, 0}, + {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_Alignment, __pyx_k_pyx_unpickle_Alignment, sizeof(__pyx_k_pyx_unpickle_Alignment), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_AlignmentWithSequ, __pyx_k_pyx_unpickle_AlignmentWithSequ, sizeof(__pyx_k_pyx_unpickle_AlignmentWithSequ), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_BowtieAlignment, __pyx_k_pyx_unpickle_BowtieAlignment, sizeof(__pyx_k_pyx_unpickle_BowtieAlignment), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_CigarOperation, __pyx_k_pyx_unpickle_CigarOperation, sizeof(__pyx_k_pyx_unpickle_CigarOperation), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_SAM_Alignment, __pyx_k_pyx_unpickle_SAM_Alignment, sizeof(__pyx_k_pyx_unpickle_SAM_Alignment), 0, 0, 1, 1}, {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1}, {&__pyx_n_s_qfrom, __pyx_k_qfrom, sizeof(__pyx_k_qfrom), 0, 0, 1, 1}, {&__pyx_n_s_qname, __pyx_k_qname, sizeof(__pyx_k_qname), 0, 0, 1, 1}, @@ -40942,11 +45637,13 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1}, {&__pyx_n_s_read_as_aligned, __pyx_k_read_as_aligned, sizeof(__pyx_k_read_as_aligned), 0, 0, 1, 1}, {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1}, {&__pyx_n_s_ref_iv, __pyx_k_ref_iv, sizeof(__pyx_k_ref_iv), 0, 0, 1, 1}, {&__pyx_n_s_ref_left, __pyx_k_ref_left, sizeof(__pyx_k_ref_left), 0, 0, 1, 1}, {&__pyx_n_s_reference_end, __pyx_k_reference_end, sizeof(__pyx_k_reference_end), 0, 0, 1, 1}, {&__pyx_n_s_reference_id, __pyx_k_reference_id, sizeof(__pyx_k_reference_id), 0, 0, 1, 1}, {&__pyx_n_s_reference_start, __pyx_k_reference_start, sizeof(__pyx_k_reference_start), 0, 0, 1, 1}, + {&__pyx_n_s_result, __pyx_k_result, sizeof(__pyx_k_result), 0, 0, 1, 1}, {&__pyx_n_u_revcomp_of, __pyx_k_revcomp_of, sizeof(__pyx_k_revcomp_of), 0, 1, 0, 1}, {&__pyx_n_s_rfrom, __pyx_k_rfrom, sizeof(__pyx_k_rfrom), 0, 0, 1, 1}, {&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1}, @@ -40975,6 +45672,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_seq_and_qualstr_do_not_have_the, __pyx_k_seq_and_qualstr_do_not_have_the, sizeof(__pyx_k_seq_and_qualstr_do_not_have_the), 0, 1, 0, 0}, {&__pyx_kp_u_sequence_matched, __pyx_k_sequence_matched, sizeof(__pyx_k_sequence_matched), 0, 1, 0, 0}, {&__pyx_kp_u_sequence_mismatched, __pyx_k_sequence_mismatched, sizeof(__pyx_k_sequence_mismatched), 0, 1, 0, 0}, + {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, {&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1}, {&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1}, {&__pyx_n_u_skipped, __pyx_k_skipped, sizeof(__pyx_k_skipped), 0, 1, 0, 1}, @@ -40998,6 +45696,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_storage_2, __pyx_k_storage_2, sizeof(__pyx_k_storage_2), 0, 0, 1, 1}, {&__pyx_n_s_strand, __pyx_k_strand, sizeof(__pyx_k_strand), 0, 0, 1, 1}, {&__pyx_n_s_stranded, __pyx_k_stranded, sizeof(__pyx_k_stranded), 0, 0, 1, 1}, + {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0}, {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1}, {&__pyx_n_s_tags, __pyx_k_tags, sizeof(__pyx_k_tags), 0, 0, 1, 1}, {&__pyx_n_s_template_length, __pyx_k_template_length, sizeof(__pyx_k_template_length), 0, 0, 1, 1}, @@ -41019,6 +45718,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, {&__pyx_kp_u_unmatched_quote, __pyx_k_unmatched_quote, sizeof(__pyx_k_unmatched_quote), 0, 1, 0, 0}, {&__pyx_n_u_unnamed, __pyx_k_unnamed, sizeof(__pyx_k_unnamed), 0, 1, 0, 1}, + {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1}, {&__pyx_n_s_upper, __pyx_k_upper, sizeof(__pyx_k_upper), 0, 0, 1, 1}, {&__pyx_n_s_values, __pyx_k_values, sizeof(__pyx_k_values), 0, 0, 1, 1}, {&__pyx_n_s_vec, __pyx_k_vec, sizeof(__pyx_k_vec), 0, 0, 1, 1}, @@ -41043,7 +45743,7 @@ static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 716, __pyx_L1_error) __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 1227, __pyx_L1_error) __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(0, 1242, __pyx_L1_error) - __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) __PYX_ERR(2, 799, __pyx_L1_error) + __pyx_builtin_RuntimeError = 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222, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__36); __Pyx_GIVEREF(__pyx_tuple__36); @@ -41270,7 +45970,7 @@ static int __Pyx_InitCachedConstants(void) { * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__37 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__37)) __PYX_ERR(2, 259, __pyx_L1_error) + __pyx_tuple__37 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__37)) __PYX_ERR(3, 259, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__37); __Pyx_GIVEREF(__pyx_tuple__37); @@ -41281,7 +45981,7 @@ static int __Pyx_InitCachedConstants(void) { * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_tuple__38 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(2, 799, __pyx_L1_error) + __pyx_tuple__38 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(3, 799, __pyx_L1_error) 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__Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) __PYX_ERR(3, 861, __pyx_L1_error) /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ @@ -41761,7 +46498,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; - goto __pyx_L9_try_end; + goto __pyx_L7_try_end; __pyx_L2_error:; __Pyx_PyThreadState_assign __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -41783,7 +46520,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); - __pyx_L9_try_end:; + __pyx_L7_try_end:; } /* "HTSeq/_HTSeq.pyx":13 @@ -42166,19 +46903,19 @@ PyMODINIT_FUNC PyInit__HTSeq(void) * * cdef class SAM_Alignment(AlignmentWithSequenceReversal): */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1227, __pyx_L12_error) 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__pyx_L12_error) + __pyx_t_9 = Py_TYPE(__pyx_t_7)->tp_iternext; if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 1227, __pyx_L10_error) } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; for (;;) { @@ -42186,17 +46923,17 @@ PyMODINIT_FUNC PyInit__HTSeq(void) if (likely(PyList_CheckExact(__pyx_t_7))) { if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_7)) break; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely(0 < 0)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely(0 < 0)) __PYX_ERR(0, 1227, __pyx_L10_error) #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_7, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = PySequence_ITEM(__pyx_t_7, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L10_error) __Pyx_GOTREF(__pyx_t_6); #endif } else { if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_7)) break; #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely(0 < 0)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++; if (unlikely(0 < 0)) __PYX_ERR(0, 1227, __pyx_L10_error) #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_7, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = PySequence_ITEM(__pyx_t_7, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L10_error) __Pyx_GOTREF(__pyx_t_6); #endif } @@ -42206,7 +46943,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else __PYX_ERR(0, 1227, __pyx_L12_error) + else __PYX_ERR(0, 1227, __pyx_L10_error) } break; } @@ -42216,12 +46953,12 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __pyx_t_6 = 0; __Pyx_INCREF(__pyx_t_1); __Pyx_XDECREF_SET(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i, __pyx_t_1); - __pyx_t_6 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = __Pyx_PyInt_AddObjC(__pyx_t_1, __pyx_int_1, 1, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L10_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = __pyx_t_6; __pyx_t_6 = 0; - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L12_error) + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1227, __pyx_L10_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_x); __Pyx_GIVEREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_x); @@ -42229,19 +46966,19 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_INCREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i); __Pyx_GIVEREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) __PYX_ERR(0, 1227, __pyx_L12_error) + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) __PYX_ERR(0, 1227, __pyx_L10_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i); __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_x); - goto __pyx_L15_exit_scope; - __pyx_L12_error:; + goto __pyx_L13_exit_scope; + __pyx_L10_error:; __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_i); __Pyx_XDECREF(__pyx_8genexpr1__pyx_v_5HTSeq_6_HTSeq_x); goto __pyx_L1_error; - __pyx_L15_exit_scope:; + __pyx_L13_exit_scope:; } /* exit inner scope */ /* "HTSeq/_HTSeq.pyx":1226 @@ -42334,6 +47071,60 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; PyType_Modified(__pyx_ptype_5HTSeq_6_HTSeq_SAM_Alignment); + /* "(tree fragment)":1 + * def __pyx_unpickle_Alignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0x77bfdf2: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_17__pyx_unpickle_Alignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_Alignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":9 + * __pyx_unpickle_Alignment__set_state( result, __pyx_state) + * return result + * cdef __pyx_unpickle_Alignment__set_state(Alignment result, tuple __pyx_state): # <<<<<<<<<<<<<< + * result._read = __pyx_state[0]; result.iv = __pyx_state[1] + * if hasattr(result, '__dict__'): + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_19__pyx_unpickle_AlignmentWithSequenceReversal, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_AlignmentWithSequ, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":1 + * def __pyx_unpickle_BowtieAlignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0x482c176: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_21__pyx_unpickle_BowtieAlignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_BowtieAlignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":9 + * __pyx_unpickle_BowtieAlignment__set_state( result, __pyx_state) + * return result + * cdef __pyx_unpickle_BowtieAlignment__set_state(BowtieAlignment result, tuple __pyx_state): # <<<<<<<<<<<<<< + * result._read = __pyx_state[0]; result._read_as_sequenced = __pyx_state[1]; result.iv = __pyx_state[2]; result.read_as_aligned = __pyx_state[3]; result.reserved = __pyx_state[4]; result.substitutions = __pyx_state[5] + * if hasattr(result, '__dict__'): + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_23__pyx_unpickle_CigarOperation, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_CigarOperation, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":1 + * def __pyx_unpickle_SAM_Alignment(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * if __pyx_checksum != 0xf6933f3: + * from pickle import PickleError + */ + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5HTSeq_6_HTSeq_25__pyx_unpickle_SAM_Alignment, NULL, __pyx_n_s_HTSeq__HTSeq); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_SAM_Alignment, __pyx_t_1) < 0) __PYX_ERR(2, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + /* "HTSeq/_HTSeq.pyx":1 * import sys # <<<<<<<<<<<<<< * import os @@ -42362,7 +47153,7 @@ PyMODINIT_FUNC PyInit__HTSeq(void) __Pyx_XDECREF(__pyx_t_7); if (__pyx_m) { if (__pyx_d) { - __Pyx_AddTraceback("init HTSeq._HTSeq", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init HTSeq._HTSeq", 0, __pyx_lineno, __pyx_filename); } Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { @@ -42786,17 +47577,22 @@ static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, P PyCFunctionObject *func = (PyCFunctionObject*)func_obj; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS))); assert(nargs >= 0); assert(nargs == 0 || args != NULL); /* _PyCFunction_FastCallDict() must not be called with an exception set, because it may clear it (directly or indirectly) and so the caller loses its exception */ assert(!PyErr_Occurred()); - return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs); + } } -#endif // CYTHON_FAST_PYCCALL +#endif /* PyFunctionFastCall */ #if CYTHON_FAST_PYCALL @@ -42915,8 +47711,8 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_LeaveRecursiveCall(); return result; } -#endif // CPython < 3.6 -#endif // CYTHON_FAST_PYCALL +#endif +#endif /* PyObjectCall */ #if CYTHON_COMPILING_IN_CPYTHON @@ -42976,11 +47772,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec return __Pyx_PyFunction_FastCall(func, &arg, 1); } #endif -#ifdef __Pyx_CyFunction_USED - if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { -#else if (likely(PyCFunction_Check(func))) { -#endif if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { return __Pyx_PyObject_CallMethO(func, arg); #if CYTHON_FAST_PYCCALL @@ -43003,7 +47795,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec #endif /* PyObjectCallNoArg */ - #if CYTHON_COMPILING_IN_CPYTHON + #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { #if CYTHON_FAST_PYCALL if (PyFunction_Check(func)) { @@ -43024,20 +47816,20 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { #endif /* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } /* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", index, (index == 1) ? "" : "s"); } /* IterFinish */ - static CYTHON_INLINE int __Pyx_IterFinish(void) { + static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_FAST_THREAD_STATE PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; @@ -43072,7 +47864,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* UnpackItemEndCheck */ - static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); @@ -43084,7 +47876,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* GetModuleGlobalName */ - static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { PyObject *result; #if !CYTHON_AVOID_BORROWED_REFS result = PyDict_GetItem(__pyx_d, name); @@ -43102,7 +47894,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* BytesEquals */ - static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { + static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else @@ -43120,7 +47912,16 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } else if (length == 1) { return (equals == Py_EQ); } else { - int result = memcmp(ps1, ps2, (size_t)length); + int result; +#if CYTHON_USE_UNICODE_INTERNALS + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { @@ -43140,7 +47941,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* UnicodeEquals */ - static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { + static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else @@ -43180,6 +47981,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { goto return_ne; } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif kind = __Pyx_PyUnicode_KIND(s1); if (kind != __Pyx_PyUnicode_KIND(s2)) { goto return_ne; @@ -43224,7 +48040,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* SliceObject */ - static CYTHON_INLINE int __Pyx_PyObject_SetSlice(PyObject* obj, PyObject* value, + static CYTHON_INLINE int __Pyx_PyObject_SetSlice(PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { @@ -43322,7 +48138,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { if (op1 == op2) { Py_RETURN_TRUE; @@ -43407,7 +48223,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED #endif /* GetItemInt */ - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; r = PyObject_GetItem(o, j); @@ -43418,9 +48234,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, i); + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); Py_INCREF(r); return r; } @@ -43433,9 +48252,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, i); + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely((0 <= wrapped_i) & (wrapped_i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); Py_INCREF(r); return r; } @@ -43488,7 +48310,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); return 0; @@ -43501,17 +48323,17 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* None */ - static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } /* None */ - static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { + static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } /* SliceObject */ - static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, + static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { @@ -43608,7 +48430,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* FetchCommonType */ - static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { PyObject* fake_module; PyTypeObject* cached_type = NULL; fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); @@ -43647,7 +48469,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, } /* CythonFunction */ - static PyObject * + static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { @@ -44229,8 +49051,39 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py Py_INCREF(dict); } +/* GetAttr */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_COMPILING_IN_CPYTHON +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +/* HasAttr */ + static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { + PyObject *r; + if (unlikely(!__Pyx_PyBaseString_Check(n))) { + PyErr_SetString(PyExc_TypeError, + "hasattr(): attribute name must be string"); + return -1; + } + r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + /* PyObjectCallMethod0 */ - static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { + static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { PyObject *method, *result = NULL; method = __Pyx_PyObject_GetAttrStr(obj, method_name); if (unlikely(!method)) goto bad; @@ -44252,12 +49105,12 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } /* UnpackTupleError */ - static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { + static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { @@ -44268,7 +49121,7 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* UnpackTuple2 */ - static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, + static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int is_tuple, int has_known_size, int decref_tuple) { Py_ssize_t index; PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; @@ -44315,17 +49168,32 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py } /* dict_iter */ - static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, + static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_source_is_dict) { is_dict = is_dict || likely(PyDict_CheckExact(iterable)); *p_source_is_dict = is_dict; -#if !CYTHON_COMPILING_IN_PYPY if (is_dict) { +#if !CYTHON_COMPILING_IN_PYPY *p_orig_length = PyDict_Size(iterable); Py_INCREF(iterable); return iterable; - } +#elif PY_MAJOR_VERSION >= 3 + static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; + const char *name = PyUnicode_AsUTF8(method_name); + PyObject **pp = NULL; + if (strcmp(name, "iteritems") == 0) pp = &py_items; + else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; + else if (strcmp(name, "itervalues") == 0) pp = &py_values; + if (pp) { + if (!*pp) { + *pp = PyUnicode_FromString(name + 4); + if (!*pp) + return NULL; + } + method_name = *pp; + } #endif + } *p_orig_length = 0; if (method_name) { PyObject* iter; @@ -44411,7 +49279,7 @@ static CYTHON_INLINE int __Pyx_dict_iter_next( } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { @@ -44527,7 +49395,7 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U #endif /* decode_c_bytes */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( + static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { @@ -44554,7 +49422,7 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U } /* unicode_tailmatch */ - static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr, + static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr, Py_ssize_t start, Py_ssize_t end, int direction) { if (unlikely(PyTuple_Check(substr))) { Py_ssize_t i, count = PyTuple_GET_SIZE(substr); @@ -44579,7 +49447,7 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U } /* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY + #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { @@ -44695,7 +49563,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED #endif /* BufferFormatCheck */ - static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } @@ -45245,26 +50113,41 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { } /* BufferIndexError */ - static void __Pyx_RaiseBufferIndexError(int axis) { + static void __Pyx_RaiseBufferIndexError(int axis) { PyErr_Format(PyExc_IndexError, "Out of bounds on buffer access (axis %d)", axis); } /* BufferFallbackError */ - static void __Pyx_RaiseBufferFallbackError(void) { + static void __Pyx_RaiseBufferFallbackError(void) { PyErr_SetString(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } +/* GetAttr3 */ + static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = __Pyx_GetAttr(o, n); + if (unlikely(!r)) { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) + goto bad; + PyErr_Clear(); + r = d; + Py_INCREF(d); + } + return r; +bad: + return NULL; +} + /* None */ - static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } /* None */ - static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); @@ -45272,7 +50155,7 @@ static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { } /* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { *type = tstate->exc_type; *value = tstate->exc_value; @@ -45296,7 +50179,7 @@ static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject #endif /* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { PyObject *exc_type = tstate->curexc_type; if (exc_type == err) return 1; @@ -45306,7 +50189,7 @@ static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tsta #endif /* GetException */ - #if CYTHON_FAST_THREAD_STATE + #if CYTHON_FAST_THREAD_STATE static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { #else static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { @@ -45367,7 +50250,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* GetItemIntUnicode */ - static CYTHON_INLINE Py_UCS4 __Pyx_GetItemInt_Unicode_Fast(PyObject* ustring, Py_ssize_t i, + static CYTHON_INLINE Py_UCS4 __Pyx_GetItemInt_Unicode_Fast(PyObject* ustring, Py_ssize_t i, int wraparound, int boundscheck) { Py_ssize_t length; if (unlikely(__Pyx_PyUnicode_READY(ustring) < 0)) return (Py_UCS4)-1; @@ -45386,7 +50269,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* PyUnicode_Substring */ - static CYTHON_INLINE PyObject* __Pyx_PyUnicode_Substring( + static CYTHON_INLINE PyObject* __Pyx_PyUnicode_Substring( PyObject* text, Py_ssize_t start, Py_ssize_t stop) { Py_ssize_t length; if (unlikely(__Pyx_PyUnicode_READY(text) == -1)) return NULL; @@ -45412,7 +50295,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; @@ -45486,7 +50369,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* bytes_index */ - static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds) { + static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds) { if (check_bounds) { Py_ssize_t size = PyBytes_GET_SIZE(bytes); if (unlikely(index >= size) | ((index < 0) & unlikely(index < -size))) { @@ -45499,8 +50382,22 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return PyBytes_AS_STRING(bytes)[index]; } +/* ImportFrom */ + static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + /* CallNextTpTraverse */ - static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { + static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_traverse != current_tp_traverse) type = type->tp_base; @@ -45512,7 +50409,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* CallNextTpClear */ - static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { + static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_clear != current_tp_clear) type = type->tp_base; @@ -45523,7 +50420,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* SetVTable */ - static int __Pyx_SetVtable(PyObject *dict, void *vtable) { + static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 PyObject *ob = PyCapsule_New(vtable, 0, 0); #else @@ -45540,22 +50437,73 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return -1; } -/* ImportFrom */ - static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { - PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); - if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { - PyErr_Format(PyExc_ImportError, - #if PY_MAJOR_VERSION < 3 - "cannot import name %.230s", PyString_AS_STRING(name)); - #else - "cannot import name %S", name); - #endif +/* SetupReduce */ + #define __Pyx_setup_reduce_GET_ATTR_OR_BAD(res, obj, name) res = PyObject_GetAttrString(obj, name); if (res == NULL) goto BAD; +static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = PyObject_GetAttrString(meth, "__name__"); + if (name_attr) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (ret < 0) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject* builtin_object = NULL; + static PyObject *object_reduce = NULL; + static PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; + if (PyObject_HasAttrString(type_obj, "__getstate__")) goto GOOD; + if (object_reduce_ex == NULL) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(builtin_object, __pyx_b, "object"); + __Pyx_setup_reduce_GET_ATTR_OR_BAD(object_reduce, builtin_object, "__reduce__"); + __Pyx_setup_reduce_GET_ATTR_OR_BAD(object_reduce_ex, builtin_object, "__reduce_ex__"); + } + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce_ex, type_obj, "__reduce_ex__"); + if (reduce_ex == object_reduce_ex) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce, type_obj, "__reduce__"); + if (object_reduce == reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(reduce_cython, type_obj, "__reduce_cython__"); + ret = PyDict_SetItemString(((PyTypeObject*)type_obj)->tp_dict, "__reduce__", reduce_cython); if (ret < 0) goto BAD; + ret = PyDict_DelItemString(((PyTypeObject*)type_obj)->tp_dict, "__reduce_cython__"); if (ret < 0) goto BAD; + setstate = PyObject_GetAttrString(type_obj, "__setstate__"); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + __Pyx_setup_reduce_GET_ATTR_OR_BAD(setstate_cython, type_obj, "__setstate_cython__"); + ret = PyDict_SetItemString(((PyTypeObject*)type_obj)->tp_dict, "__setstate__", setstate_cython); if (ret < 0) goto BAD; + ret = PyDict_DelItemString(((PyTypeObject*)type_obj)->tp_dict, "__setstate_cython__"); if (ret < 0) goto BAD; + } + PyType_Modified((PyTypeObject*)type_obj); + } } - return value; + goto GOOD; +BAD: + if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); + ret = -1; +GOOD: + Py_XDECREF(builtin_object); + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; } /* GetNameInClass */ - static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name) { + static PyObject *__Pyx_GetNameInClass(PyObject *nmspace, PyObject *name) { PyObject *result; result = __Pyx_PyObject_GetAttrStr(nmspace, name); if (!result) @@ -45564,7 +50512,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) } /* ClassMethod */ - static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { + static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { #if CYTHON_COMPILING_IN_PYPY if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { return PyClassMethod_New(method); @@ -45608,8 +50556,42 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) return NULL; } +/* CLineInTraceback */ + static int __Pyx_CLineForTraceback(int c_line) { +#ifdef CYTHON_CLINE_IN_TRACEBACK + return ((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0; +#else + PyObject **cython_runtime_dict; + PyObject *use_cline; + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (unlikely(!cython_runtime_dict)) { + PyObject *ptype, *pvalue, *ptraceback; + PyObject *use_cline_obj; + PyErr_Fetch(&ptype, &pvalue, &ptraceback); + use_cline_obj = __Pyx_PyObject_GetAttrStr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + use_cline = NULL; + } + PyErr_Restore(ptype, pvalue, ptraceback); + } else { + use_cline = PyDict_GetItem(*_PyObject_GetDictPtr(__pyx_cython_runtime), __pyx_n_s_cline_in_traceback); + } + if (!use_cline) { + c_line = 0; + PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (PyObject_Not(use_cline) != 0) { + c_line = 0; + } + return c_line; +#endif +} + /* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + 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; @@ -45689,7 +50671,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { } /* AddTraceback */ - #include "compile.h" + #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( @@ -45748,12 +50730,15 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (c_line) { + c_line = __Pyx_CLineForTraceback(c_line); + } + 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); + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); } py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ @@ -45769,29 +50754,39 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, Py_XDECREF(py_frame); } -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; +/* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); } - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } - Py_DECREF(obj); - view->obj = NULL; } -#endif - - /* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ +/* CIntFromPyVerify */ + #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) @@ -45812,8 +50807,29 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return (target_type) value;\ } -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + /* CIntToPy */ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -45843,39 +50859,8 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } } -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(int) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), - little, !is_unsigned); - } -} - /* None */ - static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { + static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { long t = b; switch (e) { case 3: @@ -45900,7 +50885,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -45931,7 +50916,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* Declarations */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); @@ -45951,7 +50936,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Arithmetic */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); @@ -46086,7 +51071,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Declarations */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); @@ -46106,7 +51091,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* Arithmetic */ - #if CYTHON_CCOMPLEX + #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); @@ -46241,7 +51226,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { @@ -46272,19 +51257,19 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (long) val; + return (int) val; } } else #endif @@ -46293,32 +51278,32 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; @@ -46332,86 +51317,86 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (long) -1; + return (int) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; } #endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } @@ -46420,7 +51405,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - long val; + int val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -46440,40 +51425,40 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return val; } #endif - return (long) -1; + return (int) -1; } } else { - long val; + int val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; + "value too large to convert to int"); + return (int) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; + "can't convert negative value to int"); + return (int) -1; } /* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } - return (int) val; + return (long) val; } } else #endif @@ -46482,32 +51467,32 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; @@ -46521,86 +51506,86 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) - return (int) -1; + return (long) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; } #endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } @@ -46609,7 +51594,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else - int val; + long val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { @@ -46629,28 +51614,28 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return val; } #endif - return (int) -1; + return (long) -1; } } else { - int val; + long val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; + "value too large to convert to long"); + return (long) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + "can't convert negative value to long"); + return (long) -1; } /* CIntFromPy */ - static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { + static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_As_Py_intptr_t(PyObject *x) { const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = (Py_intptr_t) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -46839,7 +51824,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE npy_uint8 __Pyx_PyInt_As_npy_uint8(PyObject *x) { + static CYTHON_INLINE npy_uint8 __Pyx_PyInt_As_npy_uint8(PyObject *x) { const npy_uint8 neg_one = (npy_uint8) -1, const_zero = (npy_uint8) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -47028,7 +52013,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CIntFromPy */ - static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { const char neg_one = (char) -1, const_zero = (char) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 @@ -47217,7 +52202,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { + static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); @@ -47233,7 +52218,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } /* ModuleImport */ - #ifndef __PYX_HAVE_RT_ImportModule + #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; @@ -47251,7 +52236,7 @@ static PyObject *__Pyx_ImportModule(const char *name) { #endif /* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType + #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) @@ -47316,7 +52301,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif /* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { @@ -47341,6 +52326,8 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif if (!*t->p) return -1; + if (PyObject_Hash(*t->p) == -1) + PyErr_Clear(); ++t; } return 0; @@ -47349,11 +52336,11 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); } -static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { Py_ssize_t ignore; return __Pyx_PyObject_AsStringAndSize(o, &ignore); } -static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { #if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if ( #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII