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-typedef struct {
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-struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
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- *
- */
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-struct __pyx_obj_9csamtools_IndelCallerBase {
- PyObject_HEAD
- bam_maqindel_opt_t *options;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
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- int max_depth;
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- */
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-struct __pyx_obj_9csamtools_PileupRead {
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-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2816
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-struct __pyx_obj_9csamtools_SNPCall {
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-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
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-struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
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-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
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-struct __pyx_obj_9csamtools_IteratorRowSelection {
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- *
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-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
-
-static void __Pyx_WriteUnraisable(const char *name); /*proto*/
-
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
-
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-
-static void __Pyx_AddTraceback(const char *funcname); /*proto*/
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from __builtin__ */
-
-/* Module declarations from cpython.version */
-
-/* Module declarations from cpython.ref */
-
-/* Module declarations from cpython.exc */
-
-/* Module declarations from cpython.module */
-
-/* Module declarations from cpython.mem */
-
-/* Module declarations from cpython.tuple */
-
-/* Module declarations from cpython.list */
-
-/* Module declarations from libc.stdio */
-
-/* Module declarations from cpython.object */
-
-/* Module declarations from cpython.sequence */
-
-/* Module declarations from cpython.mapping */
-
-/* Module declarations from cpython.iterator */
-
-/* Module declarations from cpython.type */
-
-/* Module declarations from cpython.number */
-
-/* Module declarations from cpython.int */
-
-/* Module declarations from __builtin__ */
-
-/* Module declarations from cpython.bool */
-
-static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
-/* Module declarations from cpython.long */
-
-/* Module declarations from cpython.float */
-
-/* Module declarations from cpython.complex */
-
-/* Module declarations from cpython.string */
-
-/* Module declarations from cpython.unicode */
-
-/* Module declarations from cpython.dict */
-
-/* Module declarations from cpython.instance */
-
-/* Module declarations from cpython.function */
-
-/* Module declarations from cpython.method */
-
-/* Module declarations from cpython.weakref */
-
-/* Module declarations from cpython.getargs */
-
-/* Module declarations from cpython.pythread */
-
-/* Module declarations from cpython.cobject */
-
-/* Module declarations from cpython.oldbuffer */
-
-/* Module declarations from cpython.set */
-
-/* Module declarations from cpython.buffer */
-
-/* Module declarations from cpython.bytes */
-
-/* Module declarations from cpython.pycapsule */
-
-/* Module declarations from cpython */
-
-/* Module declarations from csamtools */
-
-static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorSNPCalls = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
-static char *__pyx_v_9csamtools_bam_nt16_rev_table;
-static int __pyx_v_9csamtools_max_pos;
-static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
-static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *, int, int, int); /*proto*/
-static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
-static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/
-static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-#define __Pyx_MODULE_NAME "csamtools"
-int __pyx_module_is_main_csamtools = 0;
-
-/* Implementation of csamtools */
-static PyObject *__pyx_builtin_open;
-static PyObject *__pyx_builtin_object;
-static PyObject *__pyx_builtin_map;
-static PyObject *__pyx_builtin_ValueError;
-static PyObject *__pyx_builtin_IOError;
-static PyObject *__pyx_builtin_OverflowError;
-static PyObject *__pyx_builtin_NotImplementedError;
-static PyObject *__pyx_builtin_KeyError;
-static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_cmp;
-static PyObject *__pyx_builtin_chr;
-static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_range;
-static char __pyx_k_1[] = "\t";
-static char __pyx_k_2[] = "\n";
-static char __pyx_k_3[] = "calling len() on closed file";
-static char __pyx_k_4[] = "could not open file `%s`";
-static char __pyx_k_5[] = "I/O operation on closed file";
-static char __pyx_k_6[] = "no sequence/region supplied.";
-static char __pyx_k_7[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_8[] = "";
-static char __pyx_k_9[] = "start out of range (%i)";
-static char __pyx_k_10[] = "end out of range (%i)";
-static char __pyx_k_11[] = "%s:%i-%i";
-static char __pyx_k_12[] = "invalid file opening mode `%s`";
-static char __pyx_k_13[] = "http:";
-static char __pyx_k_14[] = "ftp:";
-static char __pyx_k_15[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_16[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_17[] = "-";
-static char __pyx_k_18[] = "file `%s` not found";
-static char __pyx_k_19[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_20[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_21[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_22[] = ".bai";
-static char __pyx_k_23[] = "error while opening index `%s` ";
-static char __pyx_k_24[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_25[] = "[:-]";
-static char __pyx_k_26[] = "invalid reference `%s`";
-static char __pyx_k_27[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_28[] = "seek only available in bam files";
-static char __pyx_k_30[] = "fetch called on bamfile without index";
-static char __pyx_k_31[] = "callback functionality requires a region/reference";
-static char __pyx_k_32[] = "no index available for fetch";
-static char __pyx_k_33[] = "fetch called for samfile without header";
-static char __pyx_k_34[] = "fetch for a region is not available for sam files";
-static char __pyx_k_35[] = "callback not implemented yet";
-static char __pyx_k_36[] = "read %s: is unpaired";
-static char __pyx_k_37[] = "mate %s: is unmapped";
-static char __pyx_k_38[] = "mate not found";
-static char __pyx_k_40[] = "counting functionality requires a region/reference";
-static char __pyx_k_41[] = "count for a region is not available for sam files";
-static char __pyx_k_42[] = "no index available for pileup";
-static char __pyx_k_43[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_44[] = "@";
-static char __pyx_k_45[] = "header line without '@': '%s'";
-static char __pyx_k_46[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_47[] = ":";
-static char __pyx_k_48[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_49[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_50[] = "@%s";
-static char __pyx_k_51[] = "%s:%s";
-static char __pyx_k_52[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_53[] = "incomplete sequence information in '%s'";
-static char __pyx_k_54[] = "no index available for iteration";
-static char __pyx_k_55[] = "can only use this iterator on bam files";
-static char __pyx_k_56[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_57[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_59[] = "error during iteration";
-static char __pyx_k_60[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_61[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_62[] = "%c";
-static char __pyx_k_63[] = "create_string_buffer";
-static char __pyx_k_64[] = "<cccf";
-static char __pyx_k_65[] = "<cccb";
-static char __pyx_k_66[] = "<ccch";
-static char __pyx_k_67[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_68[] = "<ccci";
-static char __pyx_k_69[] = "<cccB";
-static char __pyx_k_70[] = "<cccH";
-static char __pyx_k_71[] = "<cccI";
-static char __pyx_k_72[] = "<cccc";
-static char __pyx_k_73[] = "<ccc%is";
-static char __pyx_k_74[] = "tags field too large";
-static char __pyx_k_75[] = "tag '%s' not present";
-static char __pyx_k_76[] = "Contig index";
-static char __pyx_k_77[] = "Mapped position on contig";
-static char __pyx_k_78[] = "Contig index for mate pair";
-static char __pyx_k_79[] = "Position of mate pair";
-static char __pyx_k_80[] = "Insert size";
-static char __pyx_k_81[] = "Binary flag";
-static char __pyx_k_82[] = "Count of cigar entries";
-static char __pyx_k_83[] = "Cigar entries";
-static char __pyx_k_84[] = "Mapping quality";
-static char __pyx_k_85[] = "Bam index bin number";
-static char __pyx_k_86[] = "Length of query name";
-static char __pyx_k_87[] = "Query name";
-static char __pyx_k_88[] = "Length of query sequence";
-static char __pyx_k_89[] = "Query sequence";
-static char __pyx_k_90[] = "Quality scores";
-static char __pyx_k_91[] = "Length of auxilary data";
-static char __pyx_k_92[] = "Maximum data length";
-static char __pyx_k_93[] = "Current data length";
-static char __pyx_k_94[] = "%-30s %-10s= %s";
-static char __pyx_k_95[] = "(";
-static char __pyx_k_96[] = ")";
-static char __pyx_k_97[] = "This class cannot be instantiated from Python";
-static char __pyx_k__A[] = "A";
-static char __pyx_k__C[] = "C";
-static char __pyx_k__D[] = "D";
-static char __pyx_k__F[] = "F";
-static char __pyx_k__I[] = "I";
-static char __pyx_k__S[] = "S";
-static char __pyx_k__Z[] = "Z";
-static char __pyx_k__b[] = "b";
-static char __pyx_k__c[] = "c";
-static char __pyx_k__d[] = "d";
-static char __pyx_k__f[] = "f";
-static char __pyx_k__i[] = "i";
-static char __pyx_k__n[] = "n";
-static char __pyx_k__r[] = "r";
-static char __pyx_k__s[] = "s";
-static char __pyx_k__w[] = "w";
-static char __pyx_k__x[] = "x";
-static char __pyx_k_100[] = "No such file or directory: '%s'";
-static char __pyx_k_101[] = "-o";
-static char __pyx_k_102[] = "option -o is forbidden in samtools view";
-static char __pyx_k_103[] = "_rms_mapping_quality";
-static char __pyx_k_104[] = "--> read %i %s %i";
-static char __pyx_k_105[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
-static char __pyx_k_106[] = "-------------------------------------\n";
-static char __pyx_k_107[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
-static char __pyx_k_108[] = "position %i out of bounds on reference sequence (len=%i)";
-static char __pyx_k_109[] = "no reads in region - no call";
-static char __pyx_k_110[] = "%s/%s";
-static char __pyx_k_111[] = "IndelCallerBase requires an pileup iterator with reference sequence";
-static char __pyx_k_112[] = "can only IndexReads on bam files";
-static char __pyx_k_113[] = "read %s not found";
-static char __pyx_k_114[] = "the query name (None if not present)";
-static char __pyx_k_115[] = "the :term:`cigar` alignment (None if not present).\n ";
-static char __pyx_k_116[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_117[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_118[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
-static char __pyx_k_119[] = "aligned query sequence quality values (None if not present)";
-static char __pyx_k_120[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_121[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_122[] = "Length of the aligned query sequence";
-static char __pyx_k_123[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n ";
-static char __pyx_k_124[] = "properties flag";
-static char __pyx_k_125[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_126[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_127[] = "0-based leftmost coordinate";
-static char __pyx_k_128[] = "properties bin";
-static char __pyx_k_129[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_130[] = "aligned end position of the read (read only). Returns\n None if not available.";
-static char __pyx_k_131[] = "aligned length of the read (read only). Returns None if\n not available.";
-static char __pyx_k_132[] = "mapping quality";
-static char __pyx_k_133[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_134[] = "the position of the mate";
-static char __pyx_k_135[] = "the insert size";
-static char __pyx_k_136[] = "true if read is paired in sequencing";
-static char __pyx_k_137[] = "true if read is mapped in a proper pair";
-static char __pyx_k_138[] = "true if read itself is unmapped";
-static char __pyx_k_139[] = "true if the mate is unmapped";
-static char __pyx_k_140[] = "true if read is mapped to reverse strand";
-static char __pyx_k_141[] = "true is read is mapped to reverse strand";
-static char __pyx_k_142[] = "true if this is read1";
-static char __pyx_k_143[] = "true if this is read2";
-static char __pyx_k_144[] = "true if not primary alignment";
-static char __pyx_k_145[] = "true if QC failure";
-static char __pyx_k_146[] = "true if optical or PCR duplicate";
-static char __pyx_k_147[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_148[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_149[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_150[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_151[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_152[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_153[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
-static char __pyx_k_154[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_155[] = "number of reads mapping to this column.";
-static char __pyx_k_156[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_157[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_158[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_159[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_160[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_161[] = "current sequence length.";
-static char __pyx_k_162[] = "nucleotide position of SNP.";
-static char __pyx_k_163[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_164[] = "the genotype called.";
-static char __pyx_k_165[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_166[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_167[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_168[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_169[] = "sequence of first allele.";
-static char __pyx_k_170[] = "sequence of second allele.";
-static char __pyx_k_171[] = "reads supporting first allele.";
-static char __pyx_k_172[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_173[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
-static char __pyx_k_174[] = "\n stderr is captured. \n ";
-static char __pyx_k_175[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_176[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
-static char __pyx_k_177[] = "Fastafile._isOpen (line 265)";
-static char __pyx_k_178[] = "Fastafile._open (line 275)";
-static char __pyx_k_179[] = "Fastafile.fetch (line 306)";
-static char __pyx_k_180[] = "Samfile._isOpen (line 464)";
-static char __pyx_k_181[] = "Samfile._hasIndex (line 468)";
-static char __pyx_k_182[] = "Samfile._open (line 472)";
-static char __pyx_k_183[] = "Samfile.gettid (line 612)";
-static char __pyx_k_184[] = "Samfile.getrname (line 621)";
-static char __pyx_k_185[] = "Samfile._parseRegion (line 637)";
-static char __pyx_k_186[] = "Samfile.seek (line 691)";
-static char __pyx_k_187[] = "Samfile.tell (line 702)";
-static char __pyx_k_188[] = "Samfile.fetch (line 713)";
-static char __pyx_k_189[] = "Samfile.mate (line 782)";
-static char __pyx_k_190[] = "Samfile.count (line 825)";
-static char __pyx_k_191[] = "Samfile.pileup (line 869)";
-static char __pyx_k_192[] = "Samfile.close (line 953)";
-static char __pyx_k_193[] = "Samfile.write (line 969)";
-static char __pyx_k_194[] = "Samfile._buildLine (line 1078)";
-static char __pyx_k_195[] = "Samfile.__next__ (line 1173)";
-static char __pyx_k_196[] = "IteratorRowRegion.__next__ (line 1281)";
-static char __pyx_k_197[] = "IteratorRowAll.__next__ (line 1340)";
-static char __pyx_k_198[] = "IteratorRowAllRefs.__next__ (line 1375)";
-static char __pyx_k_199[] = "IteratorRowSelection.__next__ (line 1459)";
-static char __pyx_k_200[] = "IteratorRowSelection";
-static char __pyx_k_201[] = "IteratorColumn.addReference (line 1634)";
-static char __pyx_k_202[] = "IteratorColumn.hasReference (line 1642)";
-static char __pyx_k_203[] = "IteratorColumnRegion.__next__ (line 1724)";
-static char __pyx_k_204[] = "IteratorColumnRegion";
-static char __pyx_k_205[] = "IteratorColumnAllRefs.__next__ (line 1755)";
-static char __pyx_k_206[] = "IteratorColumnAllRefs";
-static char __pyx_k_207[] = "AlignedRead.__str__ (line 1903)";
-static char __pyx_k_208[] = "AlignedRead.compare (line 1928)";
-static char __pyx_k_209[] = "AlignedRead.overlap (line 2512)";
-static char __pyx_k_210[] = "AlignedRead.opt (line 2541)";
-static char __pyx_k_211[] = "AlignedRead.fancy_str (line 2563)";
-static char __pyx_k_212[] = "Outs.setdevice (line 2705)";
-static char __pyx_k_213[] = "Outs.setfile (line 2710)";
-static char __pyx_k_214[] = "Outs.restore (line 2723)";
-static char __pyx_k_215[] = "_samtools_dispatch (line 2734)";
-static char __pyx_k_216[] = "IteratorSNPCalls.__next__ (line 2969)";
-static char __pyx_k_217[] = "SNPCaller.call (line 3041)";
-static char __pyx_k_218[] = "IndelCaller.call (line 3306)";
-static char __pyx_k_219[] = "IteratorIndelCalls.__next__ (line 3353)";
-static char __pyx_k_220[] = "IndexedReads.build (line 3406)";
-static char __pyx_k__AS[] = "AS";
-static char __pyx_k__CL[] = "CL";
-static char __pyx_k__CN[] = "CN";
-static char __pyx_k__CO[] = "CO";
-static char __pyx_k__DS[] = "DS";
-static char __pyx_k__DT[] = "DT";
-static char __pyx_k__GO[] = "GO";
-static char __pyx_k__HD[] = "HD";
-static char __pyx_k__ID[] = "ID";
-static char __pyx_k__LB[] = "LB";
-static char __pyx_k__LN[] = "LN";
-static char __pyx_k__M5[] = "M5";
-static char __pyx_k__PG[] = "PG";
-static char __pyx_k__PI[] = "PI";
-static char __pyx_k__PL[] = "PL";
-static char __pyx_k__PN[] = "PN";
-static char __pyx_k__PU[] = "PU";
-static char __pyx_k__RG[] = "RG";
-static char __pyx_k__SM[] = "SM";
-static char __pyx_k__SN[] = "SN";
-static char __pyx_k__SO[] = "SO";
-static char __pyx_k__SP[] = "SP";
-static char __pyx_k__SQ[] = "SQ";
-static char __pyx_k__UR[] = "UR";
-static char __pyx_k__VN[] = "VN";
-static char __pyx_k___r[] = "_r";
-static char __pyx_k__fd[] = "fd";
-static char __pyx_k__fp[] = "fp";
-static char __pyx_k__id[] = "id";
-static char __pyx_k__os[] = "os";
-static char __pyx_k__rb[] = "rb";
-static char __pyx_k__re[] = "re";
-static char __pyx_k__wb[] = "wb";
-static char __pyx_k__wh[] = "wh";
-static char __pyx_k__all[] = "all";
-static char __pyx_k__bam[] = "bam";
-static char __pyx_k__beg[] = "beg";
-static char __pyx_k__bin[] = "bin";
-static char __pyx_k__chr[] = "chr";
-static char __pyx_k__cmp[] = "cmp";
-static char __pyx_k__dup[] = "dup";
-static char __pyx_k__end[] = "end";
-static char __pyx_k__map[] = "map";
-static char __pyx_k__opt[] = "opt";
-static char __pyx_k__plp[] = "plp";
-static char __pyx_k__pos[] = "pos";
-static char __pyx_k__q_r[] = "q_r";
-static char __pyx_k__raw[] = "raw";
-static char __pyx_k__seq[] = "seq";
-static char __pyx_k__sys[] = "sys";
-static char __pyx_k__tid[] = "tid";
-static char __pyx_k__wbu[] = "wbu";
-static char __pyx_k__Outs[] = "Outs";
-static char __pyx_k___pos[] = "_pos";
-static char __pyx_k___tid[] = "_tid";
-static char __pyx_k__args[] = "args";
-static char __pyx_k__call[] = "call";
-static char __pyx_k__cnt1[] = "cnt1";
-static char __pyx_k__cnt2[] = "cnt2";
-static char __pyx_k__core[] = "core";
-static char __pyx_k__data[] = "data";
-static char __pyx_k__dup2[] = "dup2";
-static char __pyx_k__flag[] = "flag";
-static char __pyx_k__hash[] = "hash";
-static char __pyx_k__iter[] = "iter";
-static char __pyx_k__join[] = "join";
-static char __pyx_k__mapq[] = "mapq";
-static char __pyx_k__mask[] = "mask";
-static char __pyx_k__mate[] = "mate";
-static char __pyx_k__mode[] = "mode";
-static char __pyx_k__mpos[] = "mpos";
-static char __pyx_k__mrnm[] = "mrnm";
-static char __pyx_k__mtid[] = "mtid";
-static char __pyx_k__n_pu[] = "n_pu";
-static char __pyx_k__name[] = "name";
-static char __pyx_k__open[] = "open";
-static char __pyx_k__path[] = "path";
-static char __pyx_k__port[] = "port";
-static char __pyx_k__qpos[] = "qpos";
-static char __pyx_k__qseq[] = "qseq";
-static char __pyx_k__qual[] = "qual";
-static char __pyx_k__rlen[] = "rlen";
-static char __pyx_k__seek[] = "seek";
-static char __pyx_k__self[] = "self";
-static char __pyx_k__tags[] = "tags";
-static char __pyx_k__tell[] = "tell";
-static char __pyx_k__text[] = "text";
-static char __pyx_k__view[] = "view";
-static char __pyx_k___call[] = "_call";
-static char __pyx_k___open[] = "_open";
-static char __pyx_k___qpos[] = "_qpos";
-static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__build[] = "build";
-static char __pyx_k__cigar[] = "cigar";
-static char __pyx_k__close[] = "close";
-static char __pyx_k__cnext[] = "cnext";
-static char __pyx_k__count[] = "count";
-static char __pyx_k__fetch[] = "fetch";
-static char __pyx_k__flush[] = "flush";
-static char __pyx_k__indel[] = "indel";
-static char __pyx_k__index[] = "index";
-static char __pyx_k__isbam[] = "isbam";
-static char __pyx_k__isize[] = "isize";
-static char __pyx_k__l_aux[] = "l_aux";
-static char __pyx_k__level[] = "level";
-static char __pyx_k__n_hap[] = "n_hap";
-static char __pyx_k__n_plp[] = "n_plp";
-static char __pyx_k__q_cns[] = "q_cns";
-static char __pyx_k__q_ref[] = "q_ref";
-static char __pyx_k__qname[] = "qname";
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-static char __pyx_k__reset[] = "reset";
-static char __pyx_k__rname[] = "rname";
-static char __pyx_k__setfd[] = "setfd";
-static char __pyx_k__split[] = "split";
-static char __pyx_k__start[] = "start";
-static char __pyx_k__strip[] = "strip";
-static char __pyx_k__theta[] = "theta";
-static char __pyx_k__types[] = "types";
-static char __pyx_k__where[] = "where";
-static char __pyx_k__write[] = "write";
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-static char __pyx_k___level[] = "_level";
-static char __pyx_k__ctypes[] = "ctypes";
-static char __pyx_k__errmod[] = "errmod";
-static char __pyx_k__exists[] = "exists";
-static char __pyx_k__fields[] = "fields";
-static char __pyx_k__fileno[] = "fileno";
-static char __pyx_k__gettid[] = "gettid";
-static char __pyx_k__header[] = "header";
-static char __pyx_k__indel1[] = "indel1";
-static char __pyx_k__indel2[] = "indel2";
-static char __pyx_k__is_del[] = "is_del";
-static char __pyx_k__l_qseq[] = "l_qseq";
-static char __pyx_k__l_text[] = "l_text";
-static char __pyx_k__m_data[] = "m_data";
-static char __pyx_k__method[] = "method";
-static char __pyx_k__object[] = "object";
-static char __pyx_k__offset[] = "offset";
-static char __pyx_k__pileup[] = "pileup";
-static char __pyx_k__record[] = "record";
-static char __pyx_k__region[] = "region";
-static char __pyx_k__remove[] = "remove";
-static char __pyx_k__reopen[] = "reopen";
-static char __pyx_k__retval[] = "retval";
-static char __pyx_k__rg2lib[] = "rg2lib";
-static char __pyx_k__stderr[] = "stderr";
-static char __pyx_k__stdout[] = "stdout";
-static char __pyx_k__struct[] = "struct";
-static char __pyx_k__system[] = "system";
-static char __pyx_k__IOError[] = "IOError";
-static char __pyx_k__IntType[] = "IntType";
-static char __pyx_k__O_CREAT[] = "O_CREAT";
-static char __pyx_k__Samfile[] = "Samfile";
-static char __pyx_k__Windows[] = "Windows";
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-static char __pyx_k____del__[] = "__del__";
-static char __pyx_k____str__[] = "__str__";
-static char __pyx_k___isOpen[] = "_isOpen";
-static char __pyx_k___is_del[] = "_is_del";
-static char __pyx_k__compare[] = "compare";
-static char __pyx_k__devnull[] = "devnull";
-static char __pyx_k__is_head[] = "is_head";
-static char __pyx_k__is_tail[] = "is_tail";
-static char __pyx_k__isupper[] = "isupper";
-static char __pyx_k__l_qname[] = "l_qname";
-static char __pyx_k__mkstemp[] = "mkstemp";
-static char __pyx_k__n_cigar[] = "n_cigar";
-static char __pyx_k__options[] = "options";
-static char __pyx_k__overlap[] = "overlap";
-static char __pyx_k__pileups[] = "pileups";
-static char __pyx_k__q_indel[] = "q_indel";
-static char __pyx_k__r_indel[] = "r_indel";
-static char __pyx_k__release[] = "release";
-static char __pyx_k__restore[] = "restore";
-static char __pyx_k__rowiter[] = "rowiter";
-static char __pyx_k__samfile[] = "samfile";
-static char __pyx_k__seq_len[] = "seq_len";
-static char __pyx_k__setfile[] = "setfile";
-static char __pyx_k__stepper[] = "stepper";
-static char __pyx_k__streams[] = "streams";
-static char __pyx_k__DictType[] = "DictType";
-static char __pyx_k__KeyError[] = "KeyError";
-static char __pyx_k__O_WRONLY[] = "O_WRONLY";
-static char __pyx_k____dict__[] = "__dict__";
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-static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
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-static char __pyx_k___is_head[] = "_is_head";
-static char __pyx_k___is_tail[] = "_is_tail";
-static char __pyx_k___logfile[] = "_logfile";
-static char __pyx_k__calcsize[] = "calcsize";
-static char __pyx_k__callback[] = "callback";
-static char __pyx_k__cap_mapQ[] = "cap_mapQ";
-static char __pyx_k__cnt_anti[] = "cnt_anti";
-static char __pyx_k__coverage[] = "coverage";
-static char __pyx_k__data_len[] = "data_len";
-static char __pyx_k__exc_type[] = "exc_type";
-static char __pyx_k__filename[] = "filename";
-static char __pyx_k__genotype[] = "genotype";
-static char __pyx_k__getrname[] = "getrname";
-static char __pyx_k__het_rate[] = "het_rate";
-static char __pyx_k__isremote[] = "isremote";
-static char __pyx_k__iterdata[] = "iterdata";
-static char __pyx_k__nextiter[] = "nextiter";
-static char __pyx_k__platform[] = "platform";
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-static char __pyx_k__stderr_f[] = "stderr_f";
-static char __pyx_k__stderr_h[] = "stderr_h";
-static char __pyx_k__tempfile[] = "tempfile";
-static char __pyx_k__template[] = "template";
-static char __pyx_k__Fastafile[] = "Fastafile";
-static char __pyx_k__FloatType[] = "FloatType";
-static char __pyx_k__SNPCaller[] = "SNPCaller";
-static char __pyx_k__TypeError[] = "TypeError";
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-static char __pyx_k___delegate[] = "_delegate";
-static char __pyx_k___filename[] = "_filename";
-static char __pyx_k___genotype[] = "_genotype";
-static char __pyx_k___hasIndex[] = "_hasIndex";
-static char __pyx_k__alignment[] = "alignment";
-static char __pyx_k__exc_value[] = "exc_value";
-static char __pyx_k__fancy_str[] = "fancy_str";
-static char __pyx_k__fastafile[] = "fastafile";
-static char __pyx_k__itertools[] = "itertools";
-static char __pyx_k__max_depth[] = "max_depth";
-static char __pyx_k__min_baseQ[] = "min_baseQ";
-static char __pyx_k__n_targets[] = "n_targets";
-static char __pyx_k__pack_into[] = "pack_into";
-static char __pyx_k__positions[] = "positions";
-static char __pyx_k__readlines[] = "readlines";
-static char __pyx_k__reference[] = "reference";
-static char __pyx_k__setdevice[] = "setdevice";
-static char __pyx_k__traceback[] = "traceback";
-static char __pyx_k__until_eof[] = "until_eof";
-static char __pyx_k__PileupRead[] = "PileupRead";
-static char __pyx_k__ValueError[] = "ValueError";
-static char __pyx_k___alignment[] = "_alignment";
-static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__reads_diff[] = "reads_diff";
-static char __pyx_k__startswith[] = "startswith";
-static char __pyx_k__target_len[] = "target_len";
-static char __pyx_k__AlignedRead[] = "AlignedRead";
-static char __pyx_k__IndelCaller[] = "IndelCaller";
-static char __pyx_k__IteratorRow[] = "IteratorRow";
-static char __pyx_k__PileupProxy[] = "PileupProxy";
-static char __pyx_k__StderrStore[] = "StderrStore";
-static char __pyx_k__collections[] = "collections";
-static char __pyx_k__current_pos[] = "current_pos";
-static char __pyx_k__defaultdict[] = "defaultdict";
-static char __pyx_k__getSequence[] = "getSequence";
-static char __pyx_k__nreferences[] = "nreferences";
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-static char __pyx_k__IteratorRowAllRefs[] = "IteratorRowAllRefs";
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- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
- #endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
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- if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- /*--- Initialize various global constants etc. ---*/
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- if (__pyx_module_is_main_csamtools) {
- if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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- /*--- Builtin init code ---*/
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- /*--- Global init code ---*/
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- /*--- Type init code ---*/
- __pyx_ptype_9csamtools_file = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "file", sizeof(PyFileObject), 0); if (unlikely(!__pyx_ptype_9csamtools_file)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_11AlignedRead___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_11AlignedRead___str__.doc = __pyx_doc_9csamtools_11AlignedRead___str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead___str__;
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- }
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
- __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
- __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
- __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
- __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
- __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._buildHeader = (void(*)(void))__pyx_f_9csamtools_7Samfile__buildHeader;
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- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.cnext = (void(*)(void))__pyx_f_9csamtools_7Samfile_cnext;
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- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_7Samfile___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_7Samfile___next__.doc = __pyx_doc_9csamtools_7Samfile___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
- __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_Fastafile._fetch = (void(*)(void))__pyx_f_9csamtools_9Fastafile__fetch;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
- __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.cnext = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
- __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__.doc = __pyx_doc_9csamtools_14IteratorRowAll___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
- __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.cnext = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_cnext;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.getSequence = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setMask = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setMask;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.reset = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_reset;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
- __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
- __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
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-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
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-
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-{
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- #else
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- return 1;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- return 0;
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- PyErr_Format(PyExc_TypeError,
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- "%s() got an unexpected keyword argument '%s'",
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- #endif
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-
-static void __Pyx_RaiseDoubleKeywordsError(
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- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
- #endif
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
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- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *number, *more_or_less;
-
- if (num_found < num_min) {
- num_expected = num_min;
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- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
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- }
- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
- #else
- "%s() takes %s %zd positional argument%s (%zd given)",
- #endif
- func_name, more_or_less, num_expected, number, num_found);
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
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- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
-
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
- values[name-argnames] = value;
- } else {
- /* unexpected keyword found */
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- }
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
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- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
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- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
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- local_value = tstate->curexc_value;
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- tstate->curexc_traceback = 0;
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- if (unlikely(tstate->curexc_type))
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
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- Py_INCREF(local_value);
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-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
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-
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
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-static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
- long q = a / b;
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- return q;
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-
-static CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
- long r = a % b;
- r += ((r != 0) & ((r ^ b) < 0)) * b;
- return r;
-}
-
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
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-
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
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- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
- PyObject *py_import = 0;
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
-bad:
- Py_XDECREF(empty_list);
- Py_XDECREF(py_import);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static PyObject *__Pyx_CreateClass(
- PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
-{
- PyObject *py_modname;
- PyObject *result = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_modname = PyString_FromString(modname);
- #else
- py_modname = PyUnicode_FromString(modname);
- #endif
- if (!py_modname)
- goto bad;
- if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- result = PyClass_New(bases, dict, name);
- #else
- result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
- #endif
-bad:
- Py_XDECREF(py_modname);
- return result;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(uint32_t) == sizeof(char)) ||
- (sizeof(uint32_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(uint32_t) == sizeof(int)) ||
- (sizeof(uint32_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
- little, !is_unsigned);
- }
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint32_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint32_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint32_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint32_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint32_t)-1;
- }
-}
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) {
- const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(int32_t) == sizeof(char)) ||
- (sizeof(int32_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(int32_t) == sizeof(int)) ||
- (sizeof(int32_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(int32_t),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
- const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(int64_t) == sizeof(char)) ||
- (sizeof(int64_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(int64_t) == sizeof(int)) ||
- (sizeof(int64_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(int64_t),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint64_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint64_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint64_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint64_t)-1;
- }
-}
-
-static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
- const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(int32_t) == sizeof(char)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(int32_t) == sizeof(short)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(int32_t) == sizeof(int)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(int32_t) == sizeof(long)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- int32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (int32_t)-1;
- }
-}
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) {
- const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(uint8_t) == sizeof(char)) ||
- (sizeof(uint8_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(uint8_t) == sizeof(int)) ||
- (sizeof(uint8_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint8_t),
- little, !is_unsigned);
- }
-}
-
-#if PY_MAJOR_VERSION < 3
-static PyObject *__Pyx_GetStdout(void) {
- PyObject *f = PySys_GetObject((char *)"stdout");
- if (!f) {
- PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
- }
- return f;
-}
-
-static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
- PyObject* v;
- int i;
-
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
- if (PyFile_SoftSpace(f, 1)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- v = PyTuple_GET_ITEM(arg_tuple, i);
- if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyString_Check(v)) {
- char *s = PyString_AsString(v);
- Py_ssize_t len = PyString_Size(v);
- if (len > 0 &&
- isspace(Py_CHARMASK(s[len-1])) &&
- s[len-1] != ' ')
- PyFile_SoftSpace(f, 0);
- }
- }
- if (newline) {
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- PyFile_SoftSpace(f, 0);
- }
- return 0;
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
- PyObject* kwargs = 0;
- PyObject* result = 0;
- PyObject* end_string;
- if (unlikely(!__pyx_print)) {
- __pyx_print = __Pyx_GetAttrString(__pyx_b, "print");
- if (!__pyx_print)
- return -1;
- }
- if (stream) {
- kwargs = PyDict_New();
- if (unlikely(!kwargs))
- return -1;
- if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0))
- goto bad;
- if (!newline) {
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- goto bad;
- if (PyDict_SetItemString(kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- goto bad;
- }
- Py_DECREF(end_string);
- }
- } else if (!newline) {
- if (unlikely(!__pyx_print_kwargs)) {
- __pyx_print_kwargs = PyDict_New();
- if (unlikely(!__pyx_print_kwargs))
- return -1;
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- return -1;
- if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- return -1;
- }
- Py_DECREF(end_string);
- }
- kwargs = __pyx_print_kwargs;
- }
- result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
- if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
- Py_DECREF(kwargs);
- if (!result)
- return -1;
- Py_DECREF(result);
- return 0;
-bad:
- if (kwargs != __pyx_print_kwargs)
- Py_XDECREF(kwargs);
- return -1;
-}
-
-#endif
-
-#if PY_MAJOR_VERSION < 3
-
-static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- if (PyFile_SoftSpace(f, 0)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- return 0;
- /* the line below is just to avoid compiler
- * compiler warnings about unused functions */
- return __Pyx_Print(f, NULL, 0);
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
- int res;
- PyObject* arg_tuple = PyTuple_New(1);
- if (unlikely(!arg_tuple))
- return -1;
- Py_INCREF(o);
- PyTuple_SET_ITEM(arg_tuple, 0, o);
- res = __Pyx_Print(stream, arg_tuple, 1);
- Py_DECREF(arg_tuple);
- return res;
-}
-
-#endif
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(uint64_t) == sizeof(char)) ||
- (sizeof(uint64_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(uint64_t) == sizeof(int)) ||
- (sizeof(uint64_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint64_t),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static void __Pyx_WriteUnraisable(const char *name) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- long size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
-
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(class_name);
- #else
- py_name = PyUnicode_FromString(class_name);
- #endif
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- PyErr_Warn(NULL, warning);
- #else
- PyErr_WarnEx(NULL, warning, 0);
- #endif
- }
- else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(name);
- #else
- py_name = PyUnicode_FromString(name);
- #endif
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-
-static void __Pyx_AddTraceback(const char *funcname) {
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- PyObject *py_globals = 0;
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(__pyx_filename);
- #else
- py_srcfile = PyUnicode_FromString(__pyx_filename);
- #endif
- if (!py_srcfile) goto bad;
- if (__pyx_clineno) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_code = PyCode_New(
- 0, /*int argcount,*/
- #if PY_MAJOR_VERSION >= 3
- 0, /*int kwonlyargcount,*/
- #endif
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- __pyx_lineno, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- if (!py_code) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = __pyx_lineno;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-/* Type Conversion Functions */
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
+++ /dev/null
-/* Generated by Cython 0.13 on Thu May 5 14:57:46 2011 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
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-
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-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
- PyObject *r;
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-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
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-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
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-static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
-static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
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-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact); /*proto*/
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-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
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-#if PY_MAJOR_VERSION >= 3
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- Py_INCREF(value);
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- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
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-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
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-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
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-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
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-static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
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-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
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-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
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-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
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-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
-
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
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-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
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-static void __Pyx_AddTraceback(const char *funcname); /*proto*/
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-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from cpython.version */
-
-/* Module declarations from cpython.ref */
-
-/* Module declarations from cpython.exc */
-
-/* Module declarations from cpython.module */
-
-/* Module declarations from cpython.mem */
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-/* Module declarations from cpython.tuple */
-
-/* Module declarations from cpython.list */
-
-/* Module declarations from libc.stdio */
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-/* Module declarations from cpython.object */
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-/* Module declarations from cpython.mapping */
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-/* Module declarations from cpython.iterator */
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-/* Module declarations from cpython.type */
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-/* Module declarations from cpython.number */
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-/* Module declarations from cpython.int */
-
-/* Module declarations from __builtin__ */
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-/* Module declarations from cpython.bool */
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-static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
-/* Module declarations from cpython.long */
-
-/* Module declarations from cpython.float */
-
-/* Module declarations from cpython.complex */
-
-/* Module declarations from cpython.string */
-
-/* Module declarations from cpython.unicode */
-
-/* Module declarations from cpython.dict */
-
-/* Module declarations from cpython.instance */
-
-/* Module declarations from cpython.function */
-
-/* Module declarations from cpython.method */
-
-/* Module declarations from cpython.weakref */
-
-/* Module declarations from cpython.getargs */
-
-/* Module declarations from cpython.pythread */
-
-/* Module declarations from cpython.cobject */
-
-/* Module declarations from cpython.oldbuffer */
-
-/* Module declarations from cpython.set */
-
-/* Module declarations from cpython.buffer */
-
-/* Module declarations from cpython.bytes */
-
-/* Module declarations from cpython.pycapsule */
-
-/* Module declarations from cpython */
-
-/* Module declarations from TabProxies */
-
-static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0;
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-static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
-/* Module declarations from ctabix */
-
-static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
-#define __Pyx_MODULE_NAME "ctabix"
-int __pyx_module_is_main_ctabix = 0;
-
-/* Implementation of ctabix */
-static PyObject *__pyx_builtin_IOError;
-static PyObject *__pyx_builtin_ValueError;
-static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_OSError;
-static PyObject *__pyx_builtin_ord;
-static PyObject *__pyx_builtin_KeyError;
-static char __pyx_k_1[] = "invalid file opening mode `%s`";
-static char __pyx_k_2[] = ".tbi";
-static char __pyx_k_3[] = "file `%s` not found";
-static char __pyx_k_4[] = "index `%s` not found";
-static char __pyx_k_5[] = "could not open file `%s`";
-static char __pyx_k_6[] = "%s:%i-%i";
-static char __pyx_k_7[] = "invalid region `%s`";
-static char __pyx_k_8[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_9[] = "start out of range (%i)";
-static char __pyx_k_10[] = "end out of range (%i)";
-static char __pyx_k_11[] = "I/O operation on closed file";
-static char __pyx_k_12[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_13[] = "can't open header.\n";
-static char __pyx_k_15[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_16[] = "could not open '%s' for writing";
-static char __pyx_k_17[] = "could not open '%s' for reading";
-static char __pyx_k_18[] = "writing failed";
-static char __pyx_k_20[] = "#";
-static char __pyx_k_22[] = "No such file '%s'";
-static char __pyx_k_23[] = ".gz";
-static char __pyx_k_24[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_25[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_26[] = ",";
-static char __pyx_k_27[] = "chromosome names";
-static char __pyx_k_28[] = "Tabixfile._isOpen (line 19)";
-static char __pyx_k_29[] = "Tabixfile._open (line 23)";
-static char __pyx_k_30[] = "Tabixfile._parseRegion (line 57)";
-static char __pyx_k_31[] = "Tabixfile.fetch (line 102)";
-static char __pyx_k_32[] = "Tabixfile.header.__get__ (line 140)";
-static char __pyx_k_33[] = "TabixIterator.__next__ (line 192)";
-static char __pyx_k_34[] = "TabixHeaderIterator.__next__ (line 239)";
-static char __pyx_k_35[] = "TabixIteratorParsed.__next__ (line 342)";
-static char __pyx_k_36[] = "tabix_compress (line 362)";
-static char __pyx_k_37[] = "tabix_index (line 407)";
-static char __pyx_k__r[] = "r";
-static char __pyx_k__w[] = "w";
-static char __pyx_k__bc[] = "bc";
-static char __pyx_k__ec[] = "ec";
-static char __pyx_k__fp[] = "fp";
-static char __pyx_k__os[] = "os";
-static char __pyx_k__sc[] = "sc";
-static char __pyx_k__bed[] = "bed";
-static char __pyx_k__end[] = "end";
-static char __pyx_k__gff[] = "gff";
-static char __pyx_k__idx[] = "idx";
-static char __pyx_k__len[] = "len";
-static char __pyx_k__ord[] = "ord";
-static char __pyx_k__sam[] = "sam";
-static char __pyx_k__sys[] = "sys";
-static char __pyx_k__tid[] = "tid";
-static char __pyx_k__vcf[] = "vcf";
-static char __pyx_k__copy[] = "copy";
-static char __pyx_k__gzip[] = "gzip";
-static char __pyx_k__join[] = "join";
-static char __pyx_k__keys[] = "keys";
-static char __pyx_k__mode[] = "mode";
-static char __pyx_k__path[] = "path";
-static char __pyx_k___open[] = "_open";
-static char __pyx_k__asBed[] = "asBed";
-static char __pyx_k__asGTF[] = "asGTF";
-static char __pyx_k__asVCF[] = "asVCF";
-static char __pyx_k__close[] = "close";
-static char __pyx_k__fetch[] = "fetch";
-static char __pyx_k__force[] = "force";
-static char __pyx_k__start[] = "start";
-static char __pyx_k__types[] = "types";
-static char __pyx_k__buffer[] = "buffer";
-static char __pyx_k__ctypes[] = "ctypes";
-static char __pyx_k__exists[] = "exists";
-static char __pyx_k__header[] = "header";
-static char __pyx_k__parser[] = "parser";
-static char __pyx_k__pileup[] = "pileup";
-static char __pyx_k__preset[] = "preset";
-static char __pyx_k__psltbl[] = "psltbl";
-static char __pyx_k__region[] = "region";
-static char __pyx_k__struct[] = "struct";
-static char __pyx_k__unlink[] = "unlink";
-static char __pyx_k__IOError[] = "IOError";
-static char __pyx_k__OSError[] = "OSError";
-static char __pyx_k____all__[] = "__all__";
-static char __pyx_k____get__[] = "__get__";
-static char __pyx_k___isOpen[] = "_isOpen";
-static char __pyx_k__asTuple[] = "asTuple";
-static char __pyx_k__end_col[] = "end_col";
-static char __pyx_k__seq_col[] = "seq_col";
-static char __pyx_k__KeyError[] = "KeyError";
-static char __pyx_k__O_RDONLY[] = "O_RDONLY";
-static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
-static char __pyx_k____test__[] = "__test__";
-static char __pyx_k__endswith[] = "endswith";
-static char __pyx_k__filename[] = "filename";
-static char __pyx_k__iterator[] = "iterator";
-static char __pyx_k__tempfile[] = "tempfile";
-static char __pyx_k__Tabixfile[] = "Tabixfile";
-static char __pyx_k__itertools[] = "itertools";
-static char __pyx_k__line_skip[] = "line_skip";
-static char __pyx_k__meta_char[] = "meta_char";
-static char __pyx_k__reference[] = "reference";
-static char __pyx_k__start_col[] = "start_col";
-static char __pyx_k__tabixfile[] = "tabixfile";
-static char __pyx_k__zerobased[] = "zerobased";
-static char __pyx_k__ValueError[] = "ValueError";
-static char __pyx_k__filename_in[] = "filename_in";
-static char __pyx_k__tabix_index[] = "tabix_index";
-static char __pyx_k___parseRegion[] = "_parseRegion";
-static char __pyx_k__filename_out[] = "filename_out";
-static char __pyx_k__StopIteration[] = "StopIteration";
-static char __pyx_k__TabixIterator[] = "TabixIterator";
-static char __pyx_k__tabix_compress[] = "tabix_compress";
-static char __pyx_k__TabixHeaderIterator[] = "TabixHeaderIterator";
-static char __pyx_k__TabixIteratorParsed[] = "TabixIteratorParsed";
-static PyObject *__pyx_kp_s_1;
-static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_12;
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-static PyObject *__pyx_kp_s_17;
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-static PyObject *__pyx_kp_s_2;
-static PyObject *__pyx_kp_s_20;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_s_23;
-static PyObject *__pyx_kp_s_24;
-static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_26;
-static PyObject *__pyx_kp_u_28;
-static PyObject *__pyx_kp_u_29;
-static PyObject *__pyx_kp_s_3;
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-static PyObject *__pyx_kp_u_32;
-static PyObject *__pyx_kp_u_33;
-static PyObject *__pyx_kp_u_34;
-static PyObject *__pyx_kp_u_35;
-static PyObject *__pyx_kp_u_36;
-static PyObject *__pyx_kp_u_37;
-static PyObject *__pyx_kp_s_4;
-static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_kp_s_7;
-static PyObject *__pyx_kp_s_8;
-static PyObject *__pyx_kp_s_9;
-static PyObject *__pyx_n_s__IOError;
-static PyObject *__pyx_n_s__KeyError;
-static PyObject *__pyx_n_s__OSError;
-static PyObject *__pyx_n_s__O_RDONLY;
-static PyObject *__pyx_n_s__StopIteration;
-static PyObject *__pyx_n_s__TabixHeaderIterator;
-static PyObject *__pyx_n_s__TabixIterator;
-static PyObject *__pyx_n_s__TabixIteratorParsed;
-static PyObject *__pyx_n_s__Tabixfile;
-static PyObject *__pyx_n_s__ValueError;
-static PyObject *__pyx_n_s____all__;
-static PyObject *__pyx_n_s____get__;
-static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____next__;
-static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s___isOpen;
-static PyObject *__pyx_n_s___open;
-static PyObject *__pyx_n_s___parseRegion;
-static PyObject *__pyx_n_s__asBed;
-static PyObject *__pyx_n_s__asGTF;
-static PyObject *__pyx_n_s__asTuple;
-static PyObject *__pyx_n_s__asVCF;
-static PyObject *__pyx_n_s__bc;
-static PyObject *__pyx_n_s__bed;
-static PyObject *__pyx_n_s__buffer;
-static PyObject *__pyx_n_s__close;
-static PyObject *__pyx_n_s__copy;
-static PyObject *__pyx_n_s__ctypes;
-static PyObject *__pyx_n_s__ec;
-static PyObject *__pyx_n_s__end;
-static PyObject *__pyx_n_s__end_col;
-static PyObject *__pyx_n_s__endswith;
-static PyObject *__pyx_n_s__exists;
-static PyObject *__pyx_n_s__fetch;
-static PyObject *__pyx_n_s__filename;
-static PyObject *__pyx_n_s__filename_in;
-static PyObject *__pyx_n_s__filename_out;
-static PyObject *__pyx_n_s__force;
-static PyObject *__pyx_n_s__fp;
-static PyObject *__pyx_n_s__gff;
-static PyObject *__pyx_n_s__gzip;
-static PyObject *__pyx_n_s__header;
-static PyObject *__pyx_n_s__idx;
-static PyObject *__pyx_n_s__iterator;
-static PyObject *__pyx_n_s__itertools;
-static PyObject *__pyx_n_s__join;
-static PyObject *__pyx_n_s__keys;
-static PyObject *__pyx_n_s__len;
-static PyObject *__pyx_n_s__line_skip;
-static PyObject *__pyx_n_s__meta_char;
-static PyObject *__pyx_n_s__mode;
-static PyObject *__pyx_n_s__ord;
-static PyObject *__pyx_n_s__os;
-static PyObject *__pyx_n_s__parser;
-static PyObject *__pyx_n_s__path;
-static PyObject *__pyx_n_s__pileup;
-static PyObject *__pyx_n_s__preset;
-static PyObject *__pyx_n_s__psltbl;
-static PyObject *__pyx_n_s__r;
-static PyObject *__pyx_n_s__reference;
-static PyObject *__pyx_n_s__region;
-static PyObject *__pyx_n_s__sam;
-static PyObject *__pyx_n_s__sc;
-static PyObject *__pyx_n_s__seq_col;
-static PyObject *__pyx_n_s__start;
-static PyObject *__pyx_n_s__start_col;
-static PyObject *__pyx_n_s__struct;
-static PyObject *__pyx_n_s__sys;
-static PyObject *__pyx_n_s__tabix_compress;
-static PyObject *__pyx_n_s__tabix_index;
-static PyObject *__pyx_n_s__tabixfile;
-static PyObject *__pyx_n_s__tempfile;
-static PyObject *__pyx_n_s__tid;
-static PyObject *__pyx_n_s__types;
-static PyObject *__pyx_n_s__unlink;
-static PyObject *__pyx_n_s__vcf;
-static PyObject *__pyx_n_s__w;
-static PyObject *__pyx_n_s__zerobased;
-static PyObject *__pyx_int_0;
-static PyObject *__pyx_int_1;
-static PyObject *__pyx_int_2;
-static PyObject *__pyx_int_3;
-static PyObject *__pyx_int_4;
-static PyObject *__pyx_int_5;
-static PyObject *__pyx_int_neg_1;
-static PyObject *__pyx_int_15;
-static PyObject *__pyx_int_17;
-static PyObject *__pyx_int_18;
-static PyObject *__pyx_int_0x10000;
-static PyObject *__pyx_k_14;
-static PyObject *__pyx_k_19;
-static PyObject *__pyx_k_21;
-
-/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":15
- * '''
- *
- * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
- * self.tabixfile = NULL
- * self._open( *args, **kwargs )
- */
-
-static int __pyx_pf_6ctabix_9Tabixfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_6ctabix_9Tabixfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- if (__pyx_m) {
- __Pyx_AddTraceback("init ctabix");
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-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
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- const char* function_name,
- int kw_allowed)
-{
- PyObject* key = 0;
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- while (PyDict_Next(kwdict, &pos, &key, 0)) {
- #if PY_MAJOR_VERSION < 3
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- goto invalid_keyword;
- return 1;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- return 0;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
- return 0;
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-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
- #endif
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
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-
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
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- more_or_less = "at most";
- }
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- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
- #else
- "%s() takes %s %zd positional argument%s (%zd given)",
- #endif
- func_name, more_or_less, num_expected, number, num_found);
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
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- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
-
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
- values[name-argnames] = value;
- } else {
- /* unexpected keyword found */
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- }
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "need more than %d value%s to unpack", (int)index,
- #else
- "need more than %zd value%s to unpack", index,
- #endif
- (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "too many values to unpack (expected %d)", (int)expected);
- #else
- "too many values to unpack (expected %zd)", expected);
- #endif
-}
-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
- }
- }
- return item;
-}
-
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
- if ((item = PyIter_Next(iter))) {
- Py_DECREF(item);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- }
- else if (!PyErr_Occurred())
- return 0;
- else
- return -1;
-}
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (Py_TYPE(obj) == type) return 1;
- }
- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
-}
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
- if (unlikely(tstate->curexc_type))
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->exc_type;
- *value = tstate->exc_value;
- *tb = tstate->exc_traceback;
- Py_XINCREF(*type);
- Py_XINCREF(*value);
- Py_XINCREF(*tb);
-}
-
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
- PyObject *py_import = 0;
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
-bad:
- Py_XDECREF(empty_list);
- Py_XDECREF(py_import);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
-static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
- const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(int32_t) == sizeof(char)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(int32_t) == sizeof(short)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(int32_t) == sizeof(int)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(int32_t) == sizeof(long)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- int32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (int32_t)-1;
- }
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return PyLong_AsUnsignedLong(x);
- } else {
- return PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return PyLong_AsUnsignedLongLong(x);
- } else {
- return PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- long size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
-
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(class_name);
- #else
- py_name = PyUnicode_FromString(class_name);
- #endif
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- PyErr_Warn(NULL, warning);
- #else
- PyErr_WarnEx(NULL, warning, 0);
- #endif
- }
- else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(name);
- #else
- py_name = PyUnicode_FromString(name);
- #endif
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
- PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
-#else
- *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!*(void **)vtabptr)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-
-static void __Pyx_AddTraceback(const char *funcname) {
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- PyObject *py_globals = 0;
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(__pyx_filename);
- #else
- py_srcfile = PyUnicode_FromString(__pyx_filename);
- #endif
- if (!py_srcfile) goto bad;
- if (__pyx_clineno) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_code = PyCode_New(
- 0, /*int argcount,*/
- #if PY_MAJOR_VERSION >= 3
- 0, /*int kwonlyargcount,*/
- #endif
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- __pyx_lineno, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- if (!py_code) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = __pyx_lineno;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-/* Type Conversion Functions */
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
projects / pysam.git / commitdiff