Generated by Cython 0.16 on Wed Oct 17 10:03:47 2012
Raw output: bam.c
1: '''
2: Created on 2012-01-17
3:
4: @author: Andrew Roth
5: '''
6: import os
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7:
8: # Global constant
9: cdef int max_pos = 2 << 29
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10:
11: cdef class BamFile:
/* "jointpysam/bam.pyx":11 * cdef int max_pos = 2<<29 * * cdef class BamFile: #<<<<<<<<<<<<<<* ''' * Heavily simplified version of pysam Samfile class. Tailored specifically for extracting data from BAM files for */ struct __pyx_vtabstruct_10jointpysam_3bam_BamFile { samfile_t *(*get_file_pointer)(struct __pyx_obj_10jointpysam_3bam_BamFile *); bam_index_t *(*get_index)(struct __pyx_obj_10jointpysam_3bam_BamFile *); }; static struct __pyx_vtabstruct_10jointpysam_3bam_BamFile *__pyx_vtabptr_10jointpysam_3bam_BamFile;
12: '''
13: Heavily simplified version of pysam Samfile class. Tailored specifically for extracting data from BAM files for
14: JointSNVMix.
15: '''
16: def __cinit__(self, char * file_name):
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17: self._file_name = strdup(file_name)
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18:
19: self._open_file()
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20:
21: self._load_index()
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22:
23: self._load_references()
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24:
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27: free(self._file_name)
/* "jointpysam/bam.pyx":27
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* free(self._file_name) # <<<<<<<<<<<<<<
*
* if self._index != NULL:
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free(__pyx_v_self->_file_name);
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__pyx_L3:;
28:
29: if self._index != NULL:
/* "jointpysam/bam.pyx":29 * free(self._file_name) * * if self._index != NULL: #<<<<<<<<<<<<<<* bam_index_destroy(self._index) * */ __pyx_t_1 = (__pyx_v_self->_index != NULL); if (__pyx_t_1) {
30: bam_index_destroy(self._index)
/* "jointpysam/bam.pyx":30
*
* if self._index != NULL:
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*
* if self._bam_file != NULL:
*/
bam_index_destroy(__pyx_v_self->_index);
goto __pyx_L4;
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__pyx_L4:;
31:
32: if self._bam_file != NULL:
/* "jointpysam/bam.pyx":32 * bam_index_destroy(self._index) * * if self._bam_file != NULL: #<<<<<<<<<<<<<<* samclose(self._bam_file) * */ __pyx_t_1 = (__pyx_v_self->_bam_file != NULL); if (__pyx_t_1) {
33: samclose(self._bam_file)
/* "jointpysam/bam.pyx":33
*
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samclose(__pyx_v_self->_bam_file);
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34:
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37:
38: if self._bam_file == NULL:
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40:
41: if self._bam_file.header == NULL:
/* "jointpysam/bam.pyx":41
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43:
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