Generated by Cython 0.29.26
Yellow lines hint at Python interaction.
Click on a line that starts with a "+" to see the C code that Cython generated for it.
Raw output: opt.c
+01: # cython: profile=False
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02: # cython: embedsignature=True
03:
04: from pysam.libcalignmentfile cimport AlignmentFile
05: from pysam.libcsamfile cimport Samfile
06: from pysam.libcfaidx cimport FastaFile
07: from pysam.libcalignedsegment cimport PileupColumn,PileupRead,pysam_bam_get_seq
08: from pysam.libchtslib cimport bam1_t, bam_pileup1_t
09: from libc.stdint cimport uint32_t, uint8_t, uint64_t, int64_t
10: from cpython cimport PyBytes_FromStringAndSize
11:
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13:
14:
15:
+16: cdef inline object get_seq_base(bam1_t *src, uint32_t k):
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17: cdef uint8_t* p
18: cdef char* s
19:
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22:
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26:
+27: s[0] = bam_nt16_rev_table[p[k//2] >> 4 * (1 - k%2) & 0xf]
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30:
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43:
44:
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88: