Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_mate.c @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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-1:000000000000 | 0:74f5ea818cea |
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1 #include <stdlib.h> | |
2 #include <string.h> | |
3 #include "bam.h" | |
4 | |
5 // currently, this function ONLY works if each read has one hit | |
6 void bam_mating_core(bamFile in, bamFile out) | |
7 { | |
8 bam_header_t *header; | |
9 bam1_t *b[2]; | |
10 int curr, has_prev; | |
11 | |
12 header = bam_header_read(in); | |
13 bam_header_write(out, header); | |
14 | |
15 b[0] = bam_init1(); | |
16 b[1] = bam_init1(); | |
17 curr = 0; has_prev = 0; | |
18 while (bam_read1(in, b[curr]) >= 0) { | |
19 bam1_t *cur = b[curr], *pre = b[1-curr]; | |
20 if (has_prev) { | |
21 if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name | |
22 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos; | |
23 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos; | |
24 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)) | |
25 && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) | |
26 { | |
27 uint32_t cur5, pre5; | |
28 cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos; | |
29 pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos; | |
30 cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5; | |
31 } else cur->core.isize = pre->core.isize = 0; | |
32 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE; | |
33 else cur->core.flag &= ~BAM_FMREVERSE; | |
34 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE; | |
35 else pre->core.flag &= ~BAM_FMREVERSE; | |
36 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; } | |
37 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; } | |
38 bam_write1(out, pre); | |
39 bam_write1(out, cur); | |
40 has_prev = 0; | |
41 } else { // unpaired or singleton | |
42 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0; | |
43 if (pre->core.flag & BAM_FPAIRED) { | |
44 pre->core.flag |= BAM_FMUNMAP; | |
45 pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR; | |
46 } | |
47 bam_write1(out, pre); | |
48 } | |
49 } else has_prev = 1; | |
50 curr = 1 - curr; | |
51 } | |
52 if (has_prev) bam_write1(out, b[1-curr]); | |
53 bam_header_destroy(header); | |
54 bam_destroy1(b[0]); | |
55 bam_destroy1(b[1]); | |
56 } | |
57 | |
58 int bam_mating(int argc, char *argv[]) | |
59 { | |
60 bamFile in, out; | |
61 if (argc < 3) { | |
62 fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n"); | |
63 return 1; | |
64 } | |
65 in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r"); | |
66 out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w"); | |
67 bam_mating_core(in, out); | |
68 bam_close(in); bam_close(out); | |
69 return 0; | |
70 } |