7 // currently, this function ONLY works if each read has one hit
8 void bam_mating_core(bamFile in, bamFile out)
14 header = bam_header_read(in);
15 bam_header_write(out, header);
19 curr = 0; has_prev = 0;
20 while (bam_read1(in, b[curr]) >= 0) {
21 bam1_t *cur = b[curr], *pre = b[1-curr];
23 if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
24 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
25 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
26 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
27 && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
30 cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
31 pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
32 cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
33 } else cur->core.isize = pre->core.isize = 0;
34 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
35 else cur->core.flag &= ~BAM_FMREVERSE;
36 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
37 else pre->core.flag &= ~BAM_FMREVERSE;
38 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
39 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
43 } else { // unpaired or singleton
44 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
45 if (pre->core.flag & BAM_FPAIRED) {
46 pre->core.flag |= BAM_FMUNMAP;
47 pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
54 if (has_prev) bam_write1(out, b[1-curr]);
55 bam_header_destroy(header);
60 int bam_mating(int argc, char *argv[])
64 fprintf(pysamerr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
67 in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
68 out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
69 bam_mating_core(in, out);
70 bam_close(in); bam_close(out);