6 void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
12 if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
13 if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
14 kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
15 kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
16 for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
17 kputw(bam_cigar_oplen(cigar[i]), str);
18 kputc(bam_cigar_opchr(cigar[i]), str);
20 end = bam_calend(&b1->core, cigar);
21 kputw(b2->core.pos - end, str);
23 kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
24 kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
25 for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
26 kputw(bam_cigar_oplen(cigar[i]), str);
27 kputc(bam_cigar_opchr(cigar[i]), str);
29 bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
32 // currently, this function ONLY works if each read has one hit
33 void bam_mating_core(bamFile in, bamFile out)
37 int curr, has_prev, pre_end = 0, cur_end;
40 str.l = str.m = 0; str.s = 0;
41 header = bam_header_read(in);
42 bam_header_write(out, header);
46 curr = 0; has_prev = 0;
47 while (bam_read1(in, b[curr]) >= 0) {
48 bam1_t *cur = b[curr], *pre = b[1-curr];
49 if (cur->core.tid < 0) continue;
50 cur_end = bam_calend(&cur->core, bam1_cigar(cur));
51 if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
52 if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
54 if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
55 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
56 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
57 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
58 && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
61 cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
62 pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
63 cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
64 } else cur->core.isize = pre->core.isize = 0;
65 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
66 else cur->core.flag &= ~BAM_FMREVERSE;
67 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
68 else pre->core.flag &= ~BAM_FMREVERSE;
69 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
70 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
71 bam_template_cigar(pre, cur, &str);
75 } else { // unpaired or singleton
76 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
77 if (pre->core.flag & BAM_FPAIRED) {
78 pre->core.flag |= BAM_FMUNMAP;
79 pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
87 if (has_prev) bam_write1(out, b[1-curr]);
88 bam_header_destroy(header);
94 int bam_mating(int argc, char *argv[])
98 fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
101 in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
102 out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
103 bam_mating_core(in, out);
104 bam_close(in); bam_close(out);