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, int remove_reads)
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)
51 if ( !remove_reads ) bam_write1(out, cur);
54 cur_end = bam_calend(&cur->core, bam1_cigar(cur));
55 if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
56 if (cur->core.flag & BAM_FSECONDARY)
58 if ( !remove_reads ) bam_write1(out, cur);
59 continue; // skip secondary alignments
62 if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
63 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
64 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
65 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
66 && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
69 cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
70 pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
71 cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
72 } else cur->core.isize = pre->core.isize = 0;
73 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
74 else cur->core.flag &= ~BAM_FMREVERSE;
75 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
76 else pre->core.flag &= ~BAM_FMREVERSE;
77 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
78 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
79 bam_template_cigar(pre, cur, &str);
83 } else { // unpaired or singleton
84 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
85 if (pre->core.flag & BAM_FPAIRED) {
86 pre->core.flag |= BAM_FMUNMAP;
87 pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
95 if (has_prev) bam_write1(out, b[1-curr]);
96 bam_header_destroy(header);
104 fprintf(stderr,"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
105 fprintf(stderr,"Options:\n");
106 fprintf(stderr," -r remove unmapped reads and secondary alignments\n");
110 int bam_mating(int argc, char *argv[])
113 int c, remove_reads=0;
114 while ((c = getopt(argc, argv, "r")) >= 0) {
116 case 'r': remove_reads=1; break;
119 if (optind+1 >= argc) usage();
120 in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
121 out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
122 bam_mating_core(in, out, remove_reads);
123 bam_close(in); bam_close(out);