sam/bam_mate.c

   1 #include <stdlib.h>
   2 #include <string.h>
   3 #include <unistd.h>
   4 #include "kstring.h"
   5 #include "bam.h"
   6
   7 void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
   8 {
   9         bam1_t *swap;
  10         int i, end;
  11         uint32_t *cigar;
  12         str->l = 0;
  13         if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
  14         if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
  15         kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
  16         kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
  17         for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
  18                 kputw(bam_cigar_oplen(cigar[i]), str);
  19                 kputc(bam_cigar_opchr(cigar[i]), str);
  20         }
  21         end = bam_calend(&b1->core, cigar);
  22         kputw(b2->core.pos - end, str);
  23         kputc('T', str);
  24         kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
  25         kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
  26         for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
  27                 kputw(bam_cigar_oplen(cigar[i]), str);
  28                 kputc(bam_cigar_opchr(cigar[i]), str);
  29         }
  30         bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
  31 }
  32
  33 // currently, this function ONLY works if each read has one hit
  34 void bam_mating_core(bamFile in, bamFile out, int remove_reads)
  35 {
  36         bam_header_t *header;
  37         bam1_t *b[2];
  38         int curr, has_prev, pre_end = 0, cur_end;
  39         kstring_t str;
  40
  41         str.l = str.m = 0; str.s = 0;
  42         header = bam_header_read(in);
  43         bam_header_write(out, header);
  44
  45         b[0] = bam_init1();
  46         b[1] = bam_init1();
  47         curr = 0; has_prev = 0;
  48         while (bam_read1(in, b[curr]) >= 0) {
  49                 bam1_t *cur = b[curr], *pre = b[1-curr];
  50                 if (cur->core.tid < 0)
  51         {
  52             if ( !remove_reads ) bam_write1(out, cur);
  53             continue;
  54         }
  55                 cur_end = bam_calend(&cur->core, bam1_cigar(cur));
  56                 if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
  57                 if (cur->core.flag & BAM_FSECONDARY)
  58         {
  59             if ( !remove_reads ) bam_write1(out, cur);
  60             continue; // skip secondary alignments
  61         }
  62                 if (has_prev) {
  63                         if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
  64                                 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
  65                                 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
  66                                 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
  67                                         && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
  68                                 {
  69                                         uint32_t cur5, pre5;
  70                                         cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
  71                                         pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
  72                                         cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
  73                                 } else cur->core.isize = pre->core.isize = 0;
  74                                 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
  75                                 else cur->core.flag &= ~BAM_FMREVERSE;
  76                                 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
  77                                 else pre->core.flag &= ~BAM_FMREVERSE;
  78                                 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
  79                                 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
  80                                 bam_template_cigar(pre, cur, &str);
  81                                 bam_write1(out, pre);
  82                                 bam_write1(out, cur);
  83                                 has_prev = 0;
  84                         } else { // unpaired or singleton
  85                                 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
  86                                 if (pre->core.flag & BAM_FPAIRED) {
  87                                         pre->core.flag |= BAM_FMUNMAP;
  88                                         pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
  89                                 }
  90                                 bam_write1(out, pre);
  91                         }
  92                 } else has_prev = 1;
  93                 curr = 1 - curr;
  94                 pre_end = cur_end;
  95         }
  96         if (has_prev) bam_write1(out, b[1-curr]);
  97         bam_header_destroy(header);
  98         bam_destroy1(b[0]);
  99         bam_destroy1(b[1]);
 100         free(str.s);
 101 }
 102
 103 void usage()
 104 {
 105     fprintf(stderr,"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
 106     fprintf(stderr,"Options:\n");
 107     fprintf(stderr,"       -r    remove unmapped reads and secondary alignments\n");
 108     exit(1);
 109 }
 110
 111 int bam_mating(int argc, char *argv[])
 112 {
 113         bamFile in, out;
 114     int c, remove_reads=0;
 115     while ((c = getopt(argc, argv, "r")) >= 0) {
 116         switch (c) {
 117             case 'r': remove_reads=1; break;
 118         }
 119     }
 120     if (optind+1 >= argc) usage();
 121         in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
 122     out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
 123         bam_mating_core(in, out, remove_reads);
 124         bam_close(in); bam_close(out);
 125         return 0;
 126 }
 127
 128