bam_mate.c

   1 #include <stdlib.h>
   2 #include <string.h>
   3 #include "kstring.h"
   4 #include "bam.h"
   5
   6 void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
   7 {
   8         bam1_t *swap;
   9         int i, end;
  10         uint32_t *cigar;
  11         str->l = 0;
  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);
  19         }
  20         end = bam_calend(&b1->core, cigar);
  21         kputw(b2->core.pos - end, str);
  22         kputc('T', 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);
  28         }
  29         bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
  30 }
  31
  32 // currently, this function ONLY works if each read has one hit
  33 void bam_mating_core(bamFile in, bamFile out)
  34 {
  35         bam_header_t *header;
  36         bam1_t *b[2];
  37         int curr, has_prev, pre_end, cur_end;
  38         kstring_t str;
  39
  40         str.l = str.m = 0; str.s = 0;
  41         header = bam_header_read(in);
  42         bam_header_write(out, header);
  43
  44         b[0] = bam_init1();
  45         b[1] = bam_init1();
  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
  53                 if (has_prev) {
  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
  59                                 {
  60                                         uint32_t cur5, pre5;
  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);
  72                                 bam_write1(out, pre);
  73                                 bam_write1(out, cur);
  74                                 has_prev = 0;
  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;
  80                                 }
  81                                 bam_write1(out, pre);
  82                         }
  83                 } else has_prev = 1;
  84                 curr = 1 - curr;
  85                 pre_end = cur_end;
  86         }
  87         if (has_prev) bam_write1(out, b[1-curr]);
  88         bam_header_destroy(header);
  89         bam_destroy1(b[0]);
  90         bam_destroy1(b[1]);
  91         free(str.s);
  92 }
  93
  94 int bam_mating(int argc, char *argv[])
  95 {
  96         bamFile in, out;
  97         if (argc < 3) {
  98                 fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
  99                 return 1;
 100         }
 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);
 105         return 0;
 106 }