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bam_mate.c

#include <stdlib.h>
#include <string.h>
#include "bam.h"

// currently, this function ONLY works if each read has one hit
void bam_mating_core(bamFile in, bamFile out)
{
      bam_header_t *header;
      bam1_t *b[2];
      int curr, has_prev;

      header = bam_header_read(in);
      bam_header_write(out, header);

      b[0] = bam_init1();
      b[1] = bam_init1();
      curr = 0; has_prev = 0;
      while (bam_read1(in, b[curr]) >= 0) {
            bam1_t *cur = b[curr], *pre = b[1-curr];
            if (has_prev) {
                  if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
                        cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
                        pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
                        if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
                              && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
                        {
                              uint32_t cur5, pre5;
                              cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
                              pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
                              cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
                        } else cur->core.isize = pre->core.isize = 0;
                        if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
                        else cur->core.flag &= ~BAM_FMREVERSE;
                        if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
                        else pre->core.flag &= ~BAM_FMREVERSE;
                        if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
                        if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
                        bam_write1(out, pre);
                        bam_write1(out, cur);
                        has_prev = 0;
                  } else { // unpaired or singleton
                        pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
                        if (pre->core.flag & BAM_FPAIRED) {
                              pre->core.flag |= BAM_FMUNMAP;
                              pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
                        }
                        bam_write1(out, pre);
                  }
            } else has_prev = 1;
            curr = 1 - curr;
      }
      if (has_prev) bam_write1(out, b[1-curr]);
      bam_header_destroy(header);
      bam_destroy1(b[0]);
      bam_destroy1(b[1]);
}

int bam_mating(int argc, char *argv[])
{
      bamFile in, out;
      if (argc < 3) {
            fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
            return 1;
      }
      in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
    out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
      bam_mating_core(in, out);
      bam_close(in); bam_close(out);
      return 0;
}

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