converted padded SAM to unpadded SAM

[samtools.git] / bam_mate.c

diff --git a/bam_mate.c b/bam_mate.c
index 61f808a26402e9bd1d332f40074b4b3ca1f89dd3..642ded68b80c0da699ba0091dc7e5dd9acc36d96 100644 (file)
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -1,14 +1,43 @@
 #include <stdlib.h>
 #include <string.h>
+#include "kstring.h"
 #include "bam.h"
 
+void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+       bam1_t *swap;
+       int i, end;
+       uint32_t *cigar;
+       str->l = 0;
+       if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
+       if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+       kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+       kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+       for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
+               kputw(bam_cigar_oplen(cigar[i]), str);
+               kputc(bam_cigar_opchr(cigar[i]), str);
+       }
+       end = bam_calend(&b1->core, cigar);
+       kputw(b2->core.pos - end, str);
+       kputc('T', str);
+       kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+       kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+       for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
+               kputw(bam_cigar_oplen(cigar[i]), str);
+               kputc(bam_cigar_opchr(cigar[i]), str);
+       }
+       bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s); 
+}
+
 // 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;
+       int curr, has_prev, pre_end, cur_end;
+       kstring_t str;
 
+       str.l = str.m = 0; str.s = 0;
        header = bam_header_read(in);
        bam_header_write(out, header);
 
@@ -17,16 +46,20 @@ void bam_mating_core(bamFile in, bamFile out)
        curr = 0; has_prev = 0;
        while (bam_read1(in, b[curr]) >= 0) {
                bam1_t *cur = b[curr], *pre = b[1-curr];
+               if (cur->core.tid < 0) continue;
+               cur_end = bam_calend(&cur->core, bam1_cigar(cur));
+               if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
+               if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
                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)))
+                                       && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
                                {
                                        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;
+                                       cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+                                       pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : 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;
@@ -35,6 +68,7 @@ void bam_mating_core(bamFile in, bamFile out)
                                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_template_cigar(pre, cur, &str);
                                bam_write1(out, pre);
                                bam_write1(out, cur);
                                has_prev = 0;
@@ -48,18 +82,20 @@ void bam_mating_core(bamFile in, bamFile out)
                        }
                } else has_prev = 1;
                curr = 1 - curr;
+               pre_end = cur_end;
        }
        if (has_prev) bam_write1(out, b[1-curr]);
        bam_header_destroy(header);
        bam_destroy1(b[0]);
        bam_destroy1(b[1]);
+       free(str.s);
 }
 
 int bam_mating(int argc, char *argv[])
 {
        bamFile in, out;
        if (argc < 3) {
-               fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+               fprintf(stderr, "Usage: 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");