#include <stdlib.h>
#include <string.h>
+#include <unistd.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)
+void bam_mating_core(bamFile in, bamFile out, int remove_reads)
{
bam_header_t *header;
bam1_t *b[2];
- int curr, has_prev;
+ int curr, has_prev, pre_end = 0, cur_end;
+ kstring_t str;
+ str.l = str.m = 0; str.s = 0;
header = bam_header_read(in);
bam_header_write(out, header);
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)
+ {
+ if ( !remove_reads ) bam_write1(out, cur);
+ 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)
+ {
+ if ( !remove_reads ) bam_write1(out, cur);
+ 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;
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;
}
} 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);
+}
+
+void usage()
+{
+ fprintf(stderr,"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+ fprintf(stderr,"Options:\n");
+ fprintf(stderr," -r remove unmapped reads and secondary alignments\n");
+ exit(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);
+ int c, remove_reads=0;
+ while ((c = getopt(argc, argv, "r")) >= 0) {
+ switch (c) {
+ case 'r': remove_reads=1; break;
+ }
+ }
+ if (optind+1 >= argc) usage();
+ in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
+ out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
+ bam_mating_core(in, out, remove_reads);
bam_close(in); bam_close(out);
return 0;
}
+
+
projects / samtools.git / blobdiff