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r114: make SAM output better

This commit is contained in:
Heng Li 2017-06-29 23:08:41 -04:00
parent 03267e8fa7
commit c4871f380c
2 changed files with 10 additions and 6 deletions
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14
format.c
View File

@ -111,18 +111,22 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
int flag = 0;
s->l = 0;
if (r->rev) flag |= 0x10;
if (r->parent != r->id) flag |= 0x80;
if (r->parent != r->id) flag |= 0x100;
if (r->id != 0) flag |= 0x800; // TODO: make sure this is always working!
mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
if (r->p) { // TODO: using hard clippings
uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
if (clip_len) mm_sprintf_lite(s, "%dS", clip_len);
int clip_char = (flag&0x800)? 'H' : 'S';
if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
clip_len = r->rev? r->qs : t->l_seq - r->qe;
if (clip_len) mm_sprintf_lite(s, "%dS", clip_len);
if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
} else mm_sprintf_lite(s, "*");
mm_sprintf_lite(s, "\t*\t0\t0\t");
sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
mm_sprintf_lite(s, "\t*");
if ((flag & 0x900) == 0) sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
else if (flag & 0x100) mm_sprintf_lite(s, "\t*");
else sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
mm_sprintf_lite(s, "\t*"); // quality
write_tags(s, r);
}

2
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r113-pre"
#define MM_VERSION "2.0-r114-pre"
void liftrlimit()
{