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separated formating printing

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for SAM in future; and for performance
This commit is contained in:
Heng Li
2017-06-25 16:13:54 -04:00
parent 7780ab792a
commit 39083be9ab
5 changed files with 94 additions and 26 deletions
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map.c
+3 -17
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@@ -4,7 +4,6 @@
#include "kvec.h"
#include "kalloc.h"
#include "sdust.h"
#include "minimap.h"
#include "mmpriv.h"
#include "bseq.h"
@@ -320,6 +319,7 @@ typedef struct {
const mm_mapopt_t *opt;
bseq_file_t *fp;
const mm_idx_t *mi;
kstring_t str;
} pipeline_t;
typedef struct {
@@ -368,22 +368,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
printf("%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
if (mi->seq[r->rid].name) fputs(mi->seq[r->rid].name, stdout);
else printf("%d", r->rid + 1);
printf("\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
if (r->p) printf("\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
else printf("\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
printf("\tcm:i:%d", r->cnt);
if (r->p) printf("\ts1:i:%d", r->score);
if (r->parent == j) printf("\ts2:i:%d", r->subsc);
if (r->p) {
uint32_t k;
printf("\tNM:i:%d\tAS:i:%d\tnn:i:%d\tcg:Z:", r->p->n_diff, r->p->score, r->p->n_ambi);
for (k = 0; k < r->p->n_cigar; ++k)
printf("%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
}
putchar('\n');
mm_write_paf(&p->str, mi, t, j, r);
puts(p->str.s);
free(r->p);
}
free(s->reg[i]);