fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-25 11:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r301: separate introns from deletions

Browse Source 
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
This commit is contained in:
Heng Li
2017-08-18 15:31:15 +08:00
parent 64c1389e1a
commit 993a2bb521
9 changed files with 41 additions and 59 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+3 -6
View File
@@ -346,24 +346,21 @@ static void *worker_pipeline(void *shared, int step, void *in)
void *km = 0;
step_t *s = (step_t*)in;
const mm_idx_t *mi = p->mi;
int intron_thres = -1;
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
free(s->buf);
if (p->opt->flag & MM_F_SPLICE)
intron_thres = mm_min_intron_len(p->opt->q, p->opt->e, p->opt->q2);
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
for (i = 0; i < s->n_seq; ++i) {
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i], intron_thres);
mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag, intron_thres);
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
puts(p->str.s);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam(&p->str, 0, t, 0, 0, 0, 0);
mm_write_sam(&p->str, 0, t, 0, 0, 0);
puts(p->str.s);
}
for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);