fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-05 07:08:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r168: fixed a bug in long join: a[] not sorted

Browse Source 
Also added length requirement for long join and changed -g in the ava mode
This commit is contained in:
Heng Li
2017-07-09 12:14:20 -04:00
parent 1ac48556ae
commit 782449975d
3 changed files with 28 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hit.c
+3 -1
View File
@@ -247,8 +247,10 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x;
min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x;
if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499); // TODO: also require length
sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499);
if (r0->score < sc_thres || r1->score < sc_thres) continue; // require good flanking chains
if (r0->re - r0->rs < max_gap>>1 || r0->qe - r0->qs < max_gap>>1) continue; // require enough flanking length
if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
// all conditions satisfied; join
a[r1->as].y |= 1ULL<<40;