fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-15 13:07:55 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1265: prefer spliced alignment

Browse Source 
mapq needs to be elevated
This commit is contained in:
Heng Li
2025-04-07 00:31:04 -04:00
parent fbb9c0fcba
commit 75619c7b51
4 changed files with 17 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
jump.c
View File

@@ -101,6 +101,8 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
else r->qe = qlen;
r->blen += clip, r->mlen += clip - mm0;
r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
r->p->dp_max += (clip - mm0) * opt->a - mm0 * opt->b;
if (!r->is_spliced) r->is_spliced = 1, r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
} else if (m > 0 && a[i0].off > r->rs) { // trim by l; l is always positive
r->p->cigar[0] -= l << 4 | MM_CIGAR_MATCH;
r->rs += l;
@@ -164,6 +166,8 @@ static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t
else r->qs = 0;
r->blen += clip, r->mlen += clip - mm0;
r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
r->p->dp_max += (clip - mm0) * opt->a - mm0 * opt->b;
if (!r->is_spliced) r->is_spliced = 1, r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
} else if (m > 0 && r->re > a[i0].off) { // trim by l; l is always positive
r->p->cigar[r->p->n_cigar - 1] -= l << 4 | MM_CIGAR_MATCH;
r->re -= l;