fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-29 19:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r85: two-round z-drop

Browse Source
This commit is contained in:
Heng Li
2017-06-27 10:36:24 -04:00
parent 490a37a599
commit c02ff4662c
4 changed files with 39 additions and 35 deletions
Download Patch File Download Diff File Expand all files Collapse all files
align.c
+4 -2
View File
@@ -188,12 +188,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_GLOBAL_ONLY, ez);
if (ez->zdropped || ez->score < 0)
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
}
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
if (ez->zdropped) { // truncated by Z-drop
int j;
for (j = i - 1; j >= 0; --j)
if ((int32_t)a[r->as + j].x < re + ez->max_t)