fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-02 12:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r655: options to map to one strand of the ref #91

Browse Source
This commit is contained in:
Heng Li
2018-01-16 10:34:30 -05:00
parent eecc06086f
commit 33f8157961
5 changed files with 29 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+12
View File
@@ -117,6 +117,11 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
{
if ((mo->flag & MM_F_FOR_ONLY) && (mo->flag & MM_F_REV_ONLY)) {
if (mm_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m --for-only and --rev-only can't be applied at the same time\033[0m\n");
return -3;
}
if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
if (mm_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");
@@ -245,6 +250,13 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
if ((opt->flag&MM_F_AVA) && cmp > 0) // all-vs-all mode: map once
continue;
}
if (opt->flag & (MM_F_FOR_ONLY|MM_F_REV_ONLY)) {
if ((r[k]&1) == (q->qpos&1)) { // forward strand
if (opt->flag & MM_F_REV_ONLY) continue;
} else {
if (opt->flag & MM_F_FOR_ONLY) continue;
}
}
p = &a[(*n_a)++];
if ((r[k]&1) == (q->qpos&1)) { // forward strand
p->x = (r[k]&0xffffffff00000000ULL) | rpos;