INNER CODE UNIT · C
as_alt
lh3/miniprot · align.c:291
int64_t as_alt = vs1 - as > opt->max_ext? vs1 - opt->max_ext : as;
ns_opt.io = opt->io_end;
ns_global_gs16b(km, (const char*)&nt[as_alt - as], vs1 - as_alt, aa, as1, &ns_opt, ss? &ss[as_alt - as] : 0, &rst);
if (rst.aa_len == as1)
nt_len = rst.nt_len, aa_len = rst.aa_len;
}
r->vs = vs1 - nt_len;
r->qs = as1 - aa_len;
ne0 = r->vs - vs0;
ae0 = r->qs;
}
if (mp_dbg_flag & MP_DBG_MORE_DP) { // apply DP to the entire region; for debugging only
score = mp_align_seq(km, opt, &ns_opt0, r->ve - r->vs, &nt[r->vs - as], r->qe - ae0, &aa[ae0], ss? &ss[r->vs - as] : 0, &cigar);
} else { // patch gaps between anchors
for (i = i0; i < r->cnt; ++i) {
int32_t ne1, ae1;
if (!(r->a[i]>>31&1)) continue;