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r1267: penalize introns without signals

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Heng Li
2025-04-07 09:51:33 -04:00
parent 3542a3d153
commit 9c3c4b1ce8
2 changed files with 8 additions and 4 deletions
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align.c
+6 -2
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@@ -1031,8 +1031,12 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
}
r = &regs[i];
r->p->trans_strand = trans_strand;
if (r->is_spliced && (trans_strand == 1 || trans_strand == 2))
r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
if (r->is_spliced) {
if (trans_strand == 1 || trans_strand == 2) // this is an *approximate* way to tell if there are splice signals.
r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
else if (trans_strand == 3)
r->p->dp_max -= opt->a + opt->b;
}
} else { // one round of alignment
mm_align1(km, opt, mi, qlen, qseq0, &regs[i], &r2, n_a, a, &ez, opt->flag);
if (opt->flag&MM_F_SPLICE)