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r122: filter contained aln after DP extension

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Heng Li
2017-06-30 15:23:30 -04:00
parent fce87ce7bd
commit 646a746cdc
4 changed files with 39 additions and 3 deletions
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map.c
+7 -1
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@@ -238,11 +238,17 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
regs = mm_gen_regs(b->km, qlen, n_u, u, a);
*n_regs = n_u;
if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
mm_join_long(b->km, opt, qlen, *n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}
if (opt->flag & MM_F_CIGAR)
if (opt->flag & MM_F_CIGAR) {
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
if (!(opt->flag & MM_F_AVA)) {
mm_update_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
}
}
mm_set_mapq(*n_regs, regs);
// free