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r148: revamped regs handling after cigar

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Heng Li
2017-07-03 10:44:26 -04:00
parent 696ebce66e
commit 2e4fd9f1d0
6 changed files with 58 additions and 92 deletions
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map.c
+1 -1
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@@ -247,7 +247,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
if (opt->flag & MM_F_CIGAR) {
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_AVA)) {
mm_update_parent(b->km, opt->mask_level, *n_regs, regs);
mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
}
} else mm_filter_regs(b->km, opt, n_regs, regs);