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command-line option to control CIGAR output

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Heng Li
2017-06-26 11:41:09 -04:00
parent 24d7f7f8b1
commit 640b1a1727
3 changed files with 10 additions and 5 deletions
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map.c
+2 -1
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@@ -290,7 +290,8 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
regs = mm_gen_reg(qlen, n_u, u, a);
*n_regs = n_u;
mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
if (opt->flag & MM_F_CIGAR)
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
// free
kfree(b->km, a);