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r465: apply option -x before other options

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Heng Li
2017-10-04 13:52:28 -04:00
parent 19c39e704f
commit 1554149158
2 changed files with 15 additions and 9 deletions
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map.c
+1 -1
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@@ -339,7 +339,7 @@ void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char *
mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len);
}
mm_seg_free(b->km, n_segs, seg);
if (n_segs == 2 && opt->pe_ori >= 0)
if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
mm_pair(b->km, max_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs);
}