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r511: fixed wrong primary sam record

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Heng Li
2017-10-12 23:02:18 -04:00
parent dea3b60918
commit 858213d513
3 changed files with 8 additions and 5 deletions
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map.c
+1 -1
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@@ -306,7 +306,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
if ((opt->flag & MM_F_SR) && rep_len > 0) {
if (opt->max_occ > opt->mid_occ && rep_len > 0) {
int rechain = 0;
if (n_regs0 > 0) { // test if the best chain has all the segments
int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;