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support RMQ

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This commit is contained in:
Heng Li
2021-05-03 09:27:04 -04:00
parent b7f4d8a0f4
commit bbb4f97e52
4 changed files with 39 additions and 24 deletions
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map.c
+8 -3
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@@ -271,10 +271,15 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
} else max_chain_gap_ref = opt->max_gap;
a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
opt->chain_gap_scale * 0.2f, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
if (opt->flag & MM_F_RMQ) {
a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
opt->chain_gap_scale * 0.2f, 0.0f, n_a, a, &n_regs0, &u, b->km);
} else {
a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
opt->chain_gap_scale * 0.2f, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
if (opt->max_occ > opt->mid_occ && rep_len > 0) {
if (opt->max_occ > opt->mid_occ && rep_len > 0 && !(opt->flag & MM_F_RMQ)) {
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;