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r1205: updated lr:hqae

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Heng Li
2024-03-20 14:06:59 -04:00
parent 27b254ed6f
commit f51ff1abac
5 changed files with 6 additions and 116 deletions
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map.c
+2 -7
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@@ -287,13 +287,8 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
for (i = 0, n_a = 0; i < n_regs0; ++i) n_a += (int32_t)u[i];
kfree(b->km, u);
radix_sort_128x(a, a + n_a);
if (opt->flag & MM_F_RMQ) {
a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
} else {
a = mg_lchain_dp_rmq(opt->max_gap, opt->bw, opt->bw_long, opt->max_chain_skip, opt->max_chain_iter, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
}
a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
}
} else if (opt->max_occ > opt->mid_occ && rep_len > 0 && !(opt->flag & MM_F_RMQ)) { // re-chain, mostly for short reads
int rechain = 0;