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prepare to backport unimap/minigraph chaining

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Heng Li
2021-05-02 18:25:49 -04:00
parent f7dc5799c5
commit e81927e7a1
6 changed files with 876 additions and 5 deletions
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map.c
+6 -2
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@@ -271,7 +271,9 @@ 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 = mm_chain_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, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
// a = mm_chain_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, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
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) {
int rechain = 0;
@@ -293,7 +295,9 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
kfree(b->km, mini_pos);
if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else a = collect_seed_hits(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
a = mm_chain_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, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
// a = mm_chain_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, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
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);
}
}
b->frag_gap = max_chain_gap_ref;