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r1047: make gap penalty proportional to k-mer 

closer to the older minimap2
This commit is contained in:
Heng Li 2021-05-24 13:18:17 -04:00
parent 8ec8866100
commit ec3bc6efd7
2 changed files with 4 additions and 4 deletions
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2
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.18-r1035-dirty"
#define MM_VERSION "2.18-r1047-dirty"
#ifdef __linux__
#include <sys/resource.h>

6
map.c
View File

@ -273,10 +273,10 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
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);
opt->chain_gap_scale * 0.01 * mi->k, 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);
opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
if (opt->max_occ > opt->mid_occ && rep_len > 0 && !(opt->flag & MM_F_RMQ)) {
@ -300,7 +300,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
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 = 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);
opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
}
b->frag_gap = max_chain_gap_ref;