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r1051: added two internal parameters 

rmq_rescue_size and rmq_rescue_ratio
This commit is contained in:
Heng Li 2021-05-24 16:38:45 -04:00
parent 9626b3e716
commit 34a41197d7
5 changed files with 9 additions and 3 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-r1050-dirty"
#define MM_VERSION "2.18-r1051-dirty"
#ifdef __linux__
#include <sys/resource.h>

4
map.c
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@ -300,9 +300,9 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
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 * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
} else if (opt->bw_long > opt->bw && !(opt->flag & (MM_F_RMQ|MM_F_NO_LJOIN)) && n_segs == 1 && n_regs0 > 1) {
} else if (opt->bw_long > opt->bw && (opt->flag & (MM_F_RMQ|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) {
int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
if (qlen_sum - (en - st) > 1000 || en - st > qlen_sum * .1) {
if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
int32_t i;
for (i = 0, n_a = 0; i < n_regs0; ++i) n_a += (int32_t)u[i];
kfree(b->km, u);

2
minimap.h
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@ -122,6 +122,8 @@ typedef struct {
int min_chain_score; // min chaining score
float chain_gap_scale;
int rmq_size_cap, rmq_inner_dist;
int rmq_rescue_size;
float rmq_rescue_ratio;
float mask_level;
int mask_len;

2
options.c
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@ -29,6 +29,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_chain_iter = 5000;
opt->rmq_inner_dist = 1000;
opt->rmq_size_cap = 100000;
opt->rmq_rescue_size = 1000;
opt->rmq_rescue_ratio = 0.1f;
opt->chain_gap_scale = 0.8f;
opt->max_max_occ = 4095;
opt->occ_dist = 500;

2
python/cmappy.pxd
View File

@ -24,6 +24,8 @@ cdef extern from "minimap.h":
int min_chain_score
float chain_gap_scale
int rmq_size_cap, rmq_inner_dist
int rmq_rescue_size
float rmq_rescue_ratio
float mask_level
int mask_len