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r1110: default --cap-kalloc=1g; test more inv 

See #816 and #823
This commit is contained in:
Heng Li 2021-10-11 14:45:15 -04:00
parent 546623dcb4
commit ac334639ce
3 changed files with 5 additions and 4 deletions
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2
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.22-r1109-dirty" #define MM_VERSION "2.22-r1110-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

6
map.c
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@ -212,7 +212,7 @@ static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_i
{ {
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s) if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 1, opt->max_gap, n_regs, regs); if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 1, opt->max_gap * 0.8, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs); else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
} }
} }
@ -223,7 +223,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs() regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s) if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 0, opt->max_gap, n_regs, regs); mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 0, opt->max_gap * 0.8, n_regs, regs);
mm_set_sam_pri(*n_regs, regs); mm_set_sam_pri(*n_regs, regs);
} }
return regs; return regs;
@ -511,7 +511,7 @@ static void merge_hits(step_t *s)
mm_hit_sort(km, &s->n_reg[k], s->reg[k], opt->alt_drop); mm_hit_sort(km, &s->n_reg[k], s->reg[k], opt->alt_drop);
mm_set_parent(km, opt->mask_level, opt->mask_len, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); mm_set_parent(km, opt->mask_level, opt->mask_len, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
if (!(opt->flag & MM_F_ALL_CHAINS)) { if (!(opt->flag & MM_F_ALL_CHAINS)) {
mm_select_sub(km, opt->pri_ratio, s->p->mi->k*2, opt->best_n, 0, opt->max_gap, &s->n_reg[k], s->reg[k]); mm_select_sub(km, opt->pri_ratio, s->p->mi->k*2, opt->best_n, 0, opt->max_gap * 0.8, &s->n_reg[k], s->reg[k]);
mm_set_sam_pri(s->n_reg[k], s->reg[k]); mm_set_sam_pri(s->n_reg[k], s->reg[k]);
} }
mm_set_mapq(km, s->n_reg[k], s->reg[k], opt->min_chain_score, opt->a, rep_len, !!(opt->flag & MM_F_SR)); mm_set_mapq(km, s->n_reg[k], s->reg[k], opt->min_chain_score, opt->a, rep_len, !!(opt->flag & MM_F_SR));

1
options.c
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@ -54,6 +54,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_clip_ratio = 1.0f; opt->max_clip_ratio = 1.0f;
opt->mini_batch_size = 500000000; opt->mini_batch_size = 500000000;
opt->max_sw_mat = 100000000; opt->max_sw_mat = 100000000;
opt->cap_kalloc = 1000000000;
opt->rank_min_len = 500; opt->rank_min_len = 500;
opt->rank_frac = 0.9f; opt->rank_frac = 0.9f;