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r443: don't filter small cm for split seg

This commit is contained in:
Heng Li 2017-09-26 16:17:58 -04:00
parent 1b1dd0cd57
commit f611edf6f2
4 changed files with 6 additions and 4 deletions
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4
hit.c
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@ -203,7 +203,7 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
for (i = k = 0; i < *n_regs; ++i) {
mm_reg1_t *r = &regs[i];
int flt = 0;
if (!r->inv && r->cnt < opt->min_cnt) flt = 1;
if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
if (r->p) {
if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max) flt = 1;
@ -342,6 +342,8 @@ mm_seg_t *mm_seg_gen(void *km, int n_segs, const int *qlens, int n_regs0, const
for (s = 0; s < n_segs; ++s) {
regs[s] = mm_gen_regs(km, qlens[s], seg[s].n_u, seg[s].u, seg[s].a);
n_regs[s] = seg[s].n_u;
for (i = 0; i < n_regs[s]; ++i)
regs[s][i].seg_split = 1;
}
return seg;
}

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r442-dirty"
#define MM_VERSION "2.2-r443-dirty"
#ifdef __linux__
#include <sys/resource.h>

2
map.c
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@ -234,7 +234,7 @@ static void chain_post(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int
if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, opt->max_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, opt->max_gap_ref, mi->k*2, opt->best_n * n_segs, n_segs, qlens, n_regs, regs);
if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR))
mm_join_long(km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}

2
minimap.h
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@ -61,7 +61,7 @@ typedef struct {
typedef struct {
int32_t id; // ID for internal uses (see also parent below)
uint32_t cnt:31, rev:1; // number of minimizers; if on the reverse strand
uint32_t cnt:30, rev:1, seg_split:1; // number of minimizers; if on the reverse strand
uint32_t rid:31, inv:1; // reference index; if this is an alignment from inversion rescue
int32_t score; // DP alignment score
int32_t qs, qe, rs, re; // query start and end; reference start and end