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r1094: for --split-prefix update max_dp at the end

This commit is contained in:
Heng Li 2021-08-06 21:40:43 -04:00
parent f7271a7c24
commit 8a1d52bcbe
4 changed files with 12 additions and 3 deletions
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4
align.c
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@ -931,7 +931,7 @@ static int32_t mm_recal_max_dp(const mm_reg1_t *r, double b2, int32_t match_sc)
return (int32_t)(match_sc * (r->mlen - b2 * n_mis - gap_cost) + .499); return (int32_t)(match_sc * (r->mlen - b2 * n_mis - gap_cost) + .499);
} }
static void mm_update_dp_max(int qlen, int n_regs, mm_reg1_t *regs, float frac, int a, int b) void mm_update_dp_max(int qlen, int n_regs, mm_reg1_t *regs, float frac, int a, int b)
{ {
int32_t max = -1, max2 = -1, i, max_i = -1; int32_t max = -1, max2 = -1, i, max_i = -1;
double div, b2; double div, b2;
@ -1011,7 +1011,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
kfree(km, qseq0[0]); kfree(km, qseq0[0]);
kfree(km, ez.cigar); kfree(km, ez.cigar);
mm_filter_regs(opt, qlen, n_regs_, regs); mm_filter_regs(opt, qlen, n_regs_, regs);
if (!(opt->flag&MM_F_SR) && qlen >= opt->rank_min_len) { if (!(opt->flag&MM_F_SR) && !opt->split_prefix && qlen >= opt->rank_min_len) {
mm_update_dp_max(qlen, *n_regs_, regs, opt->rank_frac, opt->a, opt->b); mm_update_dp_max(qlen, *n_regs_, regs, opt->rank_frac, opt->a, opt->b);
mm_filter_regs(opt, qlen, n_regs_, regs); mm_filter_regs(opt, qlen, n_regs_, regs);
} }

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 "2.21-dev-r1090-dirty" #define MM_VERSION "2.21-dev-r1094-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

8
map.c
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@ -494,6 +494,14 @@ static void merge_hits(step_t *s)
} }
} }
} }
if (!(opt->flag&MM_F_SR) && s->seq[k].l_seq >= opt->rank_min_len)
mm_update_dp_max(s->seq[k].l_seq, s->n_reg[k], s->reg[k], opt->rank_frac, opt->a, opt->b);
for (j = 0; j < s->n_reg[k]; ++j) {
mm_reg1_t *r = &s->reg[k][j];
if (r->p) r->p->dp_max2 = 0; // reset ->dp_max2 as mm_set_parent() doesn't clear it; necessary with mm_update_dp_max()
r->subsc = 0; // this may not be necessary
r->n_sub = 0; // n_sub will be an underestimate as we don't see all the chains now, but it can't be accurate anyway
}
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)) {

1
mmpriv.h
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@ -95,6 +95,7 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs); void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);
void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac); void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac);
void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr); void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);
void mm_update_dp_max(int qlen, int n_regs, mm_reg1_t *regs, float frac, int a, int b);
void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const mm128_t *a, int32_t n, const uint64_t *mini_pos); void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const mm128_t *a, int32_t n, const uint64_t *mini_pos);