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r556: bugfix - underestimate mapq for split aln

This commit is contained in:
Heng Li 2017-11-07 22:37:12 -05:00
parent 21a46ba652
commit 65deedfa96
2 changed files with 8 additions and 2 deletions
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8
hit.c
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@ -406,14 +406,20 @@ void mm_seg_free(void *km, int n_segs, mm_seg_t *segs)
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr) void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr)
{ {
static const float q_coef = 40.0f; static const float q_coef = 40.0f;
int64_t sum_sc = 0;
float uniq_ratio;
int i; int i;
for (i = 0; i < n_regs; ++i)
if (regs[i].parent == regs[i].id)
sum_sc += regs[i].score;
uniq_ratio = (float)sum_sc / (sum_sc + rep_len);
for (i = 0; i < n_regs; ++i) { for (i = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i]; mm_reg1_t *r = &regs[i];
if (r->inv) { if (r->inv) {
r->mapq = 0; r->mapq = 0;
} else if (r->parent == r->id) { } else if (r->parent == r->id) {
int mapq, subsc; int mapq, subsc;
float pen_s1 = (r->score > 100? 1.0f : 0.01f * r->score) * ((float)r->score / (r->score + rep_len)); float pen_s1 = (r->score > 100? 1.0f : 0.01f * r->score) * uniq_ratio;
float pen_cm = r->cnt > 10? 1.0f : 0.1f * r->cnt; float pen_cm = r->cnt > 10? 1.0f : 0.1f * r->cnt;
pen_cm = pen_s1 < pen_cm? pen_s1 : pen_cm; pen_cm = pen_s1 < pen_cm? pen_s1 : pen_cm;
subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc; subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.4-r555" #define MM_VERSION "2.4-r556-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>