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r543: applied some sr mapq changes to long reads

This commit is contained in:
Heng Li 2017-10-31 15:24:05 -04:00
parent fb8a1b5536
commit 311fa90030
2 changed files with 4 additions and 6 deletions
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6
hit.c
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@ -459,16 +459,14 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) { if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
float identity = (float)r->mlen / r->blen; float identity = (float)r->mlen / r->blen;
float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score; float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score;
if (is_sr) {
mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc)); mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc));
} else { if (!is_sr) {
int mapq_alt = (int)(6.02f * identity * identity * (r->p->dp_max - r->p->dp_max2) / match_sc + .499f); // BWA-MEM like mapQ, mostly for short reads int mapq_alt = (int)(6.02f * identity * identity * (r->p->dp_max - r->p->dp_max2) / match_sc + .499f); // BWA-MEM like mapQ, mostly for short reads
mapq = (int)(identity * pen_cm * q_coef * (1.0f - x) * logf(r->score)); // more for long reads
mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
} }
} else { } else {
float x = (float)subsc / r->score; float x = (float)subsc / r->score;
if (is_sr && r->p) { if (r->p) {
float identity = (float)r->mlen / r->blen; float identity = (float)r->mlen / r->blen;
mapq = (int)(identity * pen_cm * q_coef * (1.0f - x) * logf((float)r->p->dp_max / match_sc)); mapq = (int)(identity * pen_cm * q_coef * (1.0f - x) * logf((float)r->p->dp_max / match_sc));
} else { } else {

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.3-r542-dirty" #define MM_VERSION "2.3-r543-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>