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r542: tuning mapQ calculation

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Heng Li
2017-10-31 14:25:09 -04:00
parent 7f11f4c4d4
commit fb8a1b5536
4 changed files with 24 additions and 11 deletions
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hit.c
+18 -5
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@@ -442,7 +442,7 @@ void mm_seg_free(void *km, int n_segs, mm_seg_t *segs)
kfree(km, segs);
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len)
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;
int i;
@@ -458,10 +458,23 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
float identity = (float)r->mlen / r->blen;
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. - (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score) * logf(r->score)); // more for long reads
mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
} else mapq = (int)(pen_cm * q_coef * (1. - (float)subsc / r->score) * logf(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));
} else {
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
}
} else {
float x = (float)subsc / r->score;
if (is_sr && r->p) {
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));
} else {
mapq = (int)(pen_cm * q_coef * (1.0f - x) * logf(r->score));
}
}
mapq -= (int)(4.343f * logf(r->n_sub + 1) + .499f);
mapq = mapq > 0? mapq : 0;
r->mapq = mapq < 60? mapq : 60;