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r1266: fine tune mapq for short RNA-seq reads

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Heng Li
2025-04-07 00:57:39 -04:00
parent 75619c7b51
commit 3542a3d153
4 changed files with 19 additions and 11 deletions
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hit.c
+13 -5
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@@ -418,16 +418,19 @@ static void mm_set_inv_mapq(void *km, int n_regs, mm_reg1_t *regs)
kfree(km, aux);
}
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_mapq2(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr, int is_splice)
{
static const float q_coef = 40.0f;
int64_t sum_sc = 0;
float uniq_ratio;
int i;
int i, n_2nd_splice = 0;
if (n_regs == 0) return;
for (i = 0; i < n_regs; ++i)
for (i = 0; i < n_regs; ++i) {
if (regs[i].parent == regs[i].id)
sum_sc += regs[i].score;
else if (regs[i].is_spliced)
++n_2nd_splice;
}
uniq_ratio = (float)sum_sc / (sum_sc + rep_len);
for (i = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i];
@@ -440,13 +443,18 @@ void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int ma
pen_cm = pen_s1 < pen_cm? pen_s1 : pen_cm;
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;
float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score0;
float x, identity = (float)r->mlen / r->blen;
if (is_sr && is_splice)
x = (float)r->p->dp_max2 / r->p->dp_max; // ignore chaining score; for short RNA-seq reads, unspliced chaining score tends to be higher
else
x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score0;
mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc));
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
mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
}
if (is_splice && is_sr && r->is_spliced && n_2nd_splice == 0)
mapq += 10;
} else {
float x = (float)subsc / r->score0;
if (r->p) {