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support ALT mapping

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This commit is contained in:
Heng Li
2020-01-20 19:32:31 -05:00
parent d2e14705e7
commit eb3ed6993d
10 changed files with 87 additions and 22 deletions
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41
hit.c
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@@ -87,6 +87,22 @@ mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u,
return r;
}
void mm_mark_alt(const mm_idx_t *mi, int n, mm_reg1_t *r)
{
int i;
if (mi->n_alt == 0) return;
for (i = 0; i < n; ++i)
if (mi->seq[r[i].rid].is_alt)
r[i].is_alt = 1;
}
static inline int mm_alt_score(int score, float alt_diff_frac)
{
if (score < 0) return score;
score = (int)(score * (1.0 - alt_diff_frac) + .499);
return score > 0? score : 1;
}
void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
{
if (n <= 0 || n >= r->cnt) return;
@@ -106,7 +122,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
r->split |= 1, r2->split |= 2;
}
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff, int hard_mask_level) // and compute mm_reg1_t::subsc
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff, int hard_mask_level, float alt_diff_frac) // and compute mm_reg1_t::subsc
{
int i, j, k, *w;
uint64_t *cov;
@@ -147,12 +163,15 @@ skip_uncov:
max = ej - sj > ei - si? ej - sj : ei - si;
ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si); // overlap length; TODO: this can be simplified
if ((float)ol / min - (float)uncov_len / max > mask_level) {
int cnt_sub = 0;
int cnt_sub = 0, sci = ri->score;
ri->parent = rp->parent;
rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
if (!rp->is_alt && ri->is_alt) sci = mm_alt_score(sci, alt_diff_frac);
rp->subsc = rp->subsc > sci? rp->subsc : sci;
if (ri->cnt >= rp->cnt) cnt_sub = 1;
if (rp->p && ri->p && (rp->rid != ri->rid || rp->rs != ri->rs || rp->re != ri->re || ol != min)) { // the last condition excludes identical hits after DP
rp->p->dp_max2 = rp->p->dp_max2 > ri->p->dp_max? rp->p->dp_max2 : ri->p->dp_max;
sci = ri->p->dp_max;
if (!rp->is_alt && ri->is_alt) sci = mm_alt_score(sci, alt_diff_frac);
rp->p->dp_max2 = rp->p->dp_max2 > sci? rp->p->dp_max2 : sci;
if (rp->p->dp_max - ri->p->dp_max <= sub_diff) cnt_sub = 1;
}
if (cnt_sub) ++rp->n_sub;
@@ -166,7 +185,7 @@ set_parent_test:
kfree(km, w);
}
void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r)
void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac)
{
int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
mm128_t *aux;
@@ -177,13 +196,11 @@ void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r)
t = (mm_reg1_t*)kmalloc(km, n * sizeof(mm_reg1_t));
for (i = n_aux = 0; i < n; ++i) {
if (r[i].inv || r[i].cnt > 0) { // squeeze out elements with cnt==0 (soft deleted)
if (r[i].p) {
aux[n_aux].x = (uint64_t)r[i].p->dp_max << 32 | r[i].hash;
has_cigar = 1;
} else {
aux[n_aux].x = (uint64_t)r[i].score << 32 | r[i].hash;
no_cigar = 1;
}
int score;
if (r[i].p) score = r[i].p->dp_max, has_cigar = 1;
else score = r[i].score, no_cigar = 1;
if (r[i].is_alt) score = mm_alt_score(score, alt_diff_frac);
aux[n_aux].x = (uint64_t)score << 32 | r[i].hash;
aux[n_aux++].y = i;
} else if (r[i].p) {
free(r[i].p);