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r440: better chain filtering for PE reads

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Heng Li
2017-09-26 11:03:36 -04:00
parent 64c0ad6b35
commit 55d1e4f638
6 changed files with 54 additions and 9 deletions
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42
pe.c Normal file
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@@ -0,0 +1,42 @@
#include <stdlib.h>
#include "mmpriv.h"
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
int max_dist = n_segs == 2? qlens[0] + qlens[1] + max_gap_ref : 0;
for (i = k = 0; i < n; ++i) {
int to_keep = 0;
if (r[i].parent == i) { // primary
to_keep = 1;
} else if (r[i].score + min_diff >= r[r[i].parent].score) {
to_keep = 1;
} else {
mm_reg1_t *p = &r[r[i].parent], *q = &r[i];
if (p->rev == q->rev && p->rid == q->rid && q->re - p->rs < max_dist && p->re - q->rs < max_dist) { // child and parent are close on the ref
if (q->score >= p->score * pri1)
to_keep = 1;
} else {
int is_par_both = (n_segs == 2 && p->qs < qlens[0] && p->qe > qlens[0]);
int is_chi_both = (n_segs == 2 && q->qs < qlens[0] && q->qe > qlens[0]);
if (is_chi_both || is_chi_both == is_par_both) {
if (q->score >= p->score * pri_ratio)
to_keep = 1;
} else { // the remaining case: is_chi_both == 0 && is_par_both == 1
if (q->score >= p->score * pri2)
to_keep = 1;
}
}
}
if (to_keep && r[i].parent != i) {
if (n_2nd++ >= best_n) to_keep = 0; // don't keep if there are too many secondary hits
}
if (to_keep) r[k++] = r[i];
else if (r[i].p) free(r[i].p);
}
if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k;
}
}