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r783: reverted to r781 (#155)

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Heng Li
2018-05-30 15:25:34 -04:00
parent 3573784b4d
commit a3afeec0b2
5 changed files with 7 additions and 14 deletions
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hit.c
+1 -8
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@@ -106,7 +106,7 @@ 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 test_ref_ovlp) // and compute mm_reg1_t::subsc
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff) // and compute mm_reg1_t::subsc
{
int i, j, k, *w;
uint64_t *cov;
@@ -146,13 +146,6 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
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;
if (test_ref_ovlp && rp->rid == ri->rid && (rp->re > ri->rs && rp->rs < ri->re)) { // have overlap on the reference sequence
int min_r = rp->re - rp->rs < ri->re - ri->rs? rp->re - rp->rs : ri->re - ri->rs;
int min_e = rp->re < ri->re? rp->re : ri->re;
int max_s = rp->rs > ri->rs? rp->rs : ri->rs;
int rl = min_e - max_s;
if (rl > min_r * mask_level) continue;
}
ri->parent = rp->parent;
rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
if (ri->cnt >= rp->cnt) cnt_sub = 1;