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r846: added --hard-mask-level for #244

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Heng Li
2018-09-27 14:46:26 -04:00
parent c57b59f02f
commit 1077b7ddc8
6 changed files with 18 additions and 8 deletions
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hit.c
+3 -1
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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) // 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) // and compute mm_reg1_t::subsc
{
int i, j, k, *w;
uint64_t *cov;
@@ -118,6 +118,7 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
for (i = 1, k = 1; i < n; ++i) {
mm_reg1_t *ri = &r[i];
int si = ri->qs, ei = ri->qe, n_cov = 0, uncov_len = 0;
if (hard_mask_level) goto skip_uncov;
for (j = 0; j < k; ++j) { // traverse existing primary hits to find overlapping hits
mm_reg1_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe;
@@ -137,6 +138,7 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
}
if (ei > x) uncov_len += ei - x;
}
skip_uncov:
for (j = 0; j < k; ++j) { // traverse existing primary hits again
mm_reg1_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe, min, max, ol;