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fixed bug when retaining 2ndary aln; still buggy

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This commit is contained in:
Heng Li
2017-07-02 19:08:30 -04:00
parent da90b614db
commit 74d306a596
5 changed files with 31 additions and 15 deletions
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hit.c
+19 -6
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@@ -134,13 +134,13 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
kfree(km, tmp);
}
void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r)
void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_;
int i, k, n = *n_, n_2nd = 0;
for (i = k = 0; i < n; ++i)
if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
r[k++] = r[i];
if (r[i].parent == i) r[k++] = r[i];
else if (r[i].score >= r[r[i].parent].score * pri_ratio && n_2nd++ < best_n) 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;
@@ -192,9 +192,9 @@ int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
return as;
}
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a)
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
{
int i, n_aux;
int i, n_aux, n_regs = *n_regs_, n_drop = 0;
uint64_t *aux;
if (n_regs < 2) return; // nothing to join
@@ -228,8 +228,21 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg
r0->cnt += r1->cnt, r0->score += r1->score;
mm_reg_set_coor(r0, qlen, a);
r1->cnt = 0;
r1->parent = r0->id;
++n_drop;
}
kfree(km, aux);
if (n_drop > 0) { // then fix the hits hierarchy
for (i = 0; i < n_regs; ++i) { // adjust the mm_reg1_t::parent
mm_reg1_t *r = &regs[i];
if (r->parent >= 0 && r->id != r->parent) { // fix for secondary hits only
if (regs[r->parent].parent >= 0 && regs[r->parent].parent != r->parent)
r->parent = regs[r->parent].parent;
}
}
mm_filter_regs(km, opt, n_regs_, regs);
}
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs)