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r224: inversion alignment around Z-drop break

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Heng Li
2017-07-29 13:09:10 -04:00
parent 120bebc290
commit 19d6ec885e
7 changed files with 60 additions and 30 deletions
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hit.c
+6 -4
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@@ -125,11 +125,11 @@ void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r)
aux = (uint64_t*)kmalloc(km, n * 8);
t = (mm_reg1_t*)kmalloc(km, n * sizeof(mm_reg1_t));
for (i = n_aux = 0; i < n; ++i) {
if (r[i].cnt > 0) { // squeeze out elements with cnt==0 (soft deleted)
if (r[i].inv || r[i].cnt > 0) { // squeeze out elements with cnt==0 (soft deleted)
assert(r[i].p);
aux[n_aux++] = (uint64_t)r[i].p->dp_max << 32 | i;
} else if (r[i].p) {
kfree(km, r[i].p);
free(r[i].p);
r[i].p = 0;
}
}
@@ -197,7 +197,7 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
for (i = k = 0; i < *n_regs; ++i) {
mm_reg1_t *r = &regs[i];
int flt = 0;
if (r->cnt < opt->min_cnt) flt = 1;
if (!r->inv && r->cnt < opt->min_cnt) flt = 1;
if (r->p) {
if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max) flt = 1;
@@ -294,7 +294,9 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc)
int i;
for (i = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i];
if (r->parent == r->id) {
if (r->inv) {
r->mapq = 0;
} else if (r->parent == r->id) {
int mapq, subsc;
float pen_cm = r->cnt >= 10? 1.0f : 0.1f * r->cnt;
subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;