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inbananced coverage

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chhylp123
2024-04-02 10:40:11 -04:00
parent 61ceb3a4e1
commit b992a07d05
3 changed files with 14 additions and 11 deletions
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anchor.cpp
+3 -3
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@@ -126,7 +126,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
ha_mz1_t *z = &ab->mz.a[i];
seed1_t *s = &ab->seed[i];
for (j = 0; j < s->n; ++j) {
const ha_idxpos_t *y = &s->a[j];
const ha_idxpos_t *y = &s->a[j];///Improve: filter out y->rid == rid
anchor1_t *an = &ab->a[k++];
uint8_t rev = z->rev == y->rev? 0 : 1;
an->other_off = y->pos;
@@ -152,7 +152,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
cl->size = ab->m_a;
REALLOC(cl->list, cl->size);
}
for (k = 0; k < ab->n_a; ++k) {
for (k = 0; k < ab->n_a; ++k) {///Improve: direct use ab->a instead of cl->list
k_mer_hit *p = &cl->list[k];
p->readID = ab->a[k].srt >> 33;
p->strand = ab->a[k].srt >> 32 & 1;
@@ -184,7 +184,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
#endif
if ((int)overlap_list->length > max_n_chain) {
if ((int)overlap_list->length > max_n_chain) {///Improve: use HEAP to directly avoid chaining with too small scores
int32_t w, n[4], s[4];
n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
ks_introsort_or_ss(overlap_list->length, overlap_list->list);