r1105: avoid long running time occasionally (#771)

Caused by highly repetitive minimizers on a query sequence. The solution is to
filter out these query minimizers.
This commit is contained in:
Heng Li
2021-08-15 19:43:01 -04:00
parent cc14d1afdf
commit 05a8a45d44
8 changed files with 40 additions and 2 deletions
+1
View File
@@ -163,6 +163,7 @@ typedef struct {
int pe_ori, pe_bonus;
float mid_occ_frac; // only used by mm_mapopt_update(); see below
float q_occ_frac;
int32_t min_mid_occ, max_mid_occ;
int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ, max_max_occ, occ_dist;