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r1105: avoid long running time occasionally (#771)

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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
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mmpriv.h
+1
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@@ -61,6 +61,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
mm_seed_t *mm_collect_matches(void *km, int *_n_m, int qlen, int max_occ, int max_max_occ, int dist, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos);
void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac);
double mm_event_identity(const mm_reg1_t *r);
int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);