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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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python/cmappy.pxd
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@@ -51,6 +51,7 @@ cdef extern from "minimap.h":
int pe_ori, pe_bonus
float mid_occ_frac
float q_occ_frac
int32_t min_mid_occ
int32_t mid_occ
int32_t max_occ