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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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minimap2.1
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@@ -151,10 +151,16 @@ Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurr
.BR -f }}.
This option prevents excessively small or large
.B -f
estimated from the input reference. It deprecates
estimated from the input reference. Available since r1034 and deprecating
.B --min-occ-floor
in earlier versions of minimap2.
.TP
.BI --q-occ-frac \ FLOAT
Discard a query minimizer if its occurrence is higher than
.I FLOAT
fraction of query minimizers and than the reference occurrence threshold
[0.02]. Set 0 to disable. Available since r1105.
.TP
.BI -e \ INT
Sample a high-frequency minimizer every
.I INT