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added --mask-len for #659

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Heng Li
2020-08-21 11:12:50 -04:00
parent ccb0f7b05d
commit f995f55610
8 changed files with 21 additions and 8 deletions
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minimap2.1
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@@ -237,7 +237,14 @@ or more of the shorter chain [0.5]
.B --hard-mask-level
Honor option
.B -M
and disable a heurstic to save unmapped subsequences.
and disable a heurstic to save unmapped subsequences and disables
.BR --mask-len .
.TP
.BI --mask-len \ NUM
Keep an alignment if dropping it leaves an unaligned region on query longer than
.IR INT
[inf]. Effective without
.BR --hard-mask-level .
.TP
.BI --max-chain-skip \ INT
A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming