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r145: changed default -p from 2 to 0.8

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For long reads, secondary alignments can be very information.
This commit is contained in:
Heng Li
2017-07-02 22:51:45 -04:00
parent 632b8638d2
commit 51cfb60520
3 changed files with 10 additions and 5 deletions
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minimap2.1
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@@ -1,4 +1,4 @@
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r141-pre" "Bioinformatics tools"
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r145-pre" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -149,14 +149,18 @@ will be suppressed; if the query sequence name is the same as the target name,
diagonal minimizer hits will also be suppressed.
.TP
.BI -p \ FLOAT
Minimal secondary-to-primary score ratio to output secondary mappings [2].
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
Between two chains overlaping over half of the shorter chain (controled by
.BR --mask-level ),
the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
.IR FLOAT ,
the secondary chain will not be outputted or extended with DP alignment later.
The default value suppresses all secondary chains.
.TP
.BI -N \ INT
Output at most
.I INT
secondary alignments [5]
.TP
.BI -D \ FLOAT
Discard a chain if the fraction of matching bases over the length of