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r1248: support --end-bonus in splice mode

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but this is not enabled by default for now
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Heng Li
2025-04-02 21:39:41 -04:00
parent 924fc4d671
commit 9d06cef13e
6 changed files with 20 additions and 16 deletions
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minimap2.1
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@@ -1,4 +1,4 @@
.TH minimap2 1 "30 March 2025" "minimap2-2.28-dirty (r1237)" "Bioinformatics tools"
.TH minimap2 1 "2 April 2025" "minimap2-2.28-dirty (r1248)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -689,7 +689,7 @@ Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
.B splice:sr
Spliced alignment for short RNA-seq reads
.RB ( -xsplice:hq
.B --frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain
.B --frag=yes -m25 -s40 -2K50m --heap-sort=yes --pe-ind-chain
.BR --secondary=no ).
.TP
.B sr