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r1285: better --spsc support

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Heng Li
2025-05-26 15:47:14 -04:00
parent 005c9a1f6b
commit 3187782b1a
4 changed files with 29 additions and 7 deletions
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minimap2.1
+11 -2
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@@ -443,14 +443,23 @@ line corresponds to a donor site and `A' for an acceptor site.
A positive score suggests the junction is preferred and a negative score
suggests the junction is not preferred.
.TP
.BR --junc-pen \ INT
Penalty for a position not in FILE specified by
.BR --spsc0 \ INT
Penalty for positions not in
.I FILE
specified by
.B --spsc
[5]. Effective with
.B --spsc
but not
.BR --junc-bed .
.TP
.BR --spsc-scale \ FLOAT
Scale splice scores in
.B --spsc
by
.IR FLOAT
rounded to the nearest integer [0.7].
.TP
.BR --junc-bed \ FILE
Junctions to prefer during base alignment [].
Same format as