From 8ce926d279941924b7acfc29743b27ce15bbd4bf Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Fri, 28 Jun 2024 12:08:09 -0400 Subject: [PATCH] Update ClipBam.scala fix documentation --- src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala b/src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala index 1adc8c27e..190e4d04c 100644 --- a/src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala +++ b/src/main/scala/com/fulcrumgenomics/bam/ClipBam.scala @@ -55,7 +55,7 @@ import scala.collection.immutable.IndexedSeq |done in streaming fashion with, for example: | |``` - |samtools sort -n -u in.bam | fgbio ClipBam -i /dev/stdin ... + |samtools sort -n in.bam | fgbio ClipBam -i /dev/stdin ... |``` | |The output sort order may be specified with `--sort-order`. If not given, then the output will be in the same @@ -86,7 +86,7 @@ class ClipBam @arg( doc="Require at least this number of bases to be clipped on the 3' end of R2") val readTwoThreePrime: Int = 0, @arg( doc="Clip overlapping reads.") val clipOverlappingReads: Boolean = false, @arg( doc="Clip reads in FR pairs that sequence past the far end of their mate.") val clipBasesPastMate: Boolean = false, - @arg(flag='S', doc="The sort order of the output. If not given, output will be in the same order as input if the input.") + @arg(flag='S', doc="The sort order of the output. If not given, output will be in the same order as the input.") val sortOrder: Option[SamOrder] = None ) extends FgBioTool with LazyLogging { Io.assertReadable(input)