Update src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusRead…

…s.scala
fulcrumgenomics · Feb 26, 2022 · 773842a · 773842a
1 parent 4c2f9d0
commit 773842a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala b/src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala
@@ -98,7 +98,7 @@ class CallDuplexConsensusReads
  @arg(flag='2', doc="The Phred-scaled error rate for an error post the UMIs have been integrated.") val errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi,
  @arg(flag='m', doc="Ignore bases in raw reads that have Q below this value.") val minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality,
  @arg(flag='t', doc="If true, quality trim input reads in addition to masking low Q bases.") val trim: Boolean = false,
- @arg(flag='S', doc="The sort order of the output, if `:none:` then the same as the input.") val sortOrder: Option[SamOrder] = None,
+ @arg(flag='S', doc="The sort order of the output, the same as the input if not given.") val sortOrder: Option[SamOrder] = None,
  @arg(flag='M', minElements=1, maxElements=3, doc="The minimum number of input reads to a consensus read.") val minReads: Seq[Int] = Seq(1),
  @arg(doc="""
             |The maximum number of reads to use when building a single-strand consensus. If more than this many reads are