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Change default sort orders of consensus callers #781

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Feb 26, 2022
Merged

Change default sort orders of consensus callers #781

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4c2f9d0
Change default sort orders of consensus callers
nh13 Feb 20, 2022
773842a
Update src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusRead…
nh13 Feb 26, 2022
c2a3c57
Update src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusR…
nh13 Feb 26, 2022
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2 changes: 1 addition & 1 deletion src/main/scala/com/fulcrumgenomics/umi/CallDuplexConsensusReads.scala
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Expand Up @@ -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] = Some(SamOrder.Queryname),
@arg(flag='S', doc="The sort order of the output, if `:none:` then the same as the input.") val sortOrder: Option[SamOrder] = None,
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@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
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2 changes: 1 addition & 1 deletion src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala
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Expand Up @@ -121,7 +121,7 @@ class CallMolecularConsensusReads
""")
val maxReads: Option[Int] = None,
@arg(flag='B', doc="If true produce tags on consensus reads that contain per-base information.") val outputPerBaseTags: Boolean = DefaultProducePerBaseTags,
@arg(flag='S', doc="The sort order of the output, if `:none:` then the same as the input.") val sortOrder: Option[SamOrder] = Some(SamOrder.Queryname),
@arg(flag='S', doc="The sort order of the output, if `:none:` then the same as the input.") val sortOrder: Option[SamOrder] = None,
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@arg(flag='D', doc="Turn on debug logging.") val debug: Boolean = false,
@arg(doc="The number of threads to use while consensus calling.") val threads: Int = 1
) extends FgBioTool with LazyLogging {
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