diff --git a/tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala b/tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala index ae25f74c..3b2edb07 100644 --- a/tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala +++ b/tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala @@ -317,6 +317,7 @@ class VarDictJavaEndToEnd @arg(flag='a', doc="Output all sites, including reference calls.") allSites: Boolean = false, @arg(flag='A', doc="Output all variants at the same genomic site.") allVariants: Boolean = false, @arg(flag='N', doc="Count No-calls (Ns) in the total depth tag (DP)") countNsInTotalDepth: Boolean = false, + @arg(flag='E', doc="If true, add an INFO tag for the variant's end (END)") printEndTag: Boolean = false, @arg(flag='F', doc="Experimental feature: Use Java implementation of Fisher exact test (previously R Scripts: teststrandbias.R and testsomatic.R). Requires VarDictJava version 1.8.0 (b772179) or later.") fisher: Boolean = false ) extends Pipeline { @@ -367,7 +368,7 @@ class VarDictJavaEndToEnd minimumDepth = minimumDepth, minimumHighQualityAltDepth = minimumHighQualityAltDepth, minimumAf = minimumAf, - printEndTag = false + printEndTag = printEndTag ) if (fisher) var2VcfValid else { val bias = new ShellCommand(VarDictJava.TestStrandBias.toString) with PipeWithNoResources[Text, Text]