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Allow callers of Var2VcfValid to turn on printing of a variant's END tag #398

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Sep 7, 2021
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Allow callers of Var2VcfValid to turn on printing of a variant's END tag #398

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3 changes: 2 additions & 1 deletion tasks/src/main/scala/dagr/tasks/vc/VarDictJava.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {

Expand Down Expand Up @@ -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]
Expand Down