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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-01-18 09:53:42 -05:00
parent 0268da7560 b7c65cb089
commit 0133d1a901
1 changed files with 4 additions and 0 deletions
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4
public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
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@ -47,12 +47,16 @@ class SnpEff extends JavaCommandLineFunction {
@Argument(doc="verbose", required=false) @Argument(doc="verbose", required=false)
var verbose = true var verbose = true
@Argument(doc="onlyCoding", required=false)
var onlyCoding = true
@Output(doc="snp eff output") @Output(doc="snp eff output")
var outVcf: File = _ var outVcf: File = _
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("eff") + required("eff") +
conditional(verbose, "-v") + conditional(verbose, "-v") +
required("-onlyCoding", onlyCoding.toString) +
optional("-c", config) + optional("-c", config) +
required("-i", "vcf") + required("-i", "vcf") +
required("-o", "vcf") + required("-o", "vcf") +