From 742bd44728b796ac7d59865957dce6af79e32d57 Mon Sep 17 00:00:00 2001 From: fromer Date: Mon, 31 Jan 2011 22:15:26 +0000 Subject: [PATCH] Changed output file to be user-defined git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5149 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/fromer/phaseSamples.scala | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scala/qscript/oneoffs/fromer/phaseSamples.scala b/scala/qscript/oneoffs/fromer/phaseSamples.scala index fddfb392e..d341c9950 100644 --- a/scala/qscript/oneoffs/fromer/phaseSamples.scala +++ b/scala/qscript/oneoffs/fromer/phaseSamples.scala @@ -36,6 +36,9 @@ class PhaseSamples extends QScript { @Input(doc="Samples to phase together. By default is set to 1 [one job per sample].", shortName="samplesPerJob", required=false) var samplesPerJob = 1 + @Input(doc="Phased file to output", shortName="o", required=true) + var outputPhased: File = _ + trait CommandLineGATKArgs extends CommandLineGATK { this.intervalsString = List(qscript.intervals) this.jarFile = qscript.gatkJarFile @@ -46,7 +49,7 @@ class PhaseSamples extends QScript { // A target has a list of samples and bam files to use for phasing class Target(val name: String, val samples: List[String], val bams: List[File]) { - def phasedVCFFile = new File(name + ".phased.vcf") + def phasedVCFFile = new File(name + "." + outputPhased) override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams) } @@ -119,7 +122,7 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) - this.out = new File("phased.vcf") + this.out = new File(outputPhased) } }