From cf9b1d350a373fde820b4d97b2df3f321646601a Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 19 Jan 2012 00:20:49 -0500 Subject: [PATCH] Some minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs. --- .../sting/queue/library/ipf/vcf/VCFExtractIntervals.scala | 1 + .../sting/queue/library/ipf/vcf/VCFExtractSamples.scala | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala index 3935c2138..e661f1bb5 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala @@ -44,6 +44,7 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e } } } + out.printf("%s%n",cur) out.close } diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala index 54e541142..3179c327f 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala @@ -6,7 +6,7 @@ import collection.JavaConversions._ import org.broadinstitute.sting.commandline._ import java.io.{PrintWriter, PrintStream, File} -class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction { +class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction { def this(in: File, out: File, samples: File) = this(in,out, (new XReadLines(samples)).readLines.toList) @Input(doc="VCF from which to extract samples") var inputVCF : File = inVCF