From 90aef66ec5f485b647bef4afc9aa63809eebcfb2 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 23 Aug 2010 23:25:29 +0000 Subject: [PATCH] Minor fixes for my last commit git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4090 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/sequenom/SequenomValidationConverter.java | 1 - .../playground/gatk/walkers/BeagleOutputToVCFWalker.java | 4 ++-- .../sting/playground/gatk/walkers/BeagleIntegrationTest.java | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index 0dc1dad07..c74f72210 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java @@ -163,7 +163,6 @@ public class SequenomValidationConverter extends RodWalker record : records ) vcfwriter.add(record.first, record.second); - vcfwriter.close(); } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java index e1f4b7e04..dcc413a19 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java @@ -65,9 +65,9 @@ public class BeagleOutputToVCFWalker extends RodWalker { @Output(doc="File to which variants should be written",required=true) protected VCFWriter vcfWriter = null; - @Argument(fullName="output_file", shortName="output", doc="Please use --out instead") + @Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false) @Deprecated - private String oldOutputArg; + protected String oldOutputArg; @Argument(fullName="no" + "call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false) diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java index 3b0758da2..e6e0ead0d 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java @@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest { "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " + "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " + "-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " + - "-output %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0")); + "-o %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0")); executeTest("test BeagleOutputToVCF", spec); }