From 5e27e9162f2fd8d32dc4cc95611cb8717aa93b7a Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 15 Dec 2010 11:40:27 +0000 Subject: [PATCH] Huh? I thought we parsed out comma-separated command line arguments into list automatically...just change the syntax of the integration test, no need to update the md5 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4843 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 2 +- .../walkers/variantutils/VariantToTableIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index ebd13e843..7b4d05130 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -47,7 +47,7 @@ public class VariantsToTable extends RodWalker { protected PrintStream out; @Argument(fullName="fields", shortName="F", doc="Fields to emit from the VCF, allows any VCF field, any info field, and some meta fields like nHets", required=true) - public List fieldsToTake = null; + public ArrayList fieldsToTake = new ArrayList(); @Argument(fullName="showFiltered", shortName="raw", doc="Include filtered records") public boolean showFiltered = false; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java index a1efbf4a4..dfe33062a 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java @@ -40,9 +40,9 @@ public class VariantToTableIntegrationTest extends WalkerTest { "-R " + hg18Reference + " -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" + " -T VariantsToTable" + - " -F CHROM,POS,ID,REF,ALT,QUAL,FILTER,TRANSITION,DP,SB,set,RankSumP,refseq.functionalClass*" + + " -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" + " -L chr1 -o %s", Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba")); executeTest("testComplexVariantsToTable", spec).getFirst(); } -} \ No newline at end of file +}