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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
This commit is contained in:
chartl 2010-12-15 11:40:27 +00:00
parent 3e75431bc8
commit 5e27e9162f
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -47,7 +47,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
protected PrintStream out; 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) @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<String> fieldsToTake = null; public ArrayList<String> fieldsToTake = new ArrayList<String>();
@Argument(fullName="showFiltered", shortName="raw", doc="Include filtered records") @Argument(fullName="showFiltered", shortName="raw", doc="Include filtered records")
public boolean showFiltered = false; public boolean showFiltered = false;

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java
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@ -40,7 +40,7 @@ public class VariantToTableIntegrationTest extends WalkerTest {
"-R " + hg18Reference + "-R " + hg18Reference +
" -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" + " -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
" -T VariantsToTable" + " -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", " -L chr1 -o %s",
Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba")); Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba"));
executeTest("testComplexVariantsToTable", spec).getFirst(); executeTest("testComplexVariantsToTable", spec).getFirst();