From 6a431da554634b164635b299e2ef472a35fd0739 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 13 Jul 2011 14:40:01 -0400 Subject: [PATCH] Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools. --- .../walkers/variantutils/VariantsToVCF.java | 4 +-- .../utils/codecs/vcf/VCFIntegrationTest.java | 28 +++++++++++++++++++ 2 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 7eb49da34..79134b553 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker { // setup the header fields Set hInfo = new HashSet(); hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); - hInfo.add(new VCFHeaderLine("source", "VariantsToVCF")); - hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName())); + //hInfo.add(new VCFHeaderLine("source", "VariantsToVCF")); + //hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName())); allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY); for ( VCFHeaderLine field : hInfo ) { diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java new file mode 100644 index 000000000..32ff25c7b --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -0,0 +1,28 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.WalkerTest; +import org.testng.annotations.Test; + +import java.io.File; +import java.util.Arrays; +import java.util.List; + +public class VCFIntegrationTest extends WalkerTest { + + @Test + public void testReadingAndWritingWitHNoChanges() { + + String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447"; + String testVCF = validationDataLocation + "vcf4.1.example.vcf"; + + String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + + String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF)); + List result = executeTest("Test Variant Annotator with no changes", spec1).getFirst(); + + String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath(); + WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF)); + executeTest("Test Variants To VCF from new output", spec2); + } +}