From 0b181be61fb06ead1fbee278a218f421232d0524 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 7 Nov 2011 15:25:16 -0500 Subject: [PATCH] Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this. --- .../gatk/walkers/variantutils/SelectVariants.java | 6 +++--- .../variantutils/SelectVariantsIntegrationTest.java | 13 +++++++++++++ 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 2e17d68d8..609593acc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -556,9 +556,9 @@ public class SelectVariants extends RodWalker { if (vc == null) return false; - // if we're not looking at specific samples then the absense of a compVC means discordance - if (NO_SAMPLES_SPECIFIED && (compVCs == null || compVCs.isEmpty())) - return true; + // if we're not looking at specific samples then the absence of a compVC means discordance + if (NO_SAMPLES_SPECIFIED) + return (compVCs == null || compVCs.isEmpty()); // check if we find it in the variant rod Map genotypes = vc.getGenotypes(samples); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index e4ded491b..6e994be3a 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -64,6 +64,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest { executeTest("testDiscordance--" + testFile, spec); } + @Test + public void testDiscordanceNoSampleSpecified() { + String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER", + 1, + Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5") + ); + + executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec); + } + @Test public void testConcordance() { String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";