From 6e18ecfc9a44cb0e32df09dab905889536ab1756 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 13 Mar 2012 12:43:40 -0400 Subject: [PATCH] Adding integration test to cover errors from my previous commit (GENOTYPE_GIVEN_ALLELE bugs reported by Sara Pulit and Chris Hartl) --- .../genotyper/UnifiedGenotyperIntegrationTest.java | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index cfb0d11a1..65dc594ff 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -313,6 +313,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Phase1 indels with complicated records", spec4); } + @Test + public void testWithIndelAllelesPassedIn5() { + final String vcf = "small.indel.test.vcf"; + WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( + baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + vcf + " -I " + validationDataLocation + + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1, + Arrays.asList("7d069596597aee5e0d562964036141eb")); + executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec4); + } + @Test public void testSnpEffAnnotationRequestedWithoutRodBinding() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(