From ba2e7be05b7631f82115ba6017a2e689a1042706 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Tue, 7 Jun 2016 14:38:12 -0400 Subject: [PATCH] Add integration test using -maxNumPLValues for GenotypeGVCFs --- .../GenotypeGVCFsIntegrationTest.java | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index b93f5f4a9..5c27031a0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -122,7 +122,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad")); - executeTest("combineSingleSamplePipelineGVCF", spec); + executeTest("testTetraploidRun", spec); } @Test(enabled= true) @@ -134,7 +134,20 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, Arrays.asList("b1d93f4cd93093c208be2c9842f38d12")); - executeTest("combineSingleSamplePipelineGVCF", spec); + executeTest("testMixedPloidyRun", spec); + } + + @Test(enabled= true) + public void testMixedPloidyMaxNumPLValuesRun() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -V:sample1 " + privateTestDir + "haploid-gvcf-1.vcf" + + " -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" + + " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + + " -L " + privateTestDir + "tetraploid-gvcfs.intervals" + + " -maxNumPLValues 3", b37KGReference), + 1, + Arrays.asList("c0dcf62fb116c4c0baabe432eceea52c")); + executeTest("testMixedPloidyMaxNumPLValuesRun", spec); } @Test(enabled = true)