From 905b6066b203eea2b4cb6672abf989901bbde64f Mon Sep 17 00:00:00 2001 From: Valentin Ruano-Rubio Date: Tue, 18 Mar 2014 21:40:14 -0400 Subject: [PATCH] Reduce runtime of very long integration test --- .../haplotypecaller/HaplotypeCallerIntegrationTest.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 8db4d5066..d4186f610 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -301,10 +301,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testLackSensitivityDueToBadHaplotypeSelectionFix() { - final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header ", + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16", b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e2e6647f7c96e91aeead7301017dc800")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("dbe5ef6ce1a9015ff4318691f5f45fda")); spec.disableShadowBCF(); executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec); } @@ -318,5 +318,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { spec.disableShadowBCF(); executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec); } - }