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Reduce runtime of very long integration test

This commit is contained in:
Valentin Ruano-Rubio 2014-03-18 21:40:14 -04:00
parent 14eb0a8a30
commit 905b6066b2
1 changed files with 2 additions and 3 deletions
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5
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -301,10 +301,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testLackSensitivityDueToBadHaplotypeSelectionFix() { 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", b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list",
HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); 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(); spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec); executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
} }
@ -318,5 +318,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec); executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec);
} }
} }