diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java index 93ea16c2ff5..b0bce5d84a9 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java @@ -6,6 +6,7 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFUtils; import org.apache.commons.collections4.SetUtils; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.CommandLineProgramTest; @@ -1088,7 +1089,18 @@ public void testExposureOfSmithWatermanParametersIsConsistentWithPastResults(fin }; runCommandLine(args); - IntegrationTestSpec.assertEqualTextFiles(output, expected); + + // This used to be an exact text match, which cause hours of aggravation when the test passed locally and + // failed on the cloud. + final double[] outputTlods = VariantContextTestUtils.streamVcf(output) + .flatMap(vc -> vc.getAttributeAsDoubleList(GATKVCFConstants.TUMOR_LOG_10_ODDS_KEY, 0).stream()) + .mapToDouble(x -> x).toArray(); + + final double[] expectedTlods = VariantContextTestUtils.streamVcf(expected) + .flatMap(vc -> vc.getAttributeAsDoubleList(GATKVCFConstants.TUMOR_LOG_10_ODDS_KEY, 0).stream()) + .mapToDouble(x -> x).toArray(); + + Assert.assertEquals(outputTlods, expectedTlods); } @SafeVarargs