Class org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers > CombineGVCFsIntegrationTest
29

tests
0

failures
0

ignored
13.109s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@4142cba1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.157s passed
compareToExpectedResults[10]([Ljava.io.File;@6d2f0ce1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf, [-G, Standard, -G, AS_Standard], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.333s passed
compareToExpectedResults[11]([Ljava.io.File;@2056abc3, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf, [-G, Standard, -G, AS_Standard], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.235s passed
compareToExpectedResults[12]([Ljava.io.File;@3ecbc06c, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.260s passed
compareToExpectedResults[13]([Ljava.io.File;@2755b725, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf, [--break-bands-at-multiples-of, 2000000], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.218s passed
compareToExpectedResults[14]([Ljava.io.File;@8a5513a, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.528s passed
compareToExpectedResults[1]([Ljava.io.File;@57cee7df, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.187s passed
compareToExpectedResults[2]([Ljava.io.File;@17565fea, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.154s passed
compareToExpectedResults[3]([Ljava.io.File;@55c3544, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.114s passed
compareToExpectedResults[4]([Ljava.io.File;@20e0aab1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.133s passed
compareToExpectedResults[5]([Ljava.io.File;@3b499420, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.246s passed
compareToExpectedResults[6]([Ljava.io.File;@17bece64, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf, [ -L , 20:69485-69791], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.205s passed
compareToExpectedResults[7]([Ljava.io.File;@73694051, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf, [ -L , 20:69485-69791, --convert-to-base-pair-resolution], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.161s passed
compareToExpectedResults[8]([Ljava.io.File;@22ce9a87, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf, [ -L , 20:69485-69791, --break-bands-at-multiples-of, 5, -A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.150s passed
compareToExpectedResults[9]([Ljava.io.File;@5e4043c5, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.154s passed
testAddToCombinedSomaticGvcf 4.879s passed
testCombineGvcfsWithMnps 0.144s passed
testCombineReblockedGVCFs 0.179s passed
testCombineSomaticGvcfs 0.890s passed
testDropSomaticFilteringAnnotations 0.406s passed
testNoDataInInterval 0.134s passed
testOneHasAltAndTwoHasNothing 0.158s passed
testOneHasAltAndTwoHasRefBlock 0.134s passed
testOneHasDeletionAndTwoHasRefBlock 0.136s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.148s passed
testStartChromosome 0.246s passed
testTetraploidRun 0.279s passed
testTwoSpansManyBlocksInOne 0.141s passed

Standard error

[May 27, 2025 at 6:33:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=746586112
[May 27, 2025 at 6:33:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=559939584
[May 27, 2025 at 6:33:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=979369984
[May 27, 2025 at 6:33:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=979369984
[May 27, 2025 at 6:33:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160
[May 27, 2025 at 6:33:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1478492160