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

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

tests
0

failures
0

ignored
10.202s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@638ccbe2, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.131s passed
compareToExpectedResults[10]([Ljava.io.File;@551aeb3f, 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) 0.196s passed
compareToExpectedResults[11]([Ljava.io.File;@534ce92d, 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) 0.178s passed
compareToExpectedResults[12]([Ljava.io.File;@566fde67, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.167s passed
compareToExpectedResults[13]([Ljava.io.File;@18f723f2, 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) 0.170s passed
compareToExpectedResults[14]([Ljava.io.File;@25e5502, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.972s passed
compareToExpectedResults[1]([Ljava.io.File;@16bf597c, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.113s passed
compareToExpectedResults[2]([Ljava.io.File;@3840fdb9, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.106s passed
compareToExpectedResults[3]([Ljava.io.File;@508b42c9, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.103s passed
compareToExpectedResults[4]([Ljava.io.File;@7c32e788, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.118s passed
compareToExpectedResults[5]([Ljava.io.File;@33819c84, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.772s passed
compareToExpectedResults[6]([Ljava.io.File;@2874a318, 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) 0.122s passed
compareToExpectedResults[7]([Ljava.io.File;@4f85ff4c, 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) 0.140s passed
compareToExpectedResults[8]([Ljava.io.File;@43a44eb6, 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) 0.122s passed
compareToExpectedResults[9]([Ljava.io.File;@23c78c16, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.124s passed
testAddToCombinedSomaticGvcf 4.161s passed
testCombineGvcfsWithMnps 0.111s passed
testCombineReblockedGVCFs 0.140s passed
testCombineSomaticGvcfs 0.609s passed
testDropSomaticFilteringAnnotations 0.398s passed
testNoDataInInterval 0.112s passed
testOneHasAltAndTwoHasNothing 0.111s passed
testOneHasAltAndTwoHasRefBlock 0.109s passed
testOneHasDeletionAndTwoHasRefBlock 0.108s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.107s passed
testStartChromosome 0.216s passed
testTetraploidRun 0.319s passed
testTwoSpansManyBlocksInOne 0.167s passed

Standard error

[May 27, 2025 at 3:13:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824
[May 27, 2025 at 3:13:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=811597824