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

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

tests
0

failures
0

ignored
10.134s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@30e8d78b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.128s passed
compareToExpectedResults[10]([Ljava.io.File;@430f32a3, 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) 0.179s passed
compareToExpectedResults[11]([Ljava.io.File;@2d4e3001, 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) 0.171s passed
compareToExpectedResults[12]([Ljava.io.File;@5c03f43d, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.171s passed
compareToExpectedResults[13]([Ljava.io.File;@7be49850, 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) 0.168s passed
compareToExpectedResults[14]([Ljava.io.File;@15ac83ae, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.929s passed
compareToExpectedResults[1]([Ljava.io.File;@3c8a22c6, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.107s passed
compareToExpectedResults[2]([Ljava.io.File;@572ce093, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.109s passed
compareToExpectedResults[3]([Ljava.io.File;@429e83a6, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.104s passed
compareToExpectedResults[4]([Ljava.io.File;@190acc61, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.117s passed
compareToExpectedResults[5]([Ljava.io.File;@5df4df68, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.762s passed
compareToExpectedResults[6]([Ljava.io.File;@638ccbe2, 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) 0.126s passed
compareToExpectedResults[7]([Ljava.io.File;@11295499, 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) 0.129s passed
compareToExpectedResults[8]([Ljava.io.File;@33f45343, 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) 0.130s passed
compareToExpectedResults[9]([Ljava.io.File;@5b0e9b75, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.129s passed
testAddToCombinedSomaticGvcf 4.165s passed
testCombineGvcfsWithMnps 0.099s passed
testCombineReblockedGVCFs 0.142s passed
testCombineSomaticGvcfs 0.632s passed
testDropSomaticFilteringAnnotations 0.389s passed
testNoDataInInterval 0.105s passed
testOneHasAltAndTwoHasNothing 0.108s passed
testOneHasAltAndTwoHasRefBlock 0.126s passed
testOneHasDeletionAndTwoHasRefBlock 0.114s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.106s passed
testStartChromosome 0.212s passed
testTetraploidRun 0.310s passed
testTwoSpansManyBlocksInOne 0.167s passed

Standard error

[May 19, 2025 at 7:15:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=713031680
[May 19, 2025 at 7:15:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344
[May 19, 2025 at 7:15:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=832569344