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

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

tests
0

failures
0

ignored
10.789s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0.001s passed
compareToExpectedResults[0]([Ljava.io.File;@4fc4266, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.101s passed
compareToExpectedResults[10]([Ljava.io.File;@777b8029, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf, [-G, Standard, -G, AS_Standard], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.156s passed
compareToExpectedResults[11]([Ljava.io.File;@155f7bb3, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf, [-G, Standard, -G, AS_Standard], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.148s passed
compareToExpectedResults[12]([Ljava.io.File;@3908c65d, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.180s passed
compareToExpectedResults[13]([Ljava.io.File;@545ece21, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf, [--break-bands-at-multiples-of, 2000000], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.178s passed
compareToExpectedResults[14]([Ljava.io.File;@66439328, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.854s passed
compareToExpectedResults[1]([Ljava.io.File;@5979fe38, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.095s passed
compareToExpectedResults[2]([Ljava.io.File;@1605c65b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.090s passed
compareToExpectedResults[3]([Ljava.io.File;@25009c0b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.109s passed
compareToExpectedResults[4]([Ljava.io.File;@2d138e5f, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.104s passed
compareToExpectedResults[5]([Ljava.io.File;@1116137c, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.158s passed
compareToExpectedResults[6]([Ljava.io.File;@2a1cba61, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf, [ -L , 20:69485-69791], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.132s passed
compareToExpectedResults[7]([Ljava.io.File;@26338ad, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf, [ -L , 20:69485-69791, --convert-to-base-pair-resolution], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.157s passed
compareToExpectedResults[8]([Ljava.io.File;@43cf86c5, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf, [ -L , 20:69485-69791, --break-bands-at-multiples-of, 5, -A, ClippingRankSumTest], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.132s passed
compareToExpectedResults[9]([Ljava.io.File;@5e3e21f7, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.121s passed
testAddToCombinedSomaticGvcf 4.586s passed
testCombineGvcfsWithMnps 0.076s passed
testCombineReblockedGVCFs 0.137s passed
testCombineSomaticGvcfs 0.857s passed
testDropSomaticFilteringAnnotations 0.516s passed
testNoDataInInterval 0.083s passed
testOneHasAltAndTwoHasNothing 0.084s passed
testOneHasAltAndTwoHasRefBlock 0.082s passed
testOneHasDeletionAndTwoHasRefBlock 0.082s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.083s passed
testStartChromosome 0.191s passed
testTetraploidRun 0.215s passed
testTwoSpansManyBlocksInOne 0.081s passed

Standard error

[June 2, 2025 at 2:23:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=710934528
[June 2, 2025 at 2:23:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=692060160
[June 2, 2025 at 2:23:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=685768704
[June 2, 2025 at 2:23:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[June 2, 2025 at 2:23:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[June 2, 2025 at 2:23:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[June 2, 2025 at 2:23:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1042284544
[June 2, 2025 at 2:23:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1042284544
[June 2, 2025 at 2:23:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1042284544
[June 2, 2025 at 2:23:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480
[June 2, 2025 at 2:23:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1027604480