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

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

tests
0

failures
0

ignored
9.867s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@422a2376, 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) 0.103s passed
compareToExpectedResults[10]([Ljava.io.File;@5c91b4d3, 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) 0.157s passed
compareToExpectedResults[11]([Ljava.io.File;@7ae0a1a1, 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) 0.146s passed
compareToExpectedResults[12]([Ljava.io.File;@53207f44, 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) 0.185s passed
compareToExpectedResults[13]([Ljava.io.File;@50697f47, 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) 0.170s passed
compareToExpectedResults[14]([Ljava.io.File;@160562de, 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) 0.881s passed
compareToExpectedResults[1]([Ljava.io.File;@7e359877, 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) 0.080s passed
compareToExpectedResults[2]([Ljava.io.File;@3cb4ed66, 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) 0.072s passed
compareToExpectedResults[3]([Ljava.io.File;@3b57b815, 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) 0.069s passed
compareToExpectedResults[4]([Ljava.io.File;@e315a71, 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) 0.087s passed
compareToExpectedResults[5]([Ljava.io.File;@7e86261d, 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) 0.738s passed
compareToExpectedResults[6]([Ljava.io.File;@41c3a557, 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) 0.110s passed
compareToExpectedResults[7]([Ljava.io.File;@1c401e05, 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) 0.113s passed
compareToExpectedResults[8]([Ljava.io.File;@7f220ef9, 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) 0.091s passed
compareToExpectedResults[9]([Ljava.io.File;@2847fff, 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) 0.090s passed
testAddToCombinedSomaticGvcf 4.590s passed
testCombineGvcfsWithMnps 0.073s passed
testCombineReblockedGVCFs 0.120s passed
testCombineSomaticGvcfs 0.659s passed
testDropSomaticFilteringAnnotations 0.359s passed
testNoDataInInterval 0.081s passed
testOneHasAltAndTwoHasNothing 0.077s passed
testOneHasAltAndTwoHasRefBlock 0.077s passed
testOneHasDeletionAndTwoHasRefBlock 0.076s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.081s passed
testStartChromosome 0.186s passed
testTetraploidRun 0.309s passed
testTwoSpansManyBlocksInOne 0.087s passed

Standard error

[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=778043392
[May 27, 2025 at 2:59:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=685768704
[May 27, 2025 at 2:59:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[May 27, 2025 at 2:59:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[May 27, 2025 at 2:59:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=685768704
[May 27, 2025 at 2:59:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[May 27, 2025 at 2:59:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[May 27, 2025 at 2:59:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[May 27, 2025 at 2:59:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=887095296
[May 27, 2025 at 2:59:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=790626304