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

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

tests
0

failures
0

ignored
10.481s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@28b8c06, 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;@7f1cf676, 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) 0.188s passed
compareToExpectedResults[11]([Ljava.io.File;@5df44c71, 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) 0.201s passed
compareToExpectedResults[12]([Ljava.io.File;@324c95e4, 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) 0.206s passed
compareToExpectedResults[13]([Ljava.io.File;@9ef96e9, 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) 0.191s passed
compareToExpectedResults[14]([Ljava.io.File;@22e40d25, 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) 0.770s passed
compareToExpectedResults[1]([Ljava.io.File;@700631e, 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) 0.081s passed
compareToExpectedResults[2]([Ljava.io.File;@5ed1f04f, 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) 0.081s passed
compareToExpectedResults[3]([Ljava.io.File;@77d9b3bd, 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) 0.083s passed
compareToExpectedResults[4]([Ljava.io.File;@a797e58, 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) 0.095s passed
compareToExpectedResults[5]([Ljava.io.File;@731e54b5, 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) 1.092s passed
compareToExpectedResults[6]([Ljava.io.File;@10ec00a0, 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) 0.131s passed
compareToExpectedResults[7]([Ljava.io.File;@773964ec, 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) 0.150s passed
compareToExpectedResults[8]([Ljava.io.File;@db7b52b, 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) 0.129s passed
compareToExpectedResults[9]([Ljava.io.File;@7782269b, 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) 0.133s passed
testAddToCombinedSomaticGvcf 4.468s passed
testCombineGvcfsWithMnps 0.073s passed
testCombineReblockedGVCFs 0.112s passed
testCombineSomaticGvcfs 0.829s passed
testDropSomaticFilteringAnnotations 0.467s passed
testNoDataInInterval 0.081s passed
testOneHasAltAndTwoHasNothing 0.083s passed
testOneHasAltAndTwoHasRefBlock 0.083s passed
testOneHasDeletionAndTwoHasRefBlock 0.093s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.081s passed
testStartChromosome 0.189s passed
testTetraploidRun 0.206s passed
testTwoSpansManyBlocksInOne 0.082s passed

Standard error

[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=654311424
[June 12, 2025 at 8:47:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[June 12, 2025 at 8:47:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=643825664
[June 12, 2025 at 8:47:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=643825664
[June 12, 2025 at 8:47:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=643825664
[June 12, 2025 at 8:47:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984
[June 12, 2025 at 8:47:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=979369984