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

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

tests
0

failures
0

ignored
11.726s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@104e0276, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.141s passed
compareToExpectedResults[10]([Ljava.io.File;@3046745c, 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) 0.224s passed
compareToExpectedResults[11]([Ljava.io.File;@5d281cc7, 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) 0.246s passed
compareToExpectedResults[12]([Ljava.io.File;@2ce61ec5, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.217s passed
compareToExpectedResults[13]([Ljava.io.File;@7100a5de, 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) 0.184s passed
compareToExpectedResults[14]([Ljava.io.File;@1d01f5f7, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.375s passed
compareToExpectedResults[1]([Ljava.io.File;@622bcb6d, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.145s passed
compareToExpectedResults[2]([Ljava.io.File;@75188878, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.125s passed
compareToExpectedResults[3]([Ljava.io.File;@5bdc96ef, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.110s passed
compareToExpectedResults[4]([Ljava.io.File;@614f8ab4, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.119s passed
compareToExpectedResults[5]([Ljava.io.File;@7e48c82, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.158s passed
compareToExpectedResults[6]([Ljava.io.File;@303673b2, 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) 0.185s passed
compareToExpectedResults[7]([Ljava.io.File;@74e0fce4, 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) 0.209s passed
compareToExpectedResults[8]([Ljava.io.File;@283594ba, 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) 0.184s passed
compareToExpectedResults[9]([Ljava.io.File;@133c50a4, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.195s passed
testAddToCombinedSomaticGvcf 4.462s passed
testCombineGvcfsWithMnps 0.103s passed
testCombineReblockedGVCFs 0.148s passed
testCombineSomaticGvcfs 0.550s passed
testDropSomaticFilteringAnnotations 0.404s passed
testNoDataInInterval 0.167s passed
testOneHasAltAndTwoHasNothing 0.132s passed
testOneHasAltAndTwoHasRefBlock 0.139s passed
testOneHasDeletionAndTwoHasRefBlock 0.112s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.110s passed
testStartChromosome 0.223s passed
testTetraploidRun 0.243s passed
testTwoSpansManyBlocksInOne 0.116s passed

Standard error

[June 12, 2025 at 9:01:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=702545920
[June 12, 2025 at 9:01:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=702545920
[June 12, 2025 at 9:01:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=702545920
[June 12, 2025 at 9:01:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=702545920
[June 12, 2025 at 9:01:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=702545920
[June 12, 2025 at 9:01:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 9:01:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 9:01:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000