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

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

tests
0

failures
0

ignored
11.778s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@55983176, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.136s passed
compareToExpectedResults[10]([Ljava.io.File;@32765931, 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) 0.211s passed
compareToExpectedResults[11]([Ljava.io.File;@48b44489, 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) 0.269s passed
compareToExpectedResults[12]([Ljava.io.File;@30af66de, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.235s passed
compareToExpectedResults[13]([Ljava.io.File;@195ada56, 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) 0.207s passed
compareToExpectedResults[14]([Ljava.io.File;@6acadf19, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.007s passed
compareToExpectedResults[1]([Ljava.io.File;@12170b4b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.158s passed
compareToExpectedResults[2]([Ljava.io.File;@4fd78c46, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.118s passed
compareToExpectedResults[3]([Ljava.io.File;@3b6bd780, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.113s passed
compareToExpectedResults[4]([Ljava.io.File;@748b1da9, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf, [], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.120s passed
compareToExpectedResults[5]([Ljava.io.File;@4c7dad45, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 1.179s passed
compareToExpectedResults[6]([Ljava.io.File;@1e3d184c, 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) 0.192s passed
compareToExpectedResults[7]([Ljava.io.File;@1e2cccaa, 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) 0.199s passed
compareToExpectedResults[8]([Ljava.io.File;@6281b1e0, 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) 0.187s passed
compareToExpectedResults[9]([Ljava.io.File;@25b30325, src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf, [-A, ClippingRankSumTest], /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta) 0.159s passed
testAddToCombinedSomaticGvcf 4.376s passed
testCombineGvcfsWithMnps 0.106s passed
testCombineReblockedGVCFs 0.146s passed
testCombineSomaticGvcfs 0.910s passed
testDropSomaticFilteringAnnotations 0.563s passed
testNoDataInInterval 0.160s passed
testOneHasAltAndTwoHasNothing 0.113s passed
testOneHasAltAndTwoHasRefBlock 0.123s passed
testOneHasDeletionAndTwoHasRefBlock 0.109s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.106s passed
testStartChromosome 0.233s passed
testTetraploidRun 0.232s passed
testTwoSpansManyBlocksInOne 0.111s passed

Standard error

[May 27, 2025 at 2:06:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=799014912
[May 27, 2025 at 2:06:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=574619648
[May 27, 2025 at 2:06:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304
[May 27, 2025 at 2:06:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1314914304