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

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

tests
0

failures
0

ignored
10.899s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@2ceda7ae, 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;@4891f5ba, 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) 0.216s passed
compareToExpectedResults[11]([Ljava.io.File;@650d126b, 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) 0.202s passed
compareToExpectedResults[12]([Ljava.io.File;@5507cf03, 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) 0.178s passed
compareToExpectedResults[13]([Ljava.io.File;@263d59e6, 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) 0.216s passed
compareToExpectedResults[14]([Ljava.io.File;@74600f29, 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) 1.305s passed
compareToExpectedResults[1]([Ljava.io.File;@66c6a7ea, 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) 0.098s passed
compareToExpectedResults[2]([Ljava.io.File;@51f10664, 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;@5257a2fe, 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) 0.079s passed
compareToExpectedResults[4]([Ljava.io.File;@4123731a, 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) 0.090s passed
compareToExpectedResults[5]([Ljava.io.File;@57c6f3e2, 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) 0.991s passed
compareToExpectedResults[6]([Ljava.io.File;@6129c33c, 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) 0.097s passed
compareToExpectedResults[7]([Ljava.io.File;@142a0e34, 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) 0.106s passed
compareToExpectedResults[8]([Ljava.io.File;@7d2e29e6, 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) 0.096s passed
compareToExpectedResults[9]([Ljava.io.File;@6f0d552, 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) 0.104s passed
testAddToCombinedSomaticGvcf 4.384s passed
testCombineGvcfsWithMnps 0.073s passed
testCombineReblockedGVCFs 0.113s passed
testCombineSomaticGvcfs 0.902s passed
testDropSomaticFilteringAnnotations 0.489s passed
testNoDataInInterval 0.080s passed
testOneHasAltAndTwoHasNothing 0.078s passed
testOneHasAltAndTwoHasRefBlock 0.100s passed
testOneHasDeletionAndTwoHasRefBlock 0.091s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.087s passed
testStartChromosome 0.223s passed
testTetraploidRun 0.237s passed
testTwoSpansManyBlocksInOne 0.080s passed

Standard error

[May 27, 2025 at 1:51:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=643825664
[May 27, 2025 at 1:51:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=637534208
[May 27, 2025 at 1:51:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=637534208
[May 27, 2025 at 1:51:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=637534208
[May 27, 2025 at 1:51:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=637534208
[May 27, 2025 at 1:51:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:51:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:51:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:51:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288
[May 27, 2025 at 1:51:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2032140288