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

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

tests
0

failures
0

ignored
10.608s

duration
100%

successful

Tests

Test Duration Result
assertThatExpectedOutputUpdateToggleIsDisabled 0s passed
compareToExpectedResults[0]([Ljava.io.File;@111b8a53, 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) 0.100s passed
compareToExpectedResults[10]([Ljava.io.File;@23077d0a, 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) 0.200s passed
compareToExpectedResults[11]([Ljava.io.File;@42658b0b, 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) 0.204s passed
compareToExpectedResults[12]([Ljava.io.File;@4bd0e258, 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) 0.208s passed
compareToExpectedResults[13]([Ljava.io.File;@47692f1d, 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) 0.226s passed
compareToExpectedResults[14]([Ljava.io.File;@2eb593f0, 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) 1.198s passed
compareToExpectedResults[1]([Ljava.io.File;@545062d1, 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;@7df5258e, 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) 0.077s passed
compareToExpectedResults[3]([Ljava.io.File;@6731ab7b, 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;@5cef098a, 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) 0.092s passed
compareToExpectedResults[5]([Ljava.io.File;@7038d993, 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) 0.879s passed
compareToExpectedResults[6]([Ljava.io.File;@710372e7, 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) 0.091s passed
compareToExpectedResults[7]([Ljava.io.File;@349dc9c, 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) 0.152s passed
compareToExpectedResults[8]([Ljava.io.File;@7d415757, 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) 0.126s passed
compareToExpectedResults[9]([Ljava.io.File;@eb21c7b, 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) 0.130s passed
testAddToCombinedSomaticGvcf 4.346s passed
testCombineGvcfsWithMnps 0.074s passed
testCombineReblockedGVCFs 0.108s passed
testCombineSomaticGvcfs 0.850s passed
testDropSomaticFilteringAnnotations 0.466s passed
testNoDataInInterval 0.080s passed
testOneHasAltAndTwoHasNothing 0.081s passed
testOneHasAltAndTwoHasRefBlock 0.083s passed
testOneHasDeletionAndTwoHasRefBlock 0.096s passed
testOneStartsBeforeTwoAndEndsAfterwards 0.082s passed
testStartChromosome 0.217s passed
testTetraploidRun 0.206s passed
testTwoSpansManyBlocksInOne 0.077s passed

Standard error

[May 27, 2025 at 3:47:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=679477248
[May 27, 2025 at 3:47:07 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=650117120
[May 27, 2025 at 3:47:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=650117120
[May 27, 2025 at 3:47:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=721420288
[May 27, 2025 at 3:47:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=721420288
[May 27, 2025 at 3:47:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944
[May 27, 2025 at 3:47:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=937426944