Test Summary

5431

tests
2

failures
0

ignored
19m8.43s

duration
99%

successful

Packages

Package Tests Failures Ignored Duration Success rate
picard 375 0 0 9.624s 100%
picard.analysis 317 0 0 40.204s 100%
picard.analysis.artifacts 50 0 0 0.346s 100%
picard.analysis.directed 19 0 0 18.309s 100%
picard.analysis.replicates 13 0 0 0.059s 100%
picard.annotation 17 0 0 1.538s 100%
picard.arrays 77 0 0 0.422s 100%
picard.arrays.illumina 94 0 0 0.117s 100%
picard.cmdline 14 0 0 0.169s 100%
picard.fastq 3 0 0 0.012s 100%
picard.fingerprint 425 0 0 18.843s 100%
picard.flow 20 0 0 0.028s 100%
picard.illumina 227 1 0 3m9.99s 99%
picard.illumina.parser 177 0 0 0.695s 100%
picard.illumina.parser.fakers 2 0 0 0.004s 100%
picard.illumina.parser.readers 62 0 0 0.024s 100%
picard.metrics 71 0 0 0.544s 100%
picard.nio 1 0 0 0.609s 100%
picard.pedigree 20 0 0 0.001s 100%
picard.reference 2 0 0 0.010s 100%
picard.sam 753 0 0 28.492s 100%
picard.sam.SamErrorMetric 536 0 0 0.520s 100%
picard.sam.markduplicates 1098 0 0 13m44.68s 100%
picard.sam.markduplicates.util 9 0 0 0.004s 100%
picard.sam.util 61 0 0 0.196s 100%
picard.util 582 1 0 5.682s 99%
picard.util.help 1 0 0 1.830s 100%
picard.vcf 384 0 0 4.175s 100%
picard.vcf.MendelianViolations 1 0 0 0.037s 100%
picard.vcf.filter 12 0 0 0.105s 100%
picard.vcf.processor 8 0 0 1.157s 100%

Classes

Class Tests Failures Ignored Duration Success rate
picard.IntelInflaterDeflaterLoadTest 4 0 0 0.022s 100%
picard.TestDataProviders 371 0 0 9.602s 100%
picard.analysis.AbstractWgsMetricsCollectorTest 5 0 0 0.002s 100%
picard.analysis.AdapterUtilityTest 82 0 0 0.014s 100%
picard.analysis.AlignmentSummaryMetricsCollectorTest 20 0 0 0.007s 100%
picard.analysis.CollectAlignmentSummaryMetricsTest 15 0 0 2.137s 100%
picard.analysis.CollectGcBiasMetricsTest 4 0 0 2.403s 100%
picard.analysis.CollectInsertSizeMetricsTest 5 0 0 1.996s 100%
picard.analysis.CollectJumpingLibraryMetricsTest 1 0 0 0.006s 100%
picard.analysis.CollectMultipleMetricsTest 13 0 0 5.125s 100%
picard.analysis.CollectOxoGMetricsTest 9 0 0 0.026s 100%
picard.analysis.CollectQualityYieldMetricsFlowTest 1 0 0 0.070s 100%
picard.analysis.CollectQualityYieldMetricsSNVQTest 1 0 0 0.536s 100%
picard.analysis.CollectQualityYieldMetricsTest 1 0 0 0.011s 100%
picard.analysis.CollectRnaSeqMetricsTest 9 0 0 0.113s 100%
picard.analysis.CollectUmiPrevalenceMetricsTest 1 0 0 0.015s 100%
picard.analysis.CollectWgsMetricsTest 17 0 0 8.869s 100%
picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest 4 0 0 8.773s 100%
picard.analysis.CompareMetricsTest 41 0 0 1.213s 100%
picard.analysis.CounterManagerTest 9 0 0 0.001s 100%
picard.analysis.FastWgsMetricsCollectorTest 12 0 0 0.007s 100%
picard.analysis.MergeableMetricBaseTest 13 0 0 0.005s 100%
picard.analysis.MultiLevelCollectorTest 6 0 0 0.004s 100%
picard.analysis.TheoreticalSensitivityTest 36 0 0 8.795s 100%
picard.analysis.WgsMetricsProcessorImplTest 3 0 0 0.004s 100%
picard.analysis.WgsMetricsTest 9 0 0 0.072s 100%
picard.analysis.artifacts.CollectSequencingArtifactMetricsTest 8 0 0 0.312s 100%
picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest 2 0 0 0.030s 100%
picard.analysis.artifacts.TransitionTest 40 0 0 0.004s 100%
picard.analysis.directed.CollectHsMetricsTest 14 0 0 14.566s 100%
picard.analysis.directed.CollectTargetedMetricsTest 5 0 0 3.743s 100%
picard.analysis.replicates.CollectIndependentReplicatesMetricTest 13 0 0 0.059s 100%
picard.annotation.SortGffTest 17 0 0 1.538s 100%
picard.arrays.CollectArraysVariantCallingMetricsTest 67 0 0 0.354s 100%
picard.arrays.CreateBafRegressMetricsFileTest 2 0 0 0.005s 100%
picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest 2 0 0 0.004s 100%
picard.arrays.GtcToVcfTest 5 0 0 0.021s 100%
picard.arrays.MergePedIntoVcfTest 1 0 0 0.038s 100%
picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreatorTest 46 0 0 0.003s 100%
picard.arrays.illumina.Build37ExtendedIlluminaManifestTest 5 0 0 0.012s 100%
picard.arrays.illumina.CombineGenotypingArrayVcfsTest 2 0 0 0.037s 100%
picard.arrays.illumina.CreateExtendedIlluminaManifestTest 2 0 0 0.013s 100%
picard.arrays.illumina.IlluminaAdpcFileWriterTest 1 0 0 0.001s 100%
picard.arrays.illumina.IlluminaManifestTest 2 0 0 0.003s 100%
picard.arrays.illumina.InfiniumDataFileTest 23 0 0 0s 100%
picard.arrays.illumina.InfiniumNormalizationManifestTest 2 0 0 0.001s 100%
picard.arrays.illumina.InfiniumVcfFieldsTest 5 0 0 0.007s 100%
picard.arrays.illumina.VcfToAdpcTest 6 0 0 0.040s 100%
picard.cmdline.CommandLineProgramStartupErrorLogTest 2 0 0 0.003s 100%
picard.cmdline.PicardCommandLineTest 12 0 0 0.166s 100%
picard.fastq.BamToBfqTest 2 0 0 0.009s 100%
picard.fastq.Casava18ReadNameEncoderTest 1 0 0 0.003s 100%
picard.fingerprint.CalculateFingerprintMetricsTest 5 0 0 0.406s 100%
picard.fingerprint.CheckFingerprintTest 28 0 0 0.476s 100%
picard.fingerprint.ClusterCrosscheckMetricsTest 1 0 0 0.142s 100%
picard.fingerprint.ConvertHaplotypeDatabaseToVcfTest 1 0 0 0.024s 100%
picard.fingerprint.CrosscheckFingerprintsTest 216 0 0 14.325s 100%
picard.fingerprint.CrosscheckReadGroupFingerprintsTest 32 0 0 2.149s 100%
picard.fingerprint.FingerprintCheckerTest 98 0 0 1.303s 100%
picard.fingerprint.HaplotypeMapTest 5 0 0 0.008s 100%
picard.fingerprint.HaplotypeProbabilitiesTest 27 0 0 0.004s 100%
picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest 11 0 0 0s 100%
picard.fingerprint.LiftOverHaplotypeMapTest 1 0 0 0.006s 100%
picard.flow.FlowBasedKeyCodecUnitTest 19 0 0 0.001s 100%
picard.flow.FlowReadGroupInfoUnitTest 1 0 0 0.027s 100%
picard.illumina.CheckIlluminaDirectoryTest 14 0 0 0.894s 100%
picard.illumina.CollectIlluminaBasecallingMetricsTest 4 0 0 0.930s 100%
picard.illumina.DistanceMetricTest 33 0 0 0.001s 100%
picard.illumina.ExtractIlluminaBarcodesTest 17 1 0 1.189s 94%
picard.illumina.IlluminaBasecallsToFastqTest 13 0 0 48.362s 100%
picard.illumina.IlluminaBasecallsToSamAdapterClippingTest 12 0 0 6.945s 100%
picard.illumina.IlluminaBasecallsToSamTest 29 0 0 2m11.21s 100%
picard.illumina.IlluminaLaneMetricsCollectorTest 12 0 0 0.461s 100%
picard.illumina.ReadStructureTest 93 0 0 0.004s 100%
picard.illumina.parser.BclParserTest 71 0 0 0.522s 100%
picard.illumina.parser.FilterParserTest 17 0 0 0.005s 100%
picard.illumina.parser.IlluminaDataProviderTest 13 0 0 0.040s 100%
picard.illumina.parser.IlluminaFileUtilTest 30 0 0 0.120s 100%
picard.illumina.parser.MultiTileBclFileFakerTest 1 0 0 0.001s 100%
picard.illumina.parser.PerTileParserTest 17 0 0 0s 100%
picard.illumina.parser.PerTilePerCycleParserTest 10 0 0 0.003s 100%
picard.illumina.parser.PosParserTest 9 0 0 0.002s 100%
picard.illumina.parser.TileMetricsUtilTest 9 0 0 0.002s 100%
picard.illumina.parser.fakers.BclFileFakerTest 2 0 0 0.004s 100%
picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest 15 0 0 0.001s 100%
picard.illumina.parser.readers.BclReaderTest 8 0 0 0.006s 100%
picard.illumina.parser.readers.CbclReaderTest 3 0 0 0.002s 100%
picard.illumina.parser.readers.ClocsFileReaderTest 6 0 0 0.010s 100%
picard.illumina.parser.readers.FilterFileReaderTest 10 0 0 0.003s 100%
picard.illumina.parser.readers.LocsFileReaderTest 6 0 0 0.001s 100%
picard.illumina.parser.readers.MMapBackedIteratorFactoryTest 8 0 0 0.001s 100%
picard.illumina.parser.readers.PosFileReaderTest 6 0 0 0s 100%
picard.metrics.CollectRrbsMetricsTest 1 0 0 0.540s 100%
picard.metrics.MetricBaseTest 70 0 0 0.004s 100%
picard.nio.HttpNioIntegrationTest 1 0 0 0.609s 100%
picard.pedigree.PedFileTest 4 0 0 0s 100%
picard.pedigree.SexTest 16 0 0 0.001s 100%
picard.reference.NonNFastaSizeTest 2 0 0 0.010s 100%
picard.sam.AbstractAlignmentMergerTest 184 0 0 0.160s 100%
picard.sam.AddCommentsToBamTest 3 0 0 0.035s 100%
picard.sam.AddOATagTest 4 0 0 0.023s 100%
picard.sam.BuildBamIndexTest 3 0 0 0.041s 100%
picard.sam.CleanSamTest 12 0 0 0.131s 100%
picard.sam.CompareSAMsTest 58 0 0 0.665s 100%
picard.sam.CramCompatibilityTest 48 0 0 4.898s 100%
picard.sam.CreateSequenceDictionaryTest 7 0 0 0.103s 100%
picard.sam.DownsampleSamTest 84 0 0 12.236s 100%
picard.sam.DuplicationMetricsTest 7 0 0 0.003s 100%
picard.sam.FastqToSamTest 63 0 0 1.628s 100%
picard.sam.FilterSamReadsTest 48 0 0 0.807s 100%
picard.sam.FixMateInformationTest 2 0 0 0.004s 100%
picard.sam.GatherBamFilesTest 2 0 0 0.025s 100%
picard.sam.MergeBamAlignmentTest 76 0 0 0.921s 100%
picard.sam.MergeSamFilesTest 1 0 0 0.016s 100%
picard.sam.PipedDataTest 3 0 0 3.686s 100%
picard.sam.PositionBasedDownsampleSamTest 20 0 0 1.622s 100%
picard.sam.ReorderSamTest 24 0 0 0.598s 100%
picard.sam.RevertSamTest 32 0 0 0.321s 100%
picard.sam.SamFormatConverterTest 6 0 0 0.062s 100%
picard.sam.SamToFastqTest 24 0 0 0.180s 100%
picard.sam.SamToFastqWithTagsTest 13 0 0 0.084s 100%
picard.sam.SetNmMdAndUqTagsTest 6 0 0 0.033s 100%
picard.sam.SortSamTest 1 0 0 0.013s 100%
picard.sam.SplitSamByLibraryTest 3 0 0 0.003s 100%
picard.sam.SplitSamByNumberOfReadsTest 8 0 0 0.124s 100%
picard.sam.ValidateSamFileTest 9 0 0 0.065s 100%
picard.sam.ViewSamTest 2 0 0 0.005s 100%
picard.sam.SamErrorMetric.BaseErrorAggregationTest 3 0 0 0.001s 100%
picard.sam.SamErrorMetric.BaseErrorCalculationTest 3 0 0 0.319s 100%
picard.sam.SamErrorMetric.CollectSamErrorMetricsTest 186 0 0 0.194s 100%
picard.sam.SamErrorMetric.ReadBaseStratificationTest 344 0 0 0.006s 100%
picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest 8 0 0 0.063s 100%
picard.sam.markduplicates.AsIsMarkDuplicatesTest 8 0 0 7.718s 100%
picard.sam.markduplicates.CheckDuplicateMarkingTest 10 0 0 0.014s 100%
picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest 8 0 0 0.003s 100%
picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest 7 0 0 0s 100%
picard.sam.markduplicates.EstimateLibraryComplexityTest 10 0 0 1.046s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest 107 0 0 1m50.87s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest 107 0 0 1m48.44s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest 107 0 0 1m49.56s 100%
picard.sam.markduplicates.MarkDuplicatesForFlowHelperTest 25 0 0 16.412s 100%
picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest 98 0 0 1m41.79s 100%
picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest 98 0 0 1m56.54s 100%
picard.sam.markduplicates.MarkDuplicatesTest 107 0 0 1m51.36s 100%
picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted 107 0 0 1m51.18s 100%
picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest 86 0 0 7.761s 100%
picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest 80 0 0 10.673s 100%
picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest 102 0 0 11.251s 100%
picard.sam.markduplicates.UmiUtilTest 23 0 0 0.001s 100%
picard.sam.markduplicates.util.OpticalDuplicateFinderTest 9 0 0 0.004s 100%
picard.sam.util.PrimaryAlignmentKeyTest 12 0 0 0.001s 100%
picard.sam.util.ReadNameParserTests 19 0 0 0.006s 100%
picard.sam.util.SamComparisonTest 30 0 0 0.189s 100%
picard.util.AccumulateQualityYieldMetricsTest 1 0 0 0.013s 100%
picard.util.AlleleSubsettingUtilsTest 17 0 0 0.005s 100%
picard.util.BedToIntervalListTest 24 0 0 0.063s 100%
picard.util.ClippingUtilityTest 50 0 0 0.054s 100%
picard.util.DelimitedTextFileWithHeaderIteratorTest 2 0 0 0.001s 100%
picard.util.EditDistanceQueriesTest 37 0 0 0.001s 100%
picard.util.FifoBufferTest 1 0 0 2.411s 100%
picard.util.GraphUtilsTest 3 0 0 0.002s 100%
picard.util.IlluminaUtilTest 5 0 0 0.221s 100%
picard.util.IntervalListScattererTest 20 0 0 0.050s 100%
picard.util.IntervalListToBedTest 3 0 0 0.018s 100%
picard.util.IntervalListToolsTest 81 0 0 2.005s 100%
picard.util.LiftoverUtilsTest 17 0 0 0.001s 100%
picard.util.LiftoverVcfTest 179 1 0 0.351s 99%
picard.util.MathUtilTest 60 0 0 0.001s 100%
picard.util.MergingIteratorTest 3 0 0 0.001s 100%
picard.util.MiscTest 1 0 0 0s 100%
picard.util.QuerySortedReadPairIteratorUtilTest 4 0 0 0.001s 100%
picard.util.RExecutorTest 3 0 0 0.468s 100%
picard.util.ScatterIntervalsByNsTest 12 0 0 0.002s 100%
picard.util.SequenceDictionaryUtilsTest 5 0 0 0.005s 100%
picard.util.TabbedTextFileWithHeaderParserTest 2 0 0 0.001s 100%
picard.util.TextFileParsersTest 20 0 0 0.006s 100%
picard.util.UnsignedTypeUtilTest 32 0 0 0.001s 100%
picard.util.help.DocumentationGenerationIntegrationTest 1 0 0 1.830s 100%
picard.vcf.AccumulateVariantCallingMetricsTest 2 0 0 0.005s 100%
picard.vcf.ByIntervalListVariantContextIteratorTest 6 0 0 0.009s 100%
picard.vcf.CallingMetricAccumulatorTest 7 0 0 0.001s 100%
picard.vcf.CollectVariantCallingMetricsTest 3 0 0 0.246s 100%
picard.vcf.FixVcfHeaderTest 8 0 0 0.099s 100%
picard.vcf.GatherVcfsTest 10 0 0 0.203s 100%
picard.vcf.GenotypeConcordanceGA4GHSchemeTest 4 0 0 0.052s 100%
picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest 1 0 0 0.008s 100%
picard.vcf.GenotypeConcordanceTest 305 0 0 0.603s 100%
picard.vcf.MakeVcfSampleNameMapTest 2 0 0 0.004s 100%
picard.vcf.MergeVcfsTest 7 0 0 0.109s 100%
picard.vcf.SortVcfsTest 11 0 0 0.211s 100%
picard.vcf.SplitVcfsTest 1 0 0 0.232s 100%
picard.vcf.UpdateVcfSequenceDictionaryTest 4 0 0 1.063s 100%
picard.vcf.VariantContextComparatorTest 6 0 0 0.001s 100%
picard.vcf.VcfFormatConverterTest 5 0 0 1.308s 100%
picard.vcf.VcfToIntervalListTest 2 0 0 0.021s 100%
picard.vcf.MendelianViolations.FindMendelianViolationsTest 1 0 0 0.037s 100%
picard.vcf.filter.TestFilterVcf 12 0 0 0.105s 100%
picard.vcf.processor.AccumulatorExecutorTest 1 0 0 1.136s 100%
picard.vcf.processor.ByWholeContigTest 1 0 0 0.001s 100%
picard.vcf.processor.ThreadsafeTest 3 0 0 0.011s 100%
picard.vcf.processor.VcfFileSegmentGeneratorTest 1 0 0 0.004s 100%
picard.vcf.processor.VcfPathSegmentGeneratorTest 1 0 0 0.002s 100%
picard.vcf.processor.WidthLimitingDecoratorTest 1 0 0 0.003s 100%