Test Summary

1835

tests
0

failures
0

ignored
6m55.77s

duration
100%

successful

Packages

Package Tests Failures Ignored Duration Success rate
picard.analysis 41 0 0 28.800s 100%
picard.analysis.artifacts 6 0 0 0.275s 100%
picard.analysis.directed 6 0 0 5.377s 100%
picard.analysis.replicates 21 0 0 0.180s 100%
picard.cmdline 60 0 0 0.182s 100%
picard.fingerprint 57 0 0 0.024s 100%
picard.illumina 148 0 0 9.742s 100%
picard.illumina.parser 163 0 0 4.077s 100%
picard.illumina.parser.fakers 2 0 0 0.053s 100%
picard.illumina.parser.readers 59 0 0 0.087s 100%
picard.metrics 1 0 0 0.414s 100%
picard.pedigree 4 0 0 0.001s 100%
picard.reference 2 0 0 0.011s 100%
picard.sam 231 0 0 13.758s 100%
picard.sam.markduplicates 473 0 0 5m38.77s 100%
picard.sam.markduplicates.util 5 0 0 0.003s 100%
picard.sam.util 18 0 0 0.005s 100%
picard.util 173 0 0 5.284s 100%
picard.vcf 349 0 0 6.100s 100%
picard.vcf.filter 9 0 0 0.234s 100%
picard.vcf.processor 7 0 0 2.396s 100%

Classes

Class Tests Failures Ignored Duration Success rate
picard.analysis.CollectAlignmentSummaryMetricsTest 6 0 0 0.171s 100%
picard.analysis.CollectGcBiasMetricsTest 2 0 0 1.213s 100%
picard.analysis.CollectInsertSizeMetricsTest 3 0 0 0.798s 100%
picard.analysis.CollectMultipleMetricsTest 3 0 0 1.208s 100%
picard.analysis.CollectQualityYieldMetricsTest 1 0 0 0.024s 100%
picard.analysis.CollectRnaSeqMetricsTest 2 0 0 0.056s 100%
picard.analysis.CollectWgsMetricsFromQuerySortedTest 2 0 0 0.079s 100%
picard.analysis.CollectWgsMetricsFromSampledSitesTest 3 0 0 5.722s 100%
picard.analysis.CollectWgsMetricsTest 3 0 0 2.741s 100%
picard.analysis.MultiLevelCollectorTest 6 0 0 0.007s 100%
picard.analysis.TheoreticalSensitivityTest 10 0 0 16.781s 100%
picard.analysis.artifacts.CollectSequencingArtifactMetricsTest 6 0 0 0.275s 100%
picard.analysis.directed.CollectHsMetricsTest 4 0 0 3.586s 100%
picard.analysis.directed.CollectTargetedMetricsTest 2 0 0 1.791s 100%
picard.analysis.replicates.CollectIndependentReplicatesMetricTest 13 0 0 0.174s 100%
picard.analysis.replicates.MergeableMetricBaseTest 8 0 0 0.006s 100%
picard.cmdline.CommandLineParserTest 59 0 0 0.147s 100%
picard.cmdline.PicardCommandLineTest 1 0 0 0.035s 100%
picard.fingerprint.FingerprintCheckerTest 20 0 0 0.005s 100%
picard.fingerprint.HaplotypeMapTest 2 0 0 0.005s 100%
picard.fingerprint.HaplotypeProbabilitiesTest 24 0 0 0.012s 100%
picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest 11 0 0 0.002s 100%
picard.illumina.CheckIlluminaDirectoryTest 12 0 0 2.357s 100%
picard.illumina.CollectIlluminaBasecallingMetricsTest 2 0 0 0.112s 100%
picard.illumina.ExtractIlluminaBarcodesTest 12 0 0 0.514s 100%
picard.illumina.IlluminaBasecallsToFastqTest 6 0 0 3.028s 100%
picard.illumina.IlluminaBasecallsToSamAdapterClippingTest 2 0 0 1.557s 100%
picard.illumina.IlluminaBasecallsToSamTest 13 0 0 1.886s 100%
picard.illumina.IlluminaLaneMetricsCollectorTest 8 0 0 0.277s 100%
picard.illumina.ReadStructureTest 93 0 0 0.011s 100%
picard.illumina.parser.BclParserTest 71 0 0 3.364s 100%
picard.illumina.parser.FilterParserTest 17 0 0 0.013s 100%
picard.illumina.parser.IlluminaDataProviderTest 13 0 0 0.310s 100%
picard.illumina.parser.IlluminaFileUtilTest 26 0 0 0.376s 100%
picard.illumina.parser.PerTileParserTest 17 0 0 0.001s 100%
picard.illumina.parser.PerTilePerCycleParserTest 10 0 0 0.005s 100%
picard.illumina.parser.PosParserTest 9 0 0 0.008s 100%
picard.illumina.parser.fakers.BclFileFakerTest 2 0 0 0.053s 100%
picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest 15 0 0 0.012s 100%
picard.illumina.parser.readers.BclReaderTest 8 0 0 0.013s 100%
picard.illumina.parser.readers.ClocsFileReaderTest 6 0 0 0.041s 100%
picard.illumina.parser.readers.FilterFileReaderTest 10 0 0 0.006s 100%
picard.illumina.parser.readers.LocsFileReaderTest 6 0 0 0.004s 100%
picard.illumina.parser.readers.MMapBackedIteratorFactoryTest 8 0 0 0.003s 100%
picard.illumina.parser.readers.PosFileReaderTest 6 0 0 0.008s 100%
picard.metrics.CollectRrbsMetricsTest 1 0 0 0.414s 100%
picard.pedigree.PedFileTest 4 0 0 0.001s 100%
picard.reference.NonNFastaSizeTest 2 0 0 0.011s 100%
picard.sam.AddCommentsToBamTest 3 0 0 0.121s 100%
picard.sam.CleanSamTest 12 0 0 0.417s 100%
picard.sam.CompareSAMsTest 14 0 0 0.057s 100%
picard.sam.CreateSequenceDictionaryTest 2 0 0 0.049s 100%
picard.sam.FastqToSamTest 59 0 0 1.746s 100%
picard.sam.FilterSamReadsTest 4 0 0 1.374s 100%
picard.sam.FixMateInformationTest 2 0 0 0.030s 100%
picard.sam.GatherBamFilesTest 2 0 0 0.078s 100%
picard.sam.MergeBamAlignmentTest 56 0 0 3.748s 100%
picard.sam.MergeSamFilesTest 1 0 0 0.055s 100%
picard.sam.PositionBasedDownsampleSamTest 20 0 0 4.461s 100%
picard.sam.RevertSamTest 25 0 0 0.847s 100%
picard.sam.SamFileConverterTest 6 0 0 0.185s 100%
picard.sam.SamToFastqTest 17 0 0 0.504s 100%
picard.sam.SetNmAndUqTagsTest 3 0 0 0.058s 100%
picard.sam.SplitSamByLibraryTest 3 0 0 0.021s 100%
picard.sam.ViewSamTest 2 0 0 0.007s 100%
picard.sam.markduplicates.AsIsMarkDuplicatesTester 6 0 0 5.407s 100%
picard.sam.markduplicates.EstimateLibraryComplexityTest 5 0 0 0.141s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest 79 0 0 1m49.63s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest 79 0 0 1m13.83s 100%
picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest 79 0 0 1m7.70s 100%
picard.sam.markduplicates.MarkDuplicatesTest 79 0 0 1m11.87s 100%
picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest 76 0 0 4.249s 100%
picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest 70 0 0 5.943s 100%
picard.sam.markduplicates.util.OpticalDuplicateFinderTest 5 0 0 0.003s 100%
picard.sam.util.ReadNameParserTests 18 0 0 0.005s 100%
picard.util.BedToIntervalListTest 18 0 0 0.108s 100%
picard.util.ClippingUtilityTest 50 0 0 0.105s 100%
picard.util.DelimitedTextFileWithHeaderIteratorTest 2 0 0 0.002s 100%
picard.util.FifoBufferTest 1 0 0 4.338s 100%
picard.util.FileChannelJDKBugWorkAroundTest 1 0 0 0.001s 100%
picard.util.IlluminaUtilTest 5 0 0 0.499s 100%
picard.util.IntervalListScattererTest 6 0 0 0.038s 100%
picard.util.IntervalListToBedTest 1 0 0 0.008s 100%
picard.util.MathUtilTest 13 0 0 0.002s 100%
picard.util.MergingIteratorTest 3 0 0 0.003s 100%
picard.util.QuerySortedReadPairIteratorUtilTest 4 0 0 0.001s 100%
picard.util.RExecutorTest 3 0 0 0.166s 100%
picard.util.ScatterIntervalsByNsTest 12 0 0 0.004s 100%
picard.util.TabbedTextFileWithHeaderParserTest 2 0 0 0.002s 100%
picard.util.TextFileParsersTest 20 0 0 0.004s 100%
picard.util.UnsignedTypeUtilTest 32 0 0 0.003s 100%
picard.vcf.CallingMetricAccumulatorTest 7 0 0 0.053s 100%
picard.vcf.CollectVariantCallingMetricsTest 2 0 0 0.554s 100%
picard.vcf.FixVcfHeaderTest 7 0 0 0.337s 100%
picard.vcf.GenotypeConcordanceGA4GHSchemeTest 4 0 0 0.194s 100%
picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest 1 0 0 0.025s 100%
picard.vcf.GenotypeConcordanceTest 299 0 0 0.494s 100%
picard.vcf.LiftoverVcfTest 6 0 0 0.194s 100%
picard.vcf.SortVcfsTest 10 0 0 1.120s 100%
picard.vcf.SplitVcfsTest 1 0 0 0.605s 100%
picard.vcf.UpdateVcfSequenceDictionaryTest 1 0 0 0.054s 100%
picard.vcf.VariantContextComparatorTest 6 0 0 0.001s 100%
picard.vcf.VcfFormatConverterTest 5 0 0 2.469s 100%
picard.vcf.filter.TestFilterVcf 9 0 0 0.234s 100%
picard.vcf.processor.AccumulatorExecutorTest 1 0 0 2.329s 100%
picard.vcf.processor.ByWholeContigTest 1 0 0 0.003s 100%
picard.vcf.processor.ThreadsafeTest 3 0 0 0.047s 100%
picard.vcf.processor.VcfFileSegmentGeneratorTest 1 0 0 0.012s 100%
picard.vcf.processor.WidthLimitingDecoratorTest 1 0 0 0.005s 100%