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META-INF
- MANIFEST.MF
net
- sf
  - picard
    - analysis
      - AlignmentSummaryMetrics.java
      - CollectAlignmentSummaryMetrics.java
      - CollectGcBiasMetrics.java
      - CollectInsertSizeMetrics.java
      - CollectMultipleMetrics.java
      - CollectRnaSeqMetrics.java
      - directed
        CalculateHsMetrics.java
        HsMetrics.java
        HsMetricsCalculator.java
      - GcBiasDetailMetrics.java
      - GcBiasSummaryMetrics.java
      - InsertSizeMetrics.java
      - MeanQualityByCycle.java
      - MetricAccumulationLevel.java
      - QualityScoreDistribution.java
      - RnaSeqMetrics.java
      - SinglePassSamProgram.java
    - annotation
      - AnnotationException.java
      - Gene.java
      - GeneAnnotationReader.java
      - LocusFunction.java
      - RefFlatReader.java
    - cmdline
      - CommandLineParseException.java
      - CommandLineParser.java
      - CommandLineParserDefinitionException.java
      - CommandLineProgram.java
      - CreateHtmlDocForProgram.java
      - CreateHtmlDocForStandardOptions.java
      - Option.java
      - PositionalArguments.java
      - StandardOptionDefinitions.java
      - Usage.java
    - fastq
      - BamToBfq.java
      - BamToBfqWriter.java
      - FastqConstants.java
      - FastqReader.java
      - FastqRecord.java
      - FastqWriter.java
    - filter
      - AggregateFilter.java
      - DuplicateReadFilter.java
      - FailsVendorReadQualityFilter.java
      - FilteringIterator.java
      - IntervalFilter.java
      - NotPrimaryAlignmentFilter.java
      - SamRecordFilter.java
      - SolexaNoiseFilter.java
      - TagFilter.java
      - WholeReadClippedFilter.java
    - illumina
      - BarcodeUtil.java
      - ExtractIlluminaBarcodes.java
      - IlluminaBasecallsToSam.java
      - IlluminaBasecallsToSamConverter.java
      - parser
        AbstractIlluminaDataProvider.java
        AbstractIlluminaTextParser.java
        BarcodeFilter.java
        BarcodeParser.java
        CifParser.java
        ClusterIntensityFileReader.java
        CnfParser.java
        CycleFileSetIterator.java
        EndType.java
        FourChannelIntensityData.java
        IlluminaCycleFileSetParser.java
        IlluminaDataProvider.java
        IlluminaDataProviderFactory.java
        IlluminaDataType.java
        IlluminaEndData.java
        IlluminaFileNotFoundException.java
        IlluminaFileUtil.java
        IlluminaParser.java
        IlluminaReadData.java
        IntensitiesOrNoiseParser.java
        IntensityChannel.java
        IntParser.java
        NseParser.java
        PrbParser.java
        QhgParser.java
        QseqParser.java
        ReadConfiguration.java
        SeqParser.java
        Sig2Parser.java
        TiledIlluminaFile.java
    - io
      - FastLineReader.java
      - IoUtil.java
    - liftover
      - Chain.java
      - LiftOver.java
    - metrics
      - Header.java
      - MetricBase.java
      - MetricsFile.java
      - StringHeader.java
      - VersionHeader.java
    - PicardException.java
    - reference
      - AbstractFastaSequenceFile.java
      - ExtractSequences.java
      - FastaSequenceFile.java
      - FastaSequenceIndex.java
      - FastaSequenceIndexEntry.java
      - IndexedFastaSequenceFile.java
      - NormalizeFasta.java
      - ReferenceSequence.java
      - ReferenceSequenceFile.java
      - ReferenceSequenceFileFactory.java
      - ReferenceSequenceFileWalker.java
    - sam
      - AbstractAlignmentMerger.java
      - AbstractDuplicateFindingAlgorithm.java
      - AddOrReplaceReadGroups.java
      - BamIndexStats.java
      - BuildBamIndex.java
      - CleanSam.java
      - ComparableSamRecordIterator.java
      - CompareSAMs.java
      - CoordinateSortedPairInfoMap.java
      - CreateSequenceDictionary.java
      - DiskReadEndsMap.java
      - DownsampleSam.java
      - DuplicationMetrics.java
      - EstimateLibraryComplexity.java
      - FastqToSam.java
      - FixMateInformation.java
      - MarkDuplicates.java
      - MergeBamAlignment.java
      - MergeSamFiles.java
      - MergingSamRecordIterator.java
      - MultiHitAlignedReadIterator.java
      - RAMReadEndsMap.java
      - ReadEnds.java
      - ReadEndsCodec.java
      - ReadEndsMap.java
      - ReorderSam.java
      - ReplaceSamHeader.java
      - ReservedTagConstants.java
      - RevertSam.java
      - SamAlignmentMerger.java
      - SamFileHeaderMerger.java
      - SamFileValidator.java
      - SamFormatConverter.java
      - SamPairUtil.java
      - SamToFastq.java
      - SortSam.java
      - ValidateSamFile.java
      - ViewSam.java
    - util
      - AbstractInputParser.java
      - AbstractIterator.java
      - BasicInputParser.java
      - CigarUtil.java
      - ClippingUtility.java
      - CollectionUtil.java
      - FastqQualityFormat.java
      - FileAppendStreamLRUCache.java
      - FileChannelJDKBugWorkAround.java
      - FormatUtil.java
      - Histogram.java
      - IlluminaUtil.java
      - Interval.java
      - IntervalCoordinateComparator.java
      - IntervalList.java
      - IntervalListReferenceSequenceMask.java
      - IntervalListTools.java
      - IntervalTree.java
      - IntervalTreeMap.java
      - IntervalUtil.java
      - Locus.java
      - LocusComparator.java
      - LocusImpl.java
      - Log.java
      - MathUtil.java
      - MetricsDoclet.java
      - OverlapDetector.java
      - PeekableIterator.java
      - ProcessExecutor.java
      - QualityUtil.java
      - ReferenceSequenceMask.java
      - ResourceLimitedMap.java
      - ResourceLimitedMapFunctor.java
      - RExecutor.java
      - SamLocusIterator.java
      - SamRecordIntervalIterator.java
      - SamRecordIntervalIteratorFactory.java
      - SolexaQualityConverter.java
      - TabbedInputParser.java
      - TabbedTextFileWithHeaderParser.java
      - WholeGenomeReferenceSequenceMask.java