View Java Class Source Code in JAR file
- Download JD-GUI to open JAR file and explore Java source code file (.class .java)
- Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window picard-1.102.0.jar file.
Once you open a JAR file, all the java classes in the JAR file will be displayed.
org.broad.tribble.dbsnp
├─ org.broad.tribble.dbsnp.OldDbSNPCodec.class - [JAR]
├─ org.broad.tribble.dbsnp.OldDbSNPFeature.class - [JAR]
net.sf.picard.analysis.directed
├─ net.sf.picard.analysis.directed.CalculateHsMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.CollectTargetedMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.CollectTargetedPcrMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.HsMetricCollector.class - [JAR]
├─ net.sf.picard.analysis.directed.HsMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.InsertSizeCollectorArgs.class - [JAR]
├─ net.sf.picard.analysis.directed.InsertSizeMetricsCollector.class - [JAR]
├─ net.sf.picard.analysis.directed.RnaSeqMetricsCollector.class - [JAR]
├─ net.sf.picard.analysis.directed.TargetMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.TargetMetricsCollector.class - [JAR]
├─ net.sf.picard.analysis.directed.TargetedPcrMetrics.class - [JAR]
├─ net.sf.picard.analysis.directed.TargetedPcrMetricsCollector.class - [JAR]
net.sf.samtools.seekablestream
├─ net.sf.samtools.seekablestream.ISeekableStreamFactory.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableBufferedStream.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableFTPStream.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableFTPStreamHelper.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableFileStream.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableHTTPStream.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableStream.class - [JAR]
├─ net.sf.samtools.seekablestream.SeekableStreamFactory.class - [JAR]
├─ net.sf.samtools.seekablestream.UserPasswordInput.class - [JAR]
net.sf.samtools.util
├─ net.sf.samtools.util.AbstractAsyncWriter.class - [JAR]
├─ net.sf.samtools.util.AbstractIterator.class - [JAR]
├─ net.sf.samtools.util.AsciiWriter.class - [JAR]
├─ net.sf.samtools.util.BinaryCodec.class - [JAR]
├─ net.sf.samtools.util.BlockCompressedFilePointerUtil.class - [JAR]
├─ net.sf.samtools.util.BlockCompressedInputStream.class - [JAR]
├─ net.sf.samtools.util.BlockCompressedOutputStream.class - [JAR]
├─ net.sf.samtools.util.BlockCompressedStreamConstants.class - [JAR]
├─ net.sf.samtools.util.BlockGunzipper.class - [JAR]
├─ net.sf.samtools.util.BufferedLineReader.class - [JAR]
├─ net.sf.samtools.util.CloseableIterator.class - [JAR]
├─ net.sf.samtools.util.CloserUtil.class - [JAR]
├─ net.sf.samtools.util.CollectionUtil.class - [JAR]
├─ net.sf.samtools.util.CoordMath.class - [JAR]
├─ net.sf.samtools.util.DateParser.class - [JAR]
├─ net.sf.samtools.util.DelegatingIterator.class - [JAR]
├─ net.sf.samtools.util.HttpUtils.class - [JAR]
├─ net.sf.samtools.util.IOUtil.class - [JAR]
├─ net.sf.samtools.util.Iso8601Date.class - [JAR]
├─ net.sf.samtools.util.LineReader.class - [JAR]
├─ net.sf.samtools.util.Md5CalculatingInputStream.class - [JAR]
├─ net.sf.samtools.util.Md5CalculatingOutputStream.class - [JAR]
├─ net.sf.samtools.util.PeekIterator.class - [JAR]
├─ net.sf.samtools.util.RelativeIso8601Date.class - [JAR]
├─ net.sf.samtools.util.RuntimeEOFException.class - [JAR]
├─ net.sf.samtools.util.RuntimeIOException.class - [JAR]
├─ net.sf.samtools.util.SequenceUtil.class - [JAR]
├─ net.sf.samtools.util.SnappyLoader.class - [JAR]
├─ net.sf.samtools.util.SortingCollection.class - [JAR]
├─ net.sf.samtools.util.SortingLongCollection.class - [JAR]
├─ net.sf.samtools.util.StopWatch.class - [JAR]
├─ net.sf.samtools.util.StringLineReader.class - [JAR]
├─ net.sf.samtools.util.StringUtil.class - [JAR]
├─ net.sf.samtools.util.TempStreamFactory.class - [JAR]
├─ net.sf.samtools.util.TestUtil.class - [JAR]
├─ net.sf.samtools.util.Tuple.class - [JAR]
net.sf.picard.util
├─ net.sf.picard.util.AbstractInputParser.class - [JAR]
├─ net.sf.picard.util.AdapterPair.class - [JAR]
├─ net.sf.picard.util.AsyncIterator.class - [JAR]
├─ net.sf.picard.util.BasicInputParser.class - [JAR]
├─ net.sf.picard.util.CigarUtil.class - [JAR]
├─ net.sf.picard.util.ClippingUtility.class - [JAR]
├─ net.sf.picard.util.CsvInputParser.class - [JAR]
├─ net.sf.picard.util.DelimitedTextFileWithHeaderIterator.class - [JAR]
├─ net.sf.picard.util.FastqQualityFormat.class - [JAR]
├─ net.sf.picard.util.FileAppendStreamLRUCache.class - [JAR]
├─ net.sf.picard.util.FileChannelJDKBugWorkAround.class - [JAR]
├─ net.sf.picard.util.FormatUtil.class - [JAR]
├─ net.sf.picard.util.Histogram.class - [JAR]
├─ net.sf.picard.util.IlluminaUtil.class - [JAR]
├─ net.sf.picard.util.Interval.class - [JAR]
├─ net.sf.picard.util.IntervalCoordinateComparator.class - [JAR]
├─ net.sf.picard.util.IntervalList.class - [JAR]
├─ net.sf.picard.util.IntervalListReferenceSequenceMask.class - [JAR]
├─ net.sf.picard.util.IntervalListTools.class - [JAR]
├─ net.sf.picard.util.IntervalTree.class - [JAR]
├─ net.sf.picard.util.IntervalTreeMap.class - [JAR]
├─ net.sf.picard.util.IntervalUtil.class - [JAR]
├─ net.sf.picard.util.IterableAdapter.class - [JAR]
├─ net.sf.picard.util.IterableOnceIterator.class - [JAR]
├─ net.sf.picard.util.Locus.class - [JAR]
├─ net.sf.picard.util.LocusComparator.class - [JAR]
├─ net.sf.picard.util.LocusImpl.class - [JAR]
├─ net.sf.picard.util.Log.class - [JAR]
├─ net.sf.picard.util.MathUtil.class - [JAR]
├─ net.sf.picard.util.MergingIterator.class - [JAR]
├─ net.sf.picard.util.OverlapDetector.class - [JAR]
├─ net.sf.picard.util.PeekableIterator.class - [JAR]
├─ net.sf.picard.util.ProcessExecutor.class - [JAR]
├─ net.sf.picard.util.ProgressLogger.class - [JAR]
├─ net.sf.picard.util.QualityEncodingDetector.class - [JAR]
├─ net.sf.picard.util.QualityUtil.class - [JAR]
├─ net.sf.picard.util.RExecutor.class - [JAR]
├─ net.sf.picard.util.ReferenceSequenceMask.class - [JAR]
├─ net.sf.picard.util.ResourceLimitedMap.class - [JAR]
├─ net.sf.picard.util.ResourceLimitedMapFunctor.class - [JAR]
├─ net.sf.picard.util.SamLocusIterator.class - [JAR]
├─ net.sf.picard.util.SamRecordIntervalIterator.class - [JAR]
├─ net.sf.picard.util.SamRecordIntervalIteratorFactory.class - [JAR]
├─ net.sf.picard.util.SolexaQualityConverter.class - [JAR]
├─ net.sf.picard.util.TabbedInputParser.class - [JAR]
├─ net.sf.picard.util.TabbedTextFileWithHeaderParser.class - [JAR]
├─ net.sf.picard.util.UnsignedTypeUtil.class - [JAR]
├─ net.sf.picard.util.WholeGenomeReferenceSequenceMask.class - [JAR]
net.sf.picard.annotation
├─ net.sf.picard.annotation.AnnotationException.class - [JAR]
├─ net.sf.picard.annotation.Gene.class - [JAR]
├─ net.sf.picard.annotation.GeneAnnotationReader.class - [JAR]
├─ net.sf.picard.annotation.LocusFunction.class - [JAR]
├─ net.sf.picard.annotation.RefFlatReader.class - [JAR]
org.broadinstitute.variant.vcf
├─ org.broadinstitute.variant.vcf.AbstractVCFCodec.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCF3Codec.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCF3Parser.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCF4Parser.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFCodec.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFCompoundHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFConstants.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFContigHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFEncoder.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFFileReader.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFFilterHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFFormatHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeader.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeaderLineCount.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeaderLineTranslator.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeaderLineType.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFHeaderVersion.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFIDHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFInfoHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFLineParser.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFRecordCodec.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFSimpleHeaderLine.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFStandardHeaderLines.class - [JAR]
├─ org.broadinstitute.variant.vcf.VCFUtils.class - [JAR]
net.sf.picard.pedigree
├─ net.sf.picard.pedigree.PedFile.class - [JAR]
├─ net.sf.picard.pedigree.PedTrio.class - [JAR]
├─ net.sf.picard.pedigree.Sex.class - [JAR]
net.sf.picard.illumina
├─ net.sf.picard.illumina.CheckIlluminaDirectory.class - [JAR]
├─ net.sf.picard.illumina.ClusterDataToSamConverter.class - [JAR]
├─ net.sf.picard.illumina.ExtractIlluminaBarcodes.class - [JAR]
├─ net.sf.picard.illumina.IlluminaBasecallsConverter.class - [JAR]
├─ net.sf.picard.illumina.IlluminaBasecallsToFastq.class - [JAR]
├─ net.sf.picard.illumina.IlluminaBasecallsToSam.class - [JAR]
├─ net.sf.picard.illumina.MarkIlluminaAdapters.class - [JAR]
org.broad.tribble.index.linear
├─ org.broad.tribble.index.linear.LinearIndex.class - [JAR]
├─ org.broad.tribble.index.linear.LinearIndexCreator.class - [JAR]
org.broadinstitute.variant.utils
├─ org.broadinstitute.variant.utils.GeneralUtils.class - [JAR]
org.broad.tribble.exception
├─ org.broad.tribble.exception.CodecLineParsingException.class - [JAR]
├─ org.broad.tribble.exception.UnsortedFileException.class - [JAR]
net.sf.picard.reference
├─ net.sf.picard.reference.AbstractFastaSequenceFile.class - [JAR]
├─ net.sf.picard.reference.ExtractSequences.class - [JAR]
├─ net.sf.picard.reference.FastaSequenceFile.class - [JAR]
├─ net.sf.picard.reference.FastaSequenceIndex.class - [JAR]
├─ net.sf.picard.reference.FastaSequenceIndexEntry.class - [JAR]
├─ net.sf.picard.reference.IndexedFastaSequenceFile.class - [JAR]
├─ net.sf.picard.reference.NormalizeFasta.class - [JAR]
├─ net.sf.picard.reference.ReferenceSequence.class - [JAR]
├─ net.sf.picard.reference.ReferenceSequenceFile.class - [JAR]
├─ net.sf.picard.reference.ReferenceSequenceFileFactory.class - [JAR]
├─ net.sf.picard.reference.ReferenceSequenceFileWalker.class - [JAR]
org.broad.tribble.util.popgen
├─ org.broad.tribble.util.popgen.HardyWeinbergCalculation.class - [JAR]
org.broad.tribble.index
├─ org.broad.tribble.index.AbstractIndex.class - [JAR]
├─ org.broad.tribble.index.Block.class - [JAR]
├─ org.broad.tribble.index.ChrIndex.class - [JAR]
├─ org.broad.tribble.index.DynamicIndexCreator.class - [JAR]
├─ org.broad.tribble.index.Index.class - [JAR]
├─ org.broad.tribble.index.IndexCreator.class - [JAR]
├─ org.broad.tribble.index.IndexFactory.class - [JAR]
org.broadinstitute.variant.variantcontext
├─ org.broadinstitute.variant.variantcontext.Allele.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.CommonInfo.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.FastGenotype.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.Genotype.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.GenotypeBuilder.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.GenotypeType.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.GenotypesContext.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.JEXLMap.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.LazyGenotypesContext.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.VariantContext.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.VariantContextBuilder.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.VariantContextComparator.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.VariantContextUtils.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.VariantJEXLContext.class - [JAR]
net.sf.picard.analysis
├─ net.sf.picard.analysis.AlignmentSummaryMetrics.class - [JAR]
├─ net.sf.picard.analysis.AlignmentSummaryMetricsCollector.class - [JAR]
├─ net.sf.picard.analysis.CollectAlignmentSummaryMetrics.class - [JAR]
├─ net.sf.picard.analysis.CollectGcBiasMetrics.class - [JAR]
├─ net.sf.picard.analysis.CollectInsertSizeMetrics.class - [JAR]
├─ net.sf.picard.analysis.CollectMultipleMetrics.class - [JAR]
├─ net.sf.picard.analysis.CollectRnaSeqMetrics.class - [JAR]
├─ net.sf.picard.analysis.GcBiasDetailMetrics.class - [JAR]
├─ net.sf.picard.analysis.GcBiasSummaryMetrics.class - [JAR]
├─ net.sf.picard.analysis.InsertSizeMetrics.class - [JAR]
├─ net.sf.picard.analysis.MeanQualityByCycle.class - [JAR]
├─ net.sf.picard.analysis.MetricAccumulationLevel.class - [JAR]
├─ net.sf.picard.analysis.QualityScoreDistribution.class - [JAR]
├─ net.sf.picard.analysis.RnaSeqMetrics.class - [JAR]
├─ net.sf.picard.analysis.SinglePassSamProgram.class - [JAR]
net.sf.picard.sam
├─ net.sf.picard.sam.AbstractAlignmentMerger.class - [JAR]
├─ net.sf.picard.sam.AbstractDuplicateFindingAlgorithm.class - [JAR]
├─ net.sf.picard.sam.AddOrReplaceReadGroups.class - [JAR]
├─ net.sf.picard.sam.BamIndexStats.class - [JAR]
├─ net.sf.picard.sam.BestEndMapqPrimaryAlignmentStrategy.class - [JAR]
├─ net.sf.picard.sam.BestMapqPrimaryAlignmentSelectionStrategy.class - [JAR]
├─ net.sf.picard.sam.BuildBamIndex.class - [JAR]
├─ net.sf.picard.sam.CleanSam.class - [JAR]
├─ net.sf.picard.sam.ComparableSamRecordIterator.class - [JAR]
├─ net.sf.picard.sam.CompareSAMs.class - [JAR]
├─ net.sf.picard.sam.CoordinateSortedPairInfoMap.class - [JAR]
├─ net.sf.picard.sam.CreateSequenceDictionary.class - [JAR]
├─ net.sf.picard.sam.DiskReadEndsMap.class - [JAR]
├─ net.sf.picard.sam.DownsampleSam.class - [JAR]
├─ net.sf.picard.sam.DuplicationMetrics.class - [JAR]
├─ net.sf.picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy.class - [JAR]
├─ net.sf.picard.sam.EstimateLibraryComplexity.class - [JAR]
├─ net.sf.picard.sam.FastqToSam.class - [JAR]
├─ net.sf.picard.sam.FilterSamReads.class - [JAR]
├─ net.sf.picard.sam.FixMateInformation.class - [JAR]
├─ net.sf.picard.sam.HitsForInsert.class - [JAR]
├─ net.sf.picard.sam.MarkDuplicates.class - [JAR]
├─ net.sf.picard.sam.MergeBamAlignment.class - [JAR]
├─ net.sf.picard.sam.MergeSamFiles.class - [JAR]
├─ net.sf.picard.sam.MergingSamRecordIterator.class - [JAR]
├─ net.sf.picard.sam.MostDistantPrimaryAlignmentSelectionStrategy.class - [JAR]
├─ net.sf.picard.sam.MultiHitAlignedReadIterator.class - [JAR]
├─ net.sf.picard.sam.PrimaryAlignmentSelectionStrategy.class - [JAR]
├─ net.sf.picard.sam.RAMReadEndsMap.class - [JAR]
├─ net.sf.picard.sam.ReadEnds.class - [JAR]
├─ net.sf.picard.sam.ReadEndsCodec.class - [JAR]
├─ net.sf.picard.sam.ReadEndsMap.class - [JAR]
├─ net.sf.picard.sam.ReorderSam.class - [JAR]
├─ net.sf.picard.sam.ReplaceSamHeader.class - [JAR]
├─ net.sf.picard.sam.ReservedTagConstants.class - [JAR]
├─ net.sf.picard.sam.RevertSam.class - [JAR]
├─ net.sf.picard.sam.SamAlignmentMerger.class - [JAR]
├─ net.sf.picard.sam.SamFileHeaderMerger.class - [JAR]
├─ net.sf.picard.sam.SamFileValidator.class - [JAR]
├─ net.sf.picard.sam.SamFormatConverter.class - [JAR]
├─ net.sf.picard.sam.SamPairUtil.class - [JAR]
├─ net.sf.picard.sam.SamToFastq.class - [JAR]
├─ net.sf.picard.sam.SortSam.class - [JAR]
├─ net.sf.picard.sam.ValidateSamFile.class - [JAR]
├─ net.sf.picard.sam.ViewSam.class - [JAR]
org.broad.tribble.readers
├─ org.broad.tribble.readers.AsciiLineReader.class - [JAR]
├─ org.broad.tribble.readers.AsciiLineReaderIterator.class - [JAR]
├─ org.broad.tribble.readers.AsynchronousLineReader.class - [JAR]
├─ org.broad.tribble.readers.LineIterator.class - [JAR]
├─ org.broad.tribble.readers.LineIteratorImpl.class - [JAR]
├─ org.broad.tribble.readers.LineReader.class - [JAR]
├─ org.broad.tribble.readers.LineReaderUtil.class - [JAR]
├─ org.broad.tribble.readers.LocationAware.class - [JAR]
├─ org.broad.tribble.readers.LongLineBufferedReader.class - [JAR]
├─ org.broad.tribble.readers.Positional.class - [JAR]
├─ org.broad.tribble.readers.PositionalBufferedStream.class - [JAR]
├─ org.broad.tribble.readers.TabixIteratorLineReader.class - [JAR]
├─ org.broad.tribble.readers.TabixReader.class - [JAR]
org.broad.tribble.bed
├─ org.broad.tribble.bed.BEDCodec.class - [JAR]
├─ org.broad.tribble.bed.BEDFeature.class - [JAR]
├─ org.broad.tribble.bed.FullBEDFeature.class - [JAR]
├─ org.broad.tribble.bed.SimpleBEDFeature.class - [JAR]
org.broad.tribble.index.interval
├─ org.broad.tribble.index.interval.Interval.class - [JAR]
├─ org.broad.tribble.index.interval.IntervalIndexCreator.class - [JAR]
├─ org.broad.tribble.index.interval.IntervalTree.class - [JAR]
├─ org.broad.tribble.index.interval.IntervalTreeIndex.class - [JAR]
├─ org.broad.tribble.index.interval.MutableInterval.class - [JAR]
net.sf.picard.fastq
├─ net.sf.picard.fastq.AsyncFastqWriter.class - [JAR]
├─ net.sf.picard.fastq.BamToBfq.class - [JAR]
├─ net.sf.picard.fastq.BamToBfqWriter.class - [JAR]
├─ net.sf.picard.fastq.BasicFastqWriter.class - [JAR]
├─ net.sf.picard.fastq.Casava18ReadNameEncoder.class - [JAR]
├─ net.sf.picard.fastq.FastqConstants.class - [JAR]
├─ net.sf.picard.fastq.FastqReader.class - [JAR]
├─ net.sf.picard.fastq.FastqRecord.class - [JAR]
├─ net.sf.picard.fastq.FastqWriter.class - [JAR]
├─ net.sf.picard.fastq.FastqWriterFactory.class - [JAR]
├─ net.sf.picard.fastq.IlluminaReadNameEncoder.class - [JAR]
├─ net.sf.picard.fastq.ReadNameEncoder.class - [JAR]
net.sf.samtools
├─ net.sf.samtools.AbstractBAMFileIndex.class - [JAR]
├─ net.sf.samtools.AbstractSAMHeaderRecord.class - [JAR]
├─ net.sf.samtools.AlignmentBlock.class - [JAR]
├─ net.sf.samtools.AsyncSAMFileWriter.class - [JAR]
├─ net.sf.samtools.BAMFileConstants.class - [JAR]
├─ net.sf.samtools.BAMFileReader.class - [JAR]
├─ net.sf.samtools.BAMFileSpan.class - [JAR]
├─ net.sf.samtools.BAMFileWriter.class - [JAR]
├─ net.sf.samtools.BAMIndex.class - [JAR]
├─ net.sf.samtools.BAMIndexContent.class - [JAR]
├─ net.sf.samtools.BAMIndexMetaData.class - [JAR]
├─ net.sf.samtools.BAMIndexWriter.class - [JAR]
├─ net.sf.samtools.BAMIndexer.class - [JAR]
├─ net.sf.samtools.BAMRecord.class - [JAR]
├─ net.sf.samtools.BAMRecordCodec.class - [JAR]
├─ net.sf.samtools.BamIndexValidator.class - [JAR]
├─ net.sf.samtools.Bin.class - [JAR]
├─ net.sf.samtools.BinList.class - [JAR]
├─ net.sf.samtools.BinaryBAMIndexWriter.class - [JAR]
├─ net.sf.samtools.BinaryCigarCodec.class - [JAR]
├─ net.sf.samtools.BinaryTagCodec.class - [JAR]
├─ net.sf.samtools.BrowseableBAMIndex.class - [JAR]
├─ net.sf.samtools.CachingBAMFileIndex.class - [JAR]
├─ net.sf.samtools.Chunk.class - [JAR]
├─ net.sf.samtools.Cigar.class - [JAR]
├─ net.sf.samtools.CigarElement.class - [JAR]
├─ net.sf.samtools.CigarOperator.class - [JAR]
├─ net.sf.samtools.DefaultSAMRecordFactory.class - [JAR]
├─ net.sf.samtools.Defaults.class - [JAR]
├─ net.sf.samtools.DiskBasedBAMFileIndex.class - [JAR]
├─ net.sf.samtools.FileTruncatedException.class - [JAR]
├─ net.sf.samtools.FixBAMFile.class - [JAR]
├─ net.sf.samtools.LinearIndex.class - [JAR]
├─ net.sf.samtools.NotPrimarySkippingIterator.class - [JAR]
├─ net.sf.samtools.SAMBinaryTagAndUnsignedArrayValue.class - [JAR]
├─ net.sf.samtools.SAMBinaryTagAndValue.class - [JAR]
├─ net.sf.samtools.SAMException.class - [JAR]
├─ net.sf.samtools.SAMFileHeader.class - [JAR]
├─ net.sf.samtools.SAMFileReader.class - [JAR]
├─ net.sf.samtools.SAMFileSource.class - [JAR]
├─ net.sf.samtools.SAMFileSpan.class - [JAR]
├─ net.sf.samtools.SAMFileTruncatedReader.class - [JAR]
├─ net.sf.samtools.SAMFileWriter.class - [JAR]
├─ net.sf.samtools.SAMFileWriterFactory.class - [JAR]
├─ net.sf.samtools.SAMFileWriterImpl.class - [JAR]
├─ net.sf.samtools.SAMFormatException.class - [JAR]
├─ net.sf.samtools.SAMLineParser.class - [JAR]
├─ net.sf.samtools.SAMProgramRecord.class - [JAR]
├─ net.sf.samtools.SAMReadGroupRecord.class - [JAR]
├─ net.sf.samtools.SAMRecord.class - [JAR]
├─ net.sf.samtools.SAMRecordComparator.class - [JAR]
├─ net.sf.samtools.SAMRecordCoordinateComparator.class - [JAR]
├─ net.sf.samtools.SAMRecordFactory.class - [JAR]
├─ net.sf.samtools.SAMRecordIterator.class - [JAR]
├─ net.sf.samtools.SAMRecordQueryNameComparator.class - [JAR]
├─ net.sf.samtools.SAMRecordSetBuilder.class - [JAR]
├─ net.sf.samtools.SAMRecordUtil.class - [JAR]
├─ net.sf.samtools.SAMSequenceDictionary.class - [JAR]
├─ net.sf.samtools.SAMSequenceRecord.class - [JAR]
├─ net.sf.samtools.SAMSortOrderChecker.class - [JAR]
├─ net.sf.samtools.SAMTag.class - [JAR]
├─ net.sf.samtools.SAMTagUtil.class - [JAR]
├─ net.sf.samtools.SAMTestUtil.class - [JAR]
├─ net.sf.samtools.SAMTextHeaderCodec.class - [JAR]
├─ net.sf.samtools.SAMTextReader.class - [JAR]
├─ net.sf.samtools.SAMTextWriter.class - [JAR]
├─ net.sf.samtools.SAMTools.class - [JAR]
├─ net.sf.samtools.SAMUtils.class - [JAR]
├─ net.sf.samtools.SAMValidationError.class - [JAR]
├─ net.sf.samtools.SQTagUtil.class - [JAR]
├─ net.sf.samtools.SecondaryOrSupplementarySkippingIterator.class - [JAR]
├─ net.sf.samtools.TagValueAndUnsignedArrayFlag.class - [JAR]
├─ net.sf.samtools.TextCigarCodec.class - [JAR]
├─ net.sf.samtools.TextTagCodec.class - [JAR]
├─ net.sf.samtools.TextualBAMIndexWriter.class - [JAR]
net.sf.picard.metrics
├─ net.sf.picard.metrics.Header.class - [JAR]
├─ net.sf.picard.metrics.MetricBase.class - [JAR]
├─ net.sf.picard.metrics.MetricsFile.class - [JAR]
├─ net.sf.picard.metrics.MultiLevelCollector.class - [JAR]
├─ net.sf.picard.metrics.MultilevelMetrics.class - [JAR]
├─ net.sf.picard.metrics.PerUnitMetricCollector.class - [JAR]
├─ net.sf.picard.metrics.SAMRecordAndReference.class - [JAR]
├─ net.sf.picard.metrics.SAMRecordAndReferenceMultiLevelCollector.class - [JAR]
├─ net.sf.picard.metrics.SAMRecordMultiLevelCollector.class - [JAR]
├─ net.sf.picard.metrics.StringHeader.class - [JAR]
├─ net.sf.picard.metrics.VersionHeader.class - [JAR]
net.sf.samtools.example
├─ net.sf.samtools.example.ExampleSamUsage.class - [JAR]
org.broad.tribble.example
├─ org.broad.tribble.example.CountRecords.class - [JAR]
├─ org.broad.tribble.example.ExampleBinaryCodec.class - [JAR]
├─ org.broad.tribble.example.IndexToTable.class - [JAR]
├─ org.broad.tribble.example.IndicesAreEqual.class - [JAR]
├─ org.broad.tribble.example.ProfileIndexReading.class - [JAR]
org.broad.tribble.annotation
├─ org.broad.tribble.annotation.Strand.class - [JAR]
org.broadinstitute.variant.bcf2
├─ org.broadinstitute.variant.bcf2.BCF2Codec.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCF2Decoder.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCF2GenotypeFieldDecoders.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCF2LazyGenotypesDecoder.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCF2Type.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCF2Utils.class - [JAR]
├─ org.broadinstitute.variant.bcf2.BCFVersion.class - [JAR]
org.broadinstitute.variant.variantcontext.writer
├─ org.broadinstitute.variant.variantcontext.writer.BCF2Encoder.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.BCF2FieldEncoder.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.BCF2FieldWriter.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.BCF2FieldWriterManager.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.BCF2Writer.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.IndexingVariantContextWriter.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.IntGenotypeFieldAccessors.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.Options.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.PositionalOutputStream.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.SortingVariantContextWriter.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.SortingVariantContextWriterBase.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.VCFWriter.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.VariantContextWriter.class - [JAR]
├─ org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory.class - [JAR]
net.sf.picard.cmdline
├─ net.sf.picard.cmdline.CommandLineParseException.class - [JAR]
├─ net.sf.picard.cmdline.CommandLineParser.class - [JAR]
├─ net.sf.picard.cmdline.CommandLineParserDefinitionException.class - [JAR]
├─ net.sf.picard.cmdline.CommandLineProgram.class - [JAR]
├─ net.sf.picard.cmdline.CreateHtmlDocForProgram.class - [JAR]
├─ net.sf.picard.cmdline.CreateHtmlDocForStandardOptions.class - [JAR]
├─ net.sf.picard.cmdline.NestedOptions.class - [JAR]
├─ net.sf.picard.cmdline.Option.class - [JAR]
├─ net.sf.picard.cmdline.PositionalArguments.class - [JAR]
├─ net.sf.picard.cmdline.StandardOptionDefinitions.class - [JAR]
├─ net.sf.picard.cmdline.Usage.class - [JAR]
net.sf.picard.filter
├─ net.sf.picard.filter.AggregateFilter.class - [JAR]
├─ net.sf.picard.filter.AlignedFilter.class - [JAR]
├─ net.sf.picard.filter.DuplicateReadFilter.class - [JAR]
├─ net.sf.picard.filter.FailsVendorReadQualityFilter.class - [JAR]
├─ net.sf.picard.filter.FilteringIterator.class - [JAR]
├─ net.sf.picard.filter.IntervalFilter.class - [JAR]
├─ net.sf.picard.filter.NotPrimaryAlignmentFilter.class - [JAR]
├─ net.sf.picard.filter.ReadNameFilter.class - [JAR]
├─ net.sf.picard.filter.SamRecordFilter.class - [JAR]
├─ net.sf.picard.filter.SecondaryOrSupplementaryFilter.class - [JAR]
├─ net.sf.picard.filter.SolexaNoiseFilter.class - [JAR]
├─ net.sf.picard.filter.TagFilter.class - [JAR]
├─ net.sf.picard.filter.WholeReadClippedFilter.class - [JAR]
net.sf.picard
├─ net.sf.picard.PicardException.class - [JAR]
├─ net.sf.picard.Test.class - [JAR]
net.sf.picard.vcf
├─ net.sf.picard.vcf.MakeSitesOnlyVcf.class - [JAR]
├─ net.sf.picard.vcf.MergeVcfs.class - [JAR]
├─ net.sf.picard.vcf.SplitVcfs.class - [JAR]
├─ net.sf.picard.vcf.VcfFormatConverter.class - [JAR]
org.broad.tribble
├─ org.broad.tribble.AbstractFeatureCodec.class - [JAR]
├─ org.broad.tribble.AbstractFeatureReader.class - [JAR]
├─ org.broad.tribble.AsciiFeatureCodec.class - [JAR]
├─ org.broad.tribble.BasicFeature.class - [JAR]
├─ org.broad.tribble.BinaryFeatureCodec.class - [JAR]
├─ org.broad.tribble.CloseableTribbleIterator.class - [JAR]
├─ org.broad.tribble.Feature.class - [JAR]
├─ org.broad.tribble.FeatureCodec.class - [JAR]
├─ org.broad.tribble.FeatureCodecHeader.class - [JAR]
├─ org.broad.tribble.FeatureReader.class - [JAR]
├─ org.broad.tribble.NameAwareCodec.class - [JAR]
├─ org.broad.tribble.TabixFeatureReader.class - [JAR]
├─ org.broad.tribble.Tribble.class - [JAR]
├─ org.broad.tribble.TribbleException.class - [JAR]
├─ org.broad.tribble.TribbleIndexedFeatureReader.class - [JAR]
org.broad.tribble.gelitext
├─ org.broad.tribble.gelitext.DiploidGenotype.class - [JAR]
├─ org.broad.tribble.gelitext.DiploidGenotypeException.class - [JAR]
├─ org.broad.tribble.gelitext.GeliTextCodec.class - [JAR]
├─ org.broad.tribble.gelitext.GeliTextFeature.class - [JAR]
net.sf.picard.illumina.parser
├─ net.sf.picard.illumina.parser.BarcodeData.class - [JAR]
├─ net.sf.picard.illumina.parser.BarcodeParser.class - [JAR]
├─ net.sf.picard.illumina.parser.BaseData.class - [JAR]
├─ net.sf.picard.illumina.parser.BclData.class - [JAR]
├─ net.sf.picard.illumina.parser.BclParser.class - [JAR]
├─ net.sf.picard.illumina.parser.CifParser.class - [JAR]
├─ net.sf.picard.illumina.parser.ClusterData.class - [JAR]
├─ net.sf.picard.illumina.parser.ClusterIntensityFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.CnfParser.class - [JAR]
├─ net.sf.picard.illumina.parser.CycleFilesIterator.class - [JAR]
├─ net.sf.picard.illumina.parser.CycleIlluminaFileMap.class - [JAR]
├─ net.sf.picard.illumina.parser.FilterParser.class - [JAR]
├─ net.sf.picard.illumina.parser.FourChannelIntensityData.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaData.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaDataProvider.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaDataProviderFactory.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaDataType.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaFileMap.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaFileNotFoundException.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaFileUtil.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaIntensityParser.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaParser.class - [JAR]
├─ net.sf.picard.illumina.parser.IlluminaTextIterator.class - [JAR]
├─ net.sf.picard.illumina.parser.IntensityChannel.class - [JAR]
├─ net.sf.picard.illumina.parser.NoiseData.class - [JAR]
├─ net.sf.picard.illumina.parser.OutputMapping.class - [JAR]
├─ net.sf.picard.illumina.parser.PerTileParser.class - [JAR]
├─ net.sf.picard.illumina.parser.PerTilePerCycleParser.class - [JAR]
├─ net.sf.picard.illumina.parser.PfData.class - [JAR]
├─ net.sf.picard.illumina.parser.PosParser.class - [JAR]
├─ net.sf.picard.illumina.parser.PositionalData.class - [JAR]
├─ net.sf.picard.illumina.parser.QseqParser.class - [JAR]
├─ net.sf.picard.illumina.parser.QseqReadData.class - [JAR]
├─ net.sf.picard.illumina.parser.QseqReadParser.class - [JAR]
├─ net.sf.picard.illumina.parser.QualityData.class - [JAR]
├─ net.sf.picard.illumina.parser.Range.class - [JAR]
├─ net.sf.picard.illumina.parser.RawIntensityData.class - [JAR]
├─ net.sf.picard.illumina.parser.ReadData.class - [JAR]
├─ net.sf.picard.illumina.parser.ReadDescriptor.class - [JAR]
├─ net.sf.picard.illumina.parser.ReadStructure.class - [JAR]
├─ net.sf.picard.illumina.parser.ReadType.class - [JAR]
├─ net.sf.picard.illumina.parser.TileMetricsUtil.class - [JAR]
net.sf.samtools.util.ftp
├─ net.sf.samtools.util.ftp.FTPClient.class - [JAR]
├─ net.sf.samtools.util.ftp.FTPReply.class - [JAR]
├─ net.sf.samtools.util.ftp.FTPStream.class - [JAR]
├─ net.sf.samtools.util.ftp.FTPUtils.class - [JAR]
org.broad.tribble.util
├─ org.broad.tribble.util.FTPHelper.class - [JAR]
├─ org.broad.tribble.util.HTTPHelper.class - [JAR]
├─ org.broad.tribble.util.LittleEndianInputStream.class - [JAR]
├─ org.broad.tribble.util.LittleEndianOutputStream.class - [JAR]
├─ org.broad.tribble.util.MathUtils.class - [JAR]
├─ org.broad.tribble.util.ParsingUtils.class - [JAR]
├─ org.broad.tribble.util.RemoteURLHelper.class - [JAR]
├─ org.broad.tribble.util.TabixUtils.class - [JAR]
├─ org.broad.tribble.util.URLHelper.class - [JAR]
net.sf.picard.io
├─ net.sf.picard.io.CustomGzipOutputStream.class - [JAR]
├─ net.sf.picard.io.FastLineReader.class - [JAR]
├─ net.sf.picard.io.IoUtil.class - [JAR]
net.sf.picard.illumina.parser.readers
├─ net.sf.picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.BarcodeFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.BclReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.BinaryFileIterator.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.ClocsFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.FilterFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.LocsFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.MMapBackedIteratorFactory.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.PosFileReader.class - [JAR]
├─ net.sf.picard.illumina.parser.readers.TileMetricsOutReader.class - [JAR]
net.sf.samtools.apps
├─ net.sf.samtools.apps.TimeChannel.class - [JAR]
├─ net.sf.samtools.apps.TimeRandomAccessFile.class - [JAR]
net.sf.picard.liftover
├─ net.sf.picard.liftover.Chain.class - [JAR]
├─ net.sf.picard.liftover.LiftOver.class - [JAR]
