Download picard-1.86p-sources.jar
picard/picard-1.86p-sources.jar.zip( 1,071 k)
The download jar file contains the following class files or Java source files.
META-INF/MANIFEST.MF
net.sf.picard.PicardException.java
net.sf.picard.Test.java
net.sf.picard.analysis.AlignmentSummaryMetrics.java
net.sf.picard.analysis.AlignmentSummaryMetricsCollector.java
net.sf.picard.analysis.CollectAlignmentSummaryMetrics.java
net.sf.picard.analysis.CollectGcBiasMetrics.java
net.sf.picard.analysis.CollectInsertSizeMetrics.java
net.sf.picard.analysis.CollectMultipleMetrics.java
net.sf.picard.analysis.CollectRnaSeqMetrics.java
net.sf.picard.analysis.GcBiasDetailMetrics.java
net.sf.picard.analysis.GcBiasSummaryMetrics.java
net.sf.picard.analysis.InsertSizeMetrics.java
net.sf.picard.analysis.MeanQualityByCycle.java
net.sf.picard.analysis.MetricAccumulationLevel.java
net.sf.picard.analysis.QualityScoreDistribution.java
net.sf.picard.analysis.RnaSeqMetrics.java
net.sf.picard.analysis.SinglePassSamProgram.java
net.sf.picard.analysis.directed.CalculateHsMetrics.java
net.sf.picard.analysis.directed.CollectTargetedMetrics.java
net.sf.picard.analysis.directed.CollectTargetedPcrMetrics.java
net.sf.picard.analysis.directed.HsMetricCollector.java
net.sf.picard.analysis.directed.HsMetrics.java
net.sf.picard.analysis.directed.InsertSizeMetricsCollector.java
net.sf.picard.analysis.directed.RnaSeqMetricsCollector.java
net.sf.picard.analysis.directed.TargetMetricsCollector.java
net.sf.picard.analysis.directed.TargetedPcrMetrics.java
net.sf.picard.analysis.directed.TargetedPcrMetricsCollector.java
net.sf.picard.annotation.AnnotationException.java
net.sf.picard.annotation.Gene.java
net.sf.picard.annotation.GeneAnnotationReader.java
net.sf.picard.annotation.LocusFunction.java
net.sf.picard.annotation.RefFlatReader.java
net.sf.picard.cmdline.CommandLineParseException.java
net.sf.picard.cmdline.CommandLineParser.java
net.sf.picard.cmdline.CommandLineParserDefinitionException.java
net.sf.picard.cmdline.CommandLineProgram.java
net.sf.picard.cmdline.CreateHtmlDocForProgram.java
net.sf.picard.cmdline.CreateHtmlDocForStandardOptions.java
net.sf.picard.cmdline.NestedOptions.java
net.sf.picard.cmdline.Option.java
net.sf.picard.cmdline.PositionalArguments.java
net.sf.picard.cmdline.StandardOptionDefinitions.java
net.sf.picard.cmdline.Usage.java
net.sf.picard.fastq.AsyncFastqWriter.java
net.sf.picard.fastq.BamToBfq.java
net.sf.picard.fastq.BamToBfqWriter.java
net.sf.picard.fastq.BasicFastqWriter.java
net.sf.picard.fastq.FastqConstants.java
net.sf.picard.fastq.FastqReader.java
net.sf.picard.fastq.FastqRecord.java
net.sf.picard.fastq.FastqWriter.java
net.sf.picard.fastq.FastqWriterFactory.java
net.sf.picard.filter.AggregateFilter.java
net.sf.picard.filter.AlignedFilter.java
net.sf.picard.filter.DuplicateReadFilter.java
net.sf.picard.filter.FailsVendorReadQualityFilter.java
net.sf.picard.filter.FilteringIterator.java
net.sf.picard.filter.IntervalFilter.java
net.sf.picard.filter.NotPrimaryAlignmentFilter.java
net.sf.picard.filter.ReadNameFilter.java
net.sf.picard.filter.SamRecordFilter.java
net.sf.picard.filter.SolexaNoiseFilter.java
net.sf.picard.filter.TagFilter.java
net.sf.picard.filter.WholeReadClippedFilter.java
net.sf.picard.illumina.CheckIlluminaDirectory.java
net.sf.picard.illumina.ExtractIlluminaBarcodes.java
net.sf.picard.illumina.IlluminaBasecallsToSam.java
net.sf.picard.illumina.IlluminaBasecallsToSamConverter.java
net.sf.picard.illumina.parser.BarcodeParser.java
net.sf.picard.illumina.parser.BclParser.java
net.sf.picard.illumina.parser.CifParser.java
net.sf.picard.illumina.parser.ClusterData.java
net.sf.picard.illumina.parser.ClusterIntensityFileReader.java
net.sf.picard.illumina.parser.CnfParser.java
net.sf.picard.illumina.parser.CycleIlluminaFileMap.java
net.sf.picard.illumina.parser.FilterParser.java
net.sf.picard.illumina.parser.FourChannelIntensityData.java
net.sf.picard.illumina.parser.IlluminaData.java
net.sf.picard.illumina.parser.IlluminaDataProvider.java
net.sf.picard.illumina.parser.IlluminaDataProviderFactory.java
net.sf.picard.illumina.parser.IlluminaDataType.java
net.sf.picard.illumina.parser.IlluminaFileMap.java
net.sf.picard.illumina.parser.IlluminaFileNotFoundException.java
net.sf.picard.illumina.parser.IlluminaFileUtil.java
net.sf.picard.illumina.parser.IlluminaIntensityParser.java
net.sf.picard.illumina.parser.IlluminaParser.java
net.sf.picard.illumina.parser.IlluminaTextIterator.java
net.sf.picard.illumina.parser.IntensityChannel.java
net.sf.picard.illumina.parser.OutputMapping.java
net.sf.picard.illumina.parser.PerTileParser.java
net.sf.picard.illumina.parser.PerTilePerCycleParser.java
net.sf.picard.illumina.parser.PosParser.java
net.sf.picard.illumina.parser.QseqParser.java
net.sf.picard.illumina.parser.Range.java
net.sf.picard.illumina.parser.ReadData.java
net.sf.picard.illumina.parser.ReadDescriptor.java
net.sf.picard.illumina.parser.ReadStructure.java
net.sf.picard.illumina.parser.ReadType.java
net.sf.picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.java
net.sf.picard.illumina.parser.readers.BarcodeFileReader.java
net.sf.picard.illumina.parser.readers.BclReader.java
net.sf.picard.illumina.parser.readers.ClocsFileReader.java
net.sf.picard.illumina.parser.readers.FilterFileReader.java
net.sf.picard.illumina.parser.readers.LocsFileReader.java
net.sf.picard.illumina.parser.readers.MMapBackedIteratorFactory.java
net.sf.picard.illumina.parser.readers.PosFileReader.java
net.sf.picard.illumina.parser.readers.TileMetricsOutReader.java
net.sf.picard.io.FastLineReader.java
net.sf.picard.io.IoUtil.java
net.sf.picard.liftover.Chain.java
net.sf.picard.liftover.LiftOver.java
net.sf.picard.metrics.Header.java
net.sf.picard.metrics.MetricBase.java
net.sf.picard.metrics.MetricsFile.java
net.sf.picard.metrics.MultiLevelCollector.java
net.sf.picard.metrics.MultilevelMetrics.java
net.sf.picard.metrics.PerUnitMetricCollector.java
net.sf.picard.metrics.SAMRecordAndReference.java
net.sf.picard.metrics.SAMRecordAndReferenceMultiLevelCollector.java
net.sf.picard.metrics.SAMRecordMultiLevelCollector.java
net.sf.picard.metrics.StringHeader.java
net.sf.picard.metrics.VersionHeader.java
net.sf.picard.reference.AbstractFastaSequenceFile.java
net.sf.picard.reference.ExtractSequences.java
net.sf.picard.reference.FastaSequenceFile.java
net.sf.picard.reference.FastaSequenceIndex.java
net.sf.picard.reference.IndexedFastaSequenceFile.java
net.sf.picard.reference.NormalizeFasta.java
net.sf.picard.reference.ReferenceSequence.java
net.sf.picard.reference.ReferenceSequenceFile.java
net.sf.picard.reference.ReferenceSequenceFileFactory.java
net.sf.picard.reference.ReferenceSequenceFileWalker.java
net.sf.picard.sam.AbstractAlignmentMerger.java
net.sf.picard.sam.AbstractDuplicateFindingAlgorithm.java
net.sf.picard.sam.AddOrReplaceReadGroups.java
net.sf.picard.sam.BamIndexStats.java
net.sf.picard.sam.BestMapqPrimaryAlignmentSelectionStrategy.java
net.sf.picard.sam.BuildBamIndex.java
net.sf.picard.sam.CleanSam.java
net.sf.picard.sam.ComparableSamRecordIterator.java
net.sf.picard.sam.CompareSAMs.java
net.sf.picard.sam.CoordinateSortedPairInfoMap.java
net.sf.picard.sam.CreateSequenceDictionary.java
net.sf.picard.sam.DiskReadEndsMap.java
net.sf.picard.sam.DownsampleSam.java
net.sf.picard.sam.DuplicationMetrics.java
net.sf.picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy.java
net.sf.picard.sam.EstimateLibraryComplexity.java
net.sf.picard.sam.FastqToSam.java
net.sf.picard.sam.FilterSamReads.java
net.sf.picard.sam.FixMateInformation.java
net.sf.picard.sam.MarkDuplicates.java
net.sf.picard.sam.MergeBamAlignment.java
net.sf.picard.sam.MergeSamFiles.java
net.sf.picard.sam.MergingSamRecordIterator.java
net.sf.picard.sam.MultiHitAlignedReadIterator.java
net.sf.picard.sam.PrimaryAlignmentSelectionStrategy.java
net.sf.picard.sam.RAMReadEndsMap.java
net.sf.picard.sam.ReadEnds.java
net.sf.picard.sam.ReadEndsCodec.java
net.sf.picard.sam.ReadEndsMap.java
net.sf.picard.sam.ReorderSam.java
net.sf.picard.sam.ReplaceSamHeader.java
net.sf.picard.sam.ReservedTagConstants.java
net.sf.picard.sam.RevertSam.java
net.sf.picard.sam.SamAlignmentMerger.java
net.sf.picard.sam.SamFileHeaderMerger.java
net.sf.picard.sam.SamFileValidator.java
net.sf.picard.sam.SamFormatConverter.java
net.sf.picard.sam.SamPairUtil.java
net.sf.picard.sam.SamToFastq.java
net.sf.picard.sam.SortSam.java
net.sf.picard.sam.ValidateSamFile.java
net.sf.picard.sam.ViewSam.java
net.sf.picard.util.AbstractInputParser.java
net.sf.picard.util.AbstractIterator.java
net.sf.picard.util.AdapterPair.java
net.sf.picard.util.AsyncIterator.java
net.sf.picard.util.BasicInputParser.java
net.sf.picard.util.CigarUtil.java
net.sf.picard.util.ClippingUtility.java
net.sf.picard.util.CollectionUtil.java
net.sf.picard.util.FastqQualityFormat.java
net.sf.picard.util.FileAppendStreamLRUCache.java
net.sf.picard.util.FileChannelJDKBugWorkAround.java
net.sf.picard.util.FormatUtil.java
net.sf.picard.util.Histogram.java
net.sf.picard.util.IlluminaUtil.java
net.sf.picard.util.Interval.java
net.sf.picard.util.IntervalList.java
net.sf.picard.util.IntervalListReferenceSequenceMask.java
net.sf.picard.util.IntervalListTools.java
net.sf.picard.util.IntervalTree.java
net.sf.picard.util.IntervalTreeMap.java
net.sf.picard.util.IntervalUtil.java
net.sf.picard.util.Locus.java
net.sf.picard.util.LocusComparator.java
net.sf.picard.util.LocusImpl.java
net.sf.picard.util.Log.java
net.sf.picard.util.MathUtil.java
net.sf.picard.util.MergingIterator.java
net.sf.picard.util.OverlapDetector.java
net.sf.picard.util.PeekableIterator.java
net.sf.picard.util.ProcessExecutor.java
net.sf.picard.util.ProgressLogger.java
net.sf.picard.util.QualityEncodingDetector.java
net.sf.picard.util.QualityUtil.java
net.sf.picard.util.RExecutor.java
net.sf.picard.util.ReferenceSequenceMask.java
net.sf.picard.util.ResourceLimitedMap.java
net.sf.picard.util.ResourceLimitedMapFunctor.java
net.sf.picard.util.SamLocusIterator.java
net.sf.picard.util.SamRecordIntervalIterator.java
net.sf.picard.util.SamRecordIntervalIteratorFactory.java
net.sf.picard.util.SolexaQualityConverter.java
net.sf.picard.util.TabbedInputParser.java
net.sf.picard.util.TabbedTextFileWithHeaderParser.java
net.sf.picard.util.UnsignedTypeUtil.java
net.sf.picard.util.WholeGenomeReferenceSequenceMask.java
net.sf.picard.vcf.MergeVcfs.java
net.sf.picard.vcf.SplitVcfs.java
net.sf.picard.vcf.VariantContextComparator.java
net.sf.picard.vcf.VariantContextIterator.java
net.sf.picard.vcf.VariantContextUtils.java
net.sf.samtools.AbstractBAMFileIndex.java
net.sf.samtools.AbstractSAMHeaderRecord.java
net.sf.samtools.AlignmentBlock.java
net.sf.samtools.AsyncSAMFileWriter.java
net.sf.samtools.BAMFileConstants.java
net.sf.samtools.BAMFileReader.java
net.sf.samtools.BAMFileWriter.java
net.sf.samtools.BAMIndex.java
net.sf.samtools.BAMIndexContent.java
net.sf.samtools.BAMIndexMetaData.java
net.sf.samtools.BAMIndexWriter.java
net.sf.samtools.BAMIndexer.java
net.sf.samtools.BAMRecord.java
net.sf.samtools.BAMRecordCodec.java
net.sf.samtools.BamIndexValidator.java
net.sf.samtools.Bin.java
net.sf.samtools.BinList.java
net.sf.samtools.BinaryBAMIndexWriter.java
net.sf.samtools.BinaryCigarCodec.java
net.sf.samtools.BinaryTagCodec.java
net.sf.samtools.BrowseableBAMIndex.java
net.sf.samtools.CachingBAMFileIndex.java
net.sf.samtools.Chunk.java
net.sf.samtools.Cigar.java
net.sf.samtools.CigarElement.java
net.sf.samtools.CigarOperator.java
net.sf.samtools.DefaultSAMRecordFactory.java
net.sf.samtools.Defaults.java
net.sf.samtools.DiskBasedBAMFileIndex.java
net.sf.samtools.FileTruncatedException.java
net.sf.samtools.FixBAMFile.java
net.sf.samtools.LinearIndex.java
net.sf.samtools.NotPrimarySkippingIterator.java
net.sf.samtools.SAMBinaryTagAndUnsignedArrayValue.java
net.sf.samtools.SAMBinaryTagAndValue.java
net.sf.samtools.SAMException.java
net.sf.samtools.SAMFileHeader.java
net.sf.samtools.SAMFileReader.java
net.sf.samtools.SAMFileSource.java
net.sf.samtools.SAMFileSpan.java
net.sf.samtools.SAMFileTruncatedReader.java
net.sf.samtools.SAMFileWriter.java
net.sf.samtools.SAMFileWriterFactory.java
net.sf.samtools.SAMFileWriterImpl.java
net.sf.samtools.SAMFormatException.java
net.sf.samtools.SAMLineParser.java
net.sf.samtools.SAMProgramRecord.java
net.sf.samtools.SAMReadGroupRecord.java
net.sf.samtools.SAMRecord.java
net.sf.samtools.SAMRecordComparator.java
net.sf.samtools.SAMRecordCoordinateComparator.java
net.sf.samtools.SAMRecordFactory.java
net.sf.samtools.SAMRecordIterator.java
net.sf.samtools.SAMRecordQueryNameComparator.java
net.sf.samtools.SAMRecordSetBuilder.java
net.sf.samtools.SAMRecordUtil.java
net.sf.samtools.SAMSequenceDictionary.java
net.sf.samtools.SAMSequenceRecord.java
net.sf.samtools.SAMSortOrderChecker.java
net.sf.samtools.SAMTag.java
net.sf.samtools.SAMTagUtil.java
net.sf.samtools.SAMTestUtil.java
net.sf.samtools.SAMTextHeaderCodec.java
net.sf.samtools.SAMTextReader.java
net.sf.samtools.SAMTextWriter.java
net.sf.samtools.SAMTools.java
net.sf.samtools.SAMUtils.java
net.sf.samtools.SAMValidationError.java
net.sf.samtools.SQTagUtil.java
net.sf.samtools.TagValueAndUnsignedArrayFlag.java
net.sf.samtools.TextCigarCodec.java
net.sf.samtools.TextTagCodec.java
net.sf.samtools.TextualBAMIndexWriter.java
net.sf.samtools.apps.TimeChannel.java
net.sf.samtools.apps.TimeRandomAccessFile.java
net.sf.samtools.example.ExampleSamUsage.java
net.sf.samtools.seekablestream.SeekableBufferedStream.java
net.sf.samtools.seekablestream.SeekableFTPStream.java
net.sf.samtools.seekablestream.SeekableFTPStreamHelper.java
net.sf.samtools.seekablestream.SeekableFileStream.java
net.sf.samtools.seekablestream.SeekableHTTPStream.java
net.sf.samtools.seekablestream.SeekableStream.java
net.sf.samtools.seekablestream.SeekableStreamFactory.java
net.sf.samtools.seekablestream.UserPasswordInput.java
net.sf.samtools.util.AbstractAsyncWriter.java
net.sf.samtools.util.AsciiWriter.java
net.sf.samtools.util.BinaryCodec.java
net.sf.samtools.util.BlockCompressedFilePointerUtil.java
net.sf.samtools.util.BlockCompressedInputStream.java
net.sf.samtools.util.BlockCompressedOutputStream.java
net.sf.samtools.util.BlockCompressedStreamConstants.java
net.sf.samtools.util.BlockGunzipper.java
net.sf.samtools.util.BufferedLineReader.java
net.sf.samtools.util.CloseableIterator.java
net.sf.samtools.util.CloserUtil.java
net.sf.samtools.util.CoordMath.java
net.sf.samtools.util.DateParser.java
net.sf.samtools.util.DelegatingIterator.java
net.sf.samtools.util.HttpUtils.java
net.sf.samtools.util.IOUtil.java
net.sf.samtools.util.Iso8601Date.java
net.sf.samtools.util.LineReader.java
net.sf.samtools.util.Md5CalculatingInputStream.java
net.sf.samtools.util.Md5CalculatingOutputStream.java
net.sf.samtools.util.PeekIterator.java
net.sf.samtools.util.RuntimeEOFException.java
net.sf.samtools.util.RuntimeIOException.java
net.sf.samtools.util.SeekableStream.java
net.sf.samtools.util.SequenceUtil.java
net.sf.samtools.util.SnappyLoader.java
net.sf.samtools.util.SortingCollection.java
net.sf.samtools.util.SortingLongCollection.java
net.sf.samtools.util.StopWatch.java
net.sf.samtools.util.StringLineReader.java
net.sf.samtools.util.StringUtil.java
net.sf.samtools.util.TempStreamFactory.java
net.sf.samtools.util.TestUtil.java
net.sf.samtools.util.ftp.FTPClient.java
net.sf.samtools.util.ftp.FTPReply.java
net.sf.samtools.util.ftp.FTPStream.java
net.sf.samtools.util.ftp.FTPUtils.java
org.broad.tribble.AbstractFeatureCodec.java
org.broad.tribble.AbstractFeatureReader.java
org.broad.tribble.AsciiFeatureCodec.java
org.broad.tribble.BasicFeature.java
org.broad.tribble.CloseableTribbleIterator.java
org.broad.tribble.Feature.java
org.broad.tribble.FeatureCodec.java
org.broad.tribble.FeatureCodecHeader.java
org.broad.tribble.FeatureReader.java
org.broad.tribble.NameAwareCodec.java
org.broad.tribble.TabixFeatureReader.java
org.broad.tribble.Tribble.java
org.broad.tribble.TribbleException.java
org.broad.tribble.TribbleIndexedFeatureReader.java
org.broad.tribble.annotation.Strand.java
org.broad.tribble.bed.BEDCodec.java
org.broad.tribble.bed.BEDFeature.java
org.broad.tribble.bed.FullBEDFeature.java
org.broad.tribble.bed.SimpleBEDFeature.java
org.broad.tribble.dbsnp.OldDbSNPCodec.java
org.broad.tribble.dbsnp.OldDbSNPFeature.java
org.broad.tribble.example.CountRecords.java
org.broad.tribble.example.ExampleBinaryCodec.java
org.broad.tribble.example.IndexToTable.java
org.broad.tribble.example.IndicesAreEqual.java
org.broad.tribble.example.ProfileIndexReading.java
org.broad.tribble.exception.CodecLineParsingException.java
org.broad.tribble.exception.UnsortedFileException.java
org.broad.tribble.gelitext.DiploidGenotype.java
org.broad.tribble.gelitext.GeliTextCodec.java
org.broad.tribble.gelitext.GeliTextFeature.java
org.broad.tribble.index.AbstractIndex.java
org.broad.tribble.index.Block.java
org.broad.tribble.index.ChrIndex.java
org.broad.tribble.index.DynamicIndexCreator.java
org.broad.tribble.index.Index.java
org.broad.tribble.index.IndexCreator.java
org.broad.tribble.index.IndexFactory.java
org.broad.tribble.index.interval.Interval.java
org.broad.tribble.index.interval.IntervalIndexCreator.java
org.broad.tribble.index.interval.IntervalTree.java
org.broad.tribble.index.interval.IntervalTreeIndex.java
org.broad.tribble.index.linear.LinearIndex.java
org.broad.tribble.index.linear.LinearIndexCreator.java
org.broad.tribble.readers.AsciiLineReader.java
org.broad.tribble.readers.LineReader.java
org.broad.tribble.readers.Positional.java
org.broad.tribble.readers.PositionalBufferedStream.java
org.broad.tribble.readers.TabixIteratorLineReader.java
org.broad.tribble.readers.TabixReader.java
org.broad.tribble.util.HTTPHelper.java
org.broad.tribble.util.IOUtil.java
org.broad.tribble.util.LittleEndianInputStream.java
org.broad.tribble.util.LittleEndianOutputStream.java
org.broad.tribble.util.MathUtils.java
org.broad.tribble.util.ParsingUtils.java
org.broad.tribble.util.TabixUtils.java
org.broad.tribble.util.URLHelper.java
org.broad.tribble.util.popgen.HardyWeinbergCalculation.java
org.broadinstitute.variant.bcf2.BCF2Codec.java
org.broadinstitute.variant.bcf2.BCF2Decoder.java
org.broadinstitute.variant.bcf2.BCF2GenotypeFieldDecoders.java
org.broadinstitute.variant.bcf2.BCF2LazyGenotypesDecoder.java
org.broadinstitute.variant.bcf2.BCF2Type.java
org.broadinstitute.variant.bcf2.BCF2Utils.java
org.broadinstitute.variant.bcf2.BCFVersion.java
org.broadinstitute.variant.utils.GeneralUtils.java
org.broadinstitute.variant.variantcontext.Allele.java
org.broadinstitute.variant.variantcontext.CommonInfo.java
org.broadinstitute.variant.variantcontext.FastGenotype.java
org.broadinstitute.variant.variantcontext.Genotype.java
org.broadinstitute.variant.variantcontext.GenotypeBuilder.java
org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.java
org.broadinstitute.variant.variantcontext.GenotypeType.java
org.broadinstitute.variant.variantcontext.GenotypesContext.java
org.broadinstitute.variant.variantcontext.JEXLMap.java
org.broadinstitute.variant.variantcontext.LazyGenotypesContext.java
org.broadinstitute.variant.variantcontext.VariantContext.java
org.broadinstitute.variant.variantcontext.VariantContextBuilder.java
org.broadinstitute.variant.variantcontext.VariantContextUtils.java
org.broadinstitute.variant.variantcontext.VariantJEXLContext.java
org.broadinstitute.variant.variantcontext.writer.BCF2Encoder.java
org.broadinstitute.variant.variantcontext.writer.BCF2FieldEncoder.java
org.broadinstitute.variant.variantcontext.writer.BCF2FieldWriter.java
org.broadinstitute.variant.variantcontext.writer.BCF2FieldWriterManager.java
org.broadinstitute.variant.variantcontext.writer.BCF2Writer.java
org.broadinstitute.variant.variantcontext.writer.IndexingVariantContextWriter.java
org.broadinstitute.variant.variantcontext.writer.IntGenotypeFieldAccessors.java
org.broadinstitute.variant.variantcontext.writer.Options.java
org.broadinstitute.variant.variantcontext.writer.SortingVariantContextWriter.java
org.broadinstitute.variant.variantcontext.writer.SortingVariantContextWriterBase.java
org.broadinstitute.variant.variantcontext.writer.VCFWriter.java
org.broadinstitute.variant.variantcontext.writer.VariantContextWriter.java
org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory.java
org.broadinstitute.variant.vcf.AbstractVCFCodec.java
org.broadinstitute.variant.vcf.VCF3Codec.java
org.broadinstitute.variant.vcf.VCFCodec.java
org.broadinstitute.variant.vcf.VCFCompoundHeaderLine.java
org.broadinstitute.variant.vcf.VCFConstants.java
org.broadinstitute.variant.vcf.VCFContigHeaderLine.java
org.broadinstitute.variant.vcf.VCFFilterHeaderLine.java
org.broadinstitute.variant.vcf.VCFFormatHeaderLine.java
org.broadinstitute.variant.vcf.VCFHeader.java
org.broadinstitute.variant.vcf.VCFHeaderLine.java
org.broadinstitute.variant.vcf.VCFHeaderLineCount.java
org.broadinstitute.variant.vcf.VCFHeaderLineTranslator.java
org.broadinstitute.variant.vcf.VCFHeaderLineType.java
org.broadinstitute.variant.vcf.VCFHeaderVersion.java
org.broadinstitute.variant.vcf.VCFIDHeaderLine.java
org.broadinstitute.variant.vcf.VCFInfoHeaderLine.java
org.broadinstitute.variant.vcf.VCFSimpleHeaderLine.java
org.broadinstitute.variant.vcf.VCFStandardHeaderLines.java
org.broadinstitute.variant.vcf.VCFUtils.java
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