Hierarchy For All Packages

Package Hierarchies:

edu.cornell.med.icb.goby, edu.cornell.med.icb.goby.algorithmic.algorithm, edu.cornell.med.icb.goby.algorithmic.algorithm.dmr, edu.cornell.med.icb.goby.algorithmic.compression, edu.cornell.med.icb.goby.algorithmic.data, edu.cornell.med.icb.goby.algorithmic.data.ranges, edu.cornell.med.icb.goby.algorithmic.data.xml, edu.cornell.med.icb.goby.alignments, edu.cornell.med.icb.goby.alignments.filters, edu.cornell.med.icb.goby.alignments.perms, edu.cornell.med.icb.goby.alignments.processors, edu.cornell.med.icb.goby.compression, edu.cornell.med.icb.goby.config, edu.cornell.med.icb.goby.counts, edu.cornell.med.icb.goby.exception, edu.cornell.med.icb.goby.methylation, edu.cornell.med.icb.goby.modes, edu.cornell.med.icb.goby.R, edu.cornell.med.icb.goby.readers, edu.cornell.med.icb.goby.readers.sam, edu.cornell.med.icb.goby.readers.vcf, edu.cornell.med.icb.goby.reads, edu.cornell.med.icb.goby.stats, edu.cornell.med.icb.goby.util, edu.cornell.med.icb.goby.util.barcode, edu.cornell.med.icb.goby.util.dynoptions, edu.cornell.med.icb.goby.util.motifs, edu.cornell.med.icb.goby.util.pool, edu.cornell.med.icb.goby.xml, samples

Class Hierarchy

• java.lang.Object
  • edu.cornell.med.icb.goby.alignments.filters.AbstractAlignmentEntryFilter
    • edu.cornell.med.icb.goby.alignments.filters.BestScoreAmbiguityAlignmentFilter
    • edu.cornell.med.icb.goby.alignments.filters.BestScoreOnlyAlignmentFilter
    • edu.cornell.med.icb.goby.alignments.filters.TranscriptBestScoreAlignmentFilter
    • edu.cornell.med.icb.goby.alignments.filters.TranscriptsAlignmentFilter
  • edu.cornell.med.icb.goby.alignments.AbstractAlignmentReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
    • edu.cornell.med.icb.goby.alignments.AbstractConcatAlignmentReader
      • edu.cornell.med.icb.goby.alignments.ConcatAlignmentReader
        • edu.cornell.med.icb.goby.alignments.ConcatSortedAlignmentReader
    • edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl (implements edu.cornell.med.icb.goby.alignments.AlignmentReader)
  • edu.cornell.med.icb.goby.modes.AbstractAlignmentToCompactMode.TransferIds
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • it.unimi.dsi.fastutil.objects.AbstractObjectCollection<K> (implements it.unimi.dsi.fastutil.objects.ObjectCollection<K>)
      • it.unimi.dsi.fastutil.objects.AbstractObjectList<K> (implements it.unimi.dsi.fastutil.objects.ObjectList<K>, it.unimi.dsi.fastutil.Stack<K>)
        • it.unimi.dsi.fastutil.objects.ObjectArrayList<K> (implements java.lang.Cloneable, java.util.RandomAccess, java.io.Serializable)
          • edu.cornell.med.icb.goby.stats.DifferentialExpressionResults
          • edu.cornell.med.icb.goby.alignments.DiscoverVariantPositionData
      • it.unimi.dsi.fastutil.objects.AbstractObjectSet<K> (implements java.lang.Cloneable, it.unimi.dsi.fastutil.objects.ObjectSet<K>)
        • it.unimi.dsi.fastutil.objects.ObjectArraySet<K> (implements java.lang.Cloneable, java.io.Serializable)
          • edu.cornell.med.icb.goby.readers.vcf.ColumnFields
          • edu.cornell.med.icb.goby.readers.vcf.Columns
  • edu.cornell.med.icb.goby.modes.AbstractCommandLineMode
    • edu.cornell.med.icb.goby.modes.AbstractGobyMode
      • edu.cornell.med.icb.goby.modes.AbstractAlignmentToCompactMode
        • edu.cornell.med.icb.goby.modes.LastToCompactMode
        • edu.cornell.med.icb.goby.modes.SAMToCompactOldMode
      • edu.cornell.med.icb.goby.modes.AggregatePeaksByPeakDistanceMode
      • edu.cornell.med.icb.goby.modes.AggregatePeaksByRPKMDifferenceMode
      • edu.cornell.med.icb.goby.modes.AlignmentToPileupMode
      • edu.cornell.med.icb.goby.modes.AlignmentToTextMode
      • edu.cornell.med.icb.goby.modes.AnnotationPenaltyMode
      • edu.cornell.med.icb.goby.modes.AnnotationsToCountsMode
      • edu.cornell.med.icb.goby.modes.BarcodeDecoderMode
      • edu.cornell.med.icb.goby.modes.BaseStatsMode
      • edu.cornell.med.icb.goby.modes.BisulfiteConversionMode
      • edu.cornell.med.icb.goby.modes.BranchingDetectorMode
      • edu.cornell.med.icb.goby.modes.BuildSequenceCacheMode
      • edu.cornell.med.icb.goby.modes.CompactAlignmentToAnnotationCountsMode
      • edu.cornell.med.icb.goby.modes.CompactAlignmentToCountsMode
      • edu.cornell.med.icb.goby.modes.CompactAlignmentToReadSetMode
      • edu.cornell.med.icb.goby.modes.CompactAlignmentToTranscriptCountsMode
      • edu.cornell.med.icb.goby.modes.CompactFileStatsMode
      • edu.cornell.med.icb.goby.modes.CompactToFastaMode
      • edu.cornell.med.icb.goby.modes.CompactToSAMMode
      • edu.cornell.med.icb.goby.modes.ConcatenateAlignmentMode
      • edu.cornell.med.icb.goby.modes.ConcatenateCompactReadsMode
      • edu.cornell.med.icb.goby.modes.CountArchiveToPeakAnnotationsMode
      • edu.cornell.med.icb.goby.modes.CountsArchiveToBedGraphMode
      • edu.cornell.med.icb.goby.modes.CountsArchiveToUnionPeaksAnnotationMode
      • edu.cornell.med.icb.goby.modes.CountsArchiveToWiggleMode
      • edu.cornell.med.icb.goby.modes.CoverageMode
      • edu.cornell.med.icb.goby.modes.DiffAlignmentMode
      • edu.cornell.med.icb.goby.modes.DiscoverSequenceVariantsMode
      • edu.cornell.med.icb.goby.modes.DisplaySequenceVariationsMode
      • edu.cornell.med.icb.goby.modes.EmpiricalPMode
      • edu.cornell.med.icb.goby.modes.ExtractSplicingEventsMode
      • edu.cornell.med.icb.goby.modes.FalseDiscoveryRateMode
      • edu.cornell.med.icb.goby.modes.FastaToCompactMode
      • edu.cornell.med.icb.goby.modes.FilesToAttributesMode
      • edu.cornell.med.icb.goby.modes.HeptamerWeightsMode
      • edu.cornell.med.icb.goby.modes.MergeCompactAlignmentsMode
      • edu.cornell.med.icb.goby.modes.MethylStatsMode
      • edu.cornell.med.icb.goby.modes.ReadQualityStatsMode
      • edu.cornell.med.icb.goby.modes.ReadSetToTextMode
      • edu.cornell.med.icb.goby.modes.ReadsToWeightsMode
      • edu.cornell.med.icb.goby.modes.ReformatCompactReadsMode
      • edu.cornell.med.icb.goby.modes.RunParallelMode
      • edu.cornell.med.icb.goby.modes.SAMComparisonMode
      • edu.cornell.med.icb.goby.modes.SamExtractReadsMode
      • edu.cornell.med.icb.goby.modes.SampleQualityScoresMode
      • edu.cornell.med.icb.goby.modes.SAMToCompactMode
      • edu.cornell.med.icb.goby.modes.SAMToCompactSamHelperMode
      • edu.cornell.med.icb.goby.modes.SequenceVariationStats2Mode
      • edu.cornell.med.icb.goby.modes.SequenceVariationStatsMode
      • edu.cornell.med.icb.goby.modes.SimulateReadsMode
      • edu.cornell.med.icb.goby.modes.Sort1Mode
      • edu.cornell.med.icb.goby.modes.SortMode
      • edu.cornell.med.icb.goby.modes.SplitCompactReadsMode
      • edu.cornell.med.icb.goby.modes.SplitFastaMode
      • edu.cornell.med.icb.goby.modes.SplitTranscriptsMode
      • edu.cornell.med.icb.goby.modes.StatsMode
      • edu.cornell.med.icb.goby.modes.SuggestPositionSlicesMode
      • edu.cornell.med.icb.goby.modes.TabToColumnInfoMode
      • edu.cornell.med.icb.goby.modes.TallyBasesMode
      • edu.cornell.med.icb.goby.modes.TallyReadsMode
      • edu.cornell.med.icb.goby.modes.TrimMode
      • edu.cornell.med.icb.goby.modes.UpgradeMode
      • edu.cornell.med.icb.goby.modes.VCFCompareMode
      • edu.cornell.med.icb.goby.modes.VCFSubsetMode
      • edu.cornell.med.icb.goby.modes.VcfToTabMode
      • edu.cornell.med.icb.goby.modes.VersionMode
      • edu.cornell.med.icb.goby.modes.WithinGroupVariabilityMode
    • edu.cornell.med.icb.goby.modes.GenericToolsDriver
      • edu.cornell.med.icb.goby.modes.GobyDriver
  • com.google.protobuf.AbstractMessageLite (implements com.google.protobuf.MessageLite)
    • com.google.protobuf.AbstractMessage (implements com.google.protobuf.Message)
      • com.google.protobuf.GeneratedMessage (implements java.io.Serializable)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentCollection (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentCollectionOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentEntry (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentEntryOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeader (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeaderOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentIndex (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentIndexOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentTooManyHits (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentTooManyHitsOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AmbiguousLocation (implements edu.cornell.med.icb.goby.alignments.Alignments.AmbiguousLocationOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierInfo (implements edu.cornell.med.icb.goby.alignments.Alignments.IdentifierInfoOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierMapping (implements edu.cornell.med.icb.goby.alignments.Alignments.IdentifierMappingOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.ReadOriginInfo (implements edu.cornell.med.icb.goby.alignments.Alignments.ReadOriginInfoOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.RelatedAlignmentEntry (implements edu.cornell.med.icb.goby.alignments.Alignments.RelatedAlignmentEntryOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.SequenceVariation (implements edu.cornell.med.icb.goby.alignments.Alignments.SequenceVariationOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.MetaData (implements edu.cornell.med.icb.goby.reads.Reads.MetaDataOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.ReadCollection (implements edu.cornell.med.icb.goby.reads.Reads.ReadCollectionOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.ReadEntry (implements edu.cornell.med.icb.goby.reads.Reads.ReadEntryOrBuilder)
  • com.google.protobuf.AbstractMessageLite.Builder<BuilderType> (implements com.google.protobuf.MessageLite.Builder)
    • com.google.protobuf.AbstractMessage.Builder<BuilderType> (implements com.google.protobuf.Message.Builder)
      • com.google.protobuf.GeneratedMessage.Builder<BuilderType>
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentCollection.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentCollectionOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentEntry.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentEntryOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeader.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeaderOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentIndex.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentIndexOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentTooManyHits.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AlignmentTooManyHitsOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.AmbiguousLocation.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.AmbiguousLocationOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierInfo.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.IdentifierInfoOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierMapping.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.IdentifierMappingOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.ReadOriginInfo.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.ReadOriginInfoOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.RelatedAlignmentEntry.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.RelatedAlignmentEntryOrBuilder)
        • edu.cornell.med.icb.goby.alignments.Alignments.SequenceVariation.Builder (implements edu.cornell.med.icb.goby.alignments.Alignments.SequenceVariationOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.MetaData.Builder (implements edu.cornell.med.icb.goby.reads.Reads.MetaDataOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.ReadCollection.Builder (implements edu.cornell.med.icb.goby.reads.Reads.ReadCollectionOrBuilder)
        • edu.cornell.med.icb.goby.reads.Reads.ReadEntry.Builder (implements edu.cornell.med.icb.goby.reads.Reads.ReadEntryOrBuilder)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.AbstractMethylationAdapter (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.StatisticAdaptor)
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BuggyDeltaStatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.ChiSquareTestAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.DeltaStatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.FisherExactTestAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.MethylationRateDifferenceStatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.PassThroughStatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.PTestStatisticAdaptor
      • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.PTestMciProviderStatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Stat3StatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Stat4StatisticAdaptor
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Stat5StatisticAdaptor
      • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Stat5MciProviderStatisticAdaptor
  • edu.cornell.med.icb.goby.stats.AbstractOutputFormat
    • edu.cornell.med.icb.goby.modes.CompareGroupsVCFOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
    • edu.cornell.med.icb.goby.modes.MethylationRateVCFOutputFormat (implements edu.cornell.med.icb.goby.modes.MethylationFormat, edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.alignments.AlignedSequence
  • edu.cornell.med.icb.goby.alignments.AlignmentCollectionHandler (implements edu.cornell.med.icb.goby.compression.ProtobuffCollectionHandler)
  • edu.cornell.med.icb.goby.alignments.AlignmentCollectionHandler.CombinedLists
  • edu.cornell.med.icb.goby.util.AlignmentHelper
  • edu.cornell.med.icb.goby.alignments.AlignmentPositionComparator (implements java.util.Comparator<T>)
  • edu.cornell.med.icb.goby.alignments.Alignments
  • edu.cornell.med.icb.goby.alignments.AlignmentSliceHelper
  • edu.cornell.med.icb.goby.alignments.AlignmentStats
  • edu.cornell.med.icb.goby.alignments.AlignmentTooManyHitsReader
  • edu.cornell.med.icb.goby.alignments.AlignmentTooManyHitsWriter (implements java.io.Closeable)
  • edu.cornell.med.icb.goby.alignments.AlignmentToTextWriter (implements edu.cornell.med.icb.goby.alignments.AlignmentWriter)
  • edu.cornell.med.icb.goby.alignments.AlignmentWriterImpl (implements edu.cornell.med.icb.goby.alignments.AlignmentWriter)
  • edu.cornell.med.icb.goby.alignments.AlleleFrequencyOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.algorithmic.data.Annotation (implements java.lang.Comparable<T>)
    • edu.cornell.med.icb.goby.algorithmic.data.AnnotationRPKM
  • edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCountInterface)
  • edu.cornell.med.icb.goby.algorithmic.data.xml.AnnotationLength
  • edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationWeightCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCountInterface)
  • edu.cornell.med.icb.goby.counts.AnyTransitionCountsIterator (implements edu.cornell.med.icb.goby.counts.CountsAggregatorI)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.ATGCCorrectionWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.ATProportionWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.util.barcode.BarcodeMatcher
    • edu.cornell.med.icb.goby.util.barcode.PostBarcodeMatcher
    • edu.cornell.med.icb.goby.util.barcode.PreBarcodeMatcher
  • edu.cornell.med.icb.goby.util.barcode.BarcodeMatcherResult
  • edu.cornell.med.icb.goby.algorithmic.algorithm.BaseProportionWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.modes.BetweenGroupSequenceVariationOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.alignments.BufferedSortingAlignmentWriter (implements edu.cornell.med.icb.goby.alignments.AlignmentWriter)
  • edu.cornell.med.icb.goby.alignments.BufferedSortingSamBamWriter (implements net.sf.samtools.SAMFileWriter)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.By5BinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.compression.BZip2ChunkCodec (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.compression.ChunkCodecHelper
  • edu.cornell.med.icb.goby.util.CodecHelper
  • edu.cornell.med.icb.goby.reads.ColorSpaceConverter
  • edu.cornell.med.icb.goby.readers.vcf.ColumnField
  • edu.cornell.med.icb.goby.readers.vcf.ColumnInfo (implements java.lang.Cloneable)
  • edu.cornell.med.icb.goby.readers.vcf.ColumnMetaInfo
  • edu.cornell.med.icb.goby.reads.CompressedRead
  • edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeCountInterface)
    • edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeStartCount
  • edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeWeightCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeCountInterface)
  • edu.cornell.med.icb.goby.counts.CountAdaptiveBinningAdaptor (implements edu.cornell.med.icb.goby.counts.CountBinningAdapterI)
  • edu.cornell.med.icb.goby.counts.CountBinningAdaptor (implements edu.cornell.med.icb.goby.counts.CountBinningAdapterI)
  • edu.cornell.med.icb.goby.alignments.CountFixer (implements edu.cornell.med.icb.goby.alignments.CountFixerInterface)
    • edu.cornell.med.icb.goby.alignments.CountFixerNoThresholdingEffect
  • edu.cornell.med.icb.goby.counts.CountIndexBuilder
  • edu.cornell.med.icb.goby.counts.CountsArchiveReader (implements java.io.Closeable)
    • edu.cornell.med.icb.goby.counts.CachingCountsArchiveReader
  • edu.cornell.med.icb.goby.counts.CountsArchiveWriter (implements java.io.Closeable)
  • edu.cornell.med.icb.goby.counts.CountsReader (implements edu.cornell.med.icb.goby.counts.CountsReaderI)
  • edu.cornell.med.icb.goby.counts.CountsWriter (implements edu.cornell.med.icb.goby.counts.CountsWriterI)
  • edu.cornell.med.icb.goby.counts.CountWriterHelper (implements edu.cornell.med.icb.goby.counts.CountsWriterHelperI)
  • edu.cornell.med.icb.goby.counts.CountWriterHelper2 (implements edu.cornell.med.icb.goby.counts.CountsWriterHelperI)
  • edu.cornell.med.icb.goby.algorithmic.data.CovariateInfo
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.CovariateStrategy (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.CoverageAnalysis
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.CumulativeArrayKeeperFast
  • edu.cornell.med.icb.goby.alignments.processors.DefaultAlignmentProcessorFactory (implements edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorFactory)
  • edu.cornell.med.icb.goby.alignments.DefaultAlignmentReaderFactory (implements edu.cornell.med.icb.goby.alignments.AlignmentReaderFactory)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.DeNovoDMRfinder
  • edu.cornell.med.icb.goby.stats.DifferentialExpressionAnalysis
  • edu.cornell.med.icb.goby.stats.DifferentialExpressionCalculator
  • edu.cornell.med.icb.goby.stats.DifferentialExpressionInfo
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.DifferentiallyMethylatedRegion
  • edu.cornell.med.icb.goby.methylation.DifferentiallyMethylatedRegion
  • edu.cornell.med.icb.goby.alignments.DiscoverVariantIterateSortedAlignments.PositionBaseInfo
  • edu.cornell.med.icb.goby.algorithmic.data.DistinctIntValueCounterBitSet (implements edu.cornell.med.icb.goby.algorithmic.data.DistinctIntValueCounterInterface)
  • edu.cornell.med.icb.goby.util.DoInParallel
  • edu.cornell.med.icb.goby.reads.DualRandomAccessSequenceCache (implements edu.cornell.med.icb.goby.reads.RandomAccessSequenceInterface)
  • edu.cornell.med.icb.goby.alignments.processors.DummyProcessor (implements edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorInterface)
  • edu.cornell.med.icb.goby.alignments.processors.DummyProcessorUnsorted (implements edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorInterface)
  • edu.cornell.med.icb.goby.util.DumpTargetInfo
  • edu.cornell.med.icb.goby.util.dynoptions.DynamicOptionClient (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.util.dynoptions.DynamicOptionRegistry
  • edu.cornell.med.icb.goby.stats.ElementIndexComparator (implements java.util.Comparator<T>)
  • edu.cornell.med.icb.goby.stats.EmpiricalPValueEstimator
  • edu.cornell.med.icb.goby.alignments.EntryFlagHelper
  • edu.cornell.med.icb.goby.algorithmic.data.EquivalentIndelRegion
  • edu.cornell.med.icb.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.EstimatedDistribution (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.stats.EstimatedTestDistributions (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.alignments.ExportableAlignmentEntryData
  • edu.cornell.med.icb.goby.algorithmic.algorithm.ExportSplicingEvents
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoder (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderI)
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderOrder1 (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderI)
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderPlus (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderI)
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoder (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderI)
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderOrder1 (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderI)
  • edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderPlus (implements edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderI)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.FastSmallAndLog10BinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.readers.FastXEntry (implements java.lang.Cloneable)
  • edu.cornell.med.icb.goby.readers.FastXReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  • edu.cornell.med.icb.goby.stats.FDRAdjustment
    • edu.cornell.med.icb.goby.stats.BenjaminiHochbergAdjustment
    • edu.cornell.med.icb.goby.stats.BonferroniAdjustment
  • edu.cornell.med.icb.goby.algorithmic.algorithm.FenwickTree (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.FenwickTree.answer
  • edu.cornell.med.icb.goby.util.FileExtensionHelper
  • edu.cornell.med.icb.goby.alignments.FileSlice
  • edu.cornell.med.icb.goby.R.FisherExact
  • edu.cornell.med.icb.goby.R.FisherExact.Result
  • edu.cornell.med.icb.goby.util.FoldChangeForExonPairs
  • edu.cornell.med.icb.goby.modes.FormatConfigurator<T>
    • edu.cornell.med.icb.goby.modes.DummyFormatConfigurator
  • edu.cornell.med.icb.goby.stats.FormatFieldCounter
  • edu.cornell.med.icb.goby.algorithmic.algorithm.FormulaWeightAnnotationCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCountInterface)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.FormulaWeightCount (implements edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeCountInterface)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.FrequencyTable
  • edu.cornell.med.icb.goby.algorithmic.algorithm.GCProportionWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.alignments.GenomicRange
  • edu.cornell.med.icb.goby.alignments.GenotypeFilter
    • edu.cornell.med.icb.goby.alignments.AtLeastAQuarterFilter
    • edu.cornell.med.icb.goby.alignments.CommonIndelArtifactFilter
    • edu.cornell.med.icb.goby.alignments.DiploidFilter
    • edu.cornell.med.icb.goby.alignments.EntropicIndelArtifactFilter
    • edu.cornell.med.icb.goby.alignments.LeftOverFilter
    • edu.cornell.med.icb.goby.alignments.QualityScoreFilter
    • edu.cornell.med.icb.goby.alignments.RemoveIndelArtifactsFilter
  • edu.cornell.med.icb.goby.alignments.GenotypesOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.config.GobyConfiguration
  • edu.cornell.med.icb.goby.readers.sam.GobyQuickSeqvar (implements edu.cornell.med.icb.goby.util.pool.Resettable)
  • edu.cornell.med.icb.goby.R.GobyRengine
  • edu.cornell.med.icb.goby.readers.sam.GobySamRecord (implements edu.cornell.med.icb.goby.util.pool.Resettable)
  • edu.cornell.med.icb.goby.readers.sam.GobySamSegment (implements edu.cornell.med.icb.goby.util.pool.Resettable)
  • edu.cornell.med.icb.goby.GobyVersion
  • edu.cornell.med.icb.goby.readers.vcf.GroupAssociations
  • edu.cornell.med.icb.goby.algorithmic.data.GroupComparison
  • edu.cornell.med.icb.goby.compression.GZipChunkCodec (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.util.HeaderUtil
  • edu.cornell.med.icb.goby.algorithmic.data.HeptamerInfo (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.HeptamerWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.HiCMerge
  • edu.cornell.med.icb.goby.util.HitBoundedPriorityQueue
  • edu.cornell.med.icb.goby.compression.HybridChunkCodec1 (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.compression.HybridChunkCodec2 (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.modes.IndelCountOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.alignments.processors.InfoForTarget
  • edu.cornell.med.icb.goby.algorithmic.data.xml.InfoOutput
  • edu.cornell.med.icb.goby.stats.InformativeColumns
  • edu.cornell.med.icb.goby.stats.InformativeNonZeroNonNaN (implements edu.cornell.med.icb.goby.stats.InformativeDouble)
  • java.io.InputStream (implements java.io.Closeable)
    • edu.cornell.med.icb.goby.alignments.RepositionableInputStream (implements it.unimi.dsi.fastutil.io.RepositionableStream)
  • edu.cornell.med.icb.goby.algorithmic.data.Interval
  • edu.cornell.med.icb.goby.util.IOUtil
  • edu.cornell.med.icb.goby.util.IsDone
  • edu.cornell.med.icb.goby.alignments.IterateAlignments
    • edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCountIterateAlignments
    • edu.cornell.med.icb.goby.alignments.SortIterateAlignments
  • samples.IterateAlignmentsCodeSample
  • edu.cornell.med.icb.goby.alignments.IterateSortedAlignments<T>
    • edu.cornell.med.icb.goby.alignments.IterateSortedAlignmentsListImpl
      • edu.cornell.med.icb.goby.alignments.DiscoverVariantIterateSortedAlignments
    • edu.cornell.med.icb.goby.alignments.IterateSortedAlignmentsListImpl2
      • edu.cornell.med.icb.goby.alignments.IterateSortedAlignmentsToPileup
  • edu.cornell.med.icb.goby.alignments.IterateSortedAlignmentsListImpl2.PositionBaseInfo2
  • edu.cornell.med.icb.goby.alignments.LastParser (implements java.io.Closeable)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.LinearBinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.alignments.processors.LocalSortProcessor (implements edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorInterface)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Log10BinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.Log2BinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.LogGCCorrectionWeight (implements edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator)
  • edu.cornell.med.icb.goby.util.LongNamedCounter
  • edu.cornell.med.icb.goby.util.MakeBisulfiteFastaExample
  • edu.cornell.med.icb.goby.algorithmic.algorithm.MaxCombinator (implements edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.MedianCombinator (implements edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator)
  • edu.cornell.med.icb.goby.alignments.Merge
  • edu.cornell.med.icb.goby.compression.MessageChunksReader (implements java.io.Closeable)
    • edu.cornell.med.icb.goby.compression.FastBufferedMessageChunksReader
  • edu.cornell.med.icb.goby.compression.MessageChunksWriter
  • edu.cornell.med.icb.goby.methylation.MethylationData (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.methylation.MethylationRegion
  • edu.cornell.med.icb.goby.modes.MethylationRegionsOutputFormat (implements edu.cornell.med.icb.goby.modes.MethylationFormat, edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.methylation.MethylationSimilarityMatch
  • edu.cornell.med.icb.goby.methylation.MethylationSite (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.methylation.MethylationSiteIterator
  • edu.cornell.med.icb.goby.algorithmic.data.MethylCountInfo
  • edu.cornell.med.icb.goby.stats.MethylCountProviderFromRegionsOutputFormat (implements edu.cornell.med.icb.goby.stats.MethylCountProvider)
  • edu.cornell.med.icb.goby.stats.MethylCountProviderTestSupport (implements edu.cornell.med.icb.goby.stats.MethylCountProvider)
  • edu.cornell.med.icb.goby.algorithmic.data.MethylRateInfo
  • edu.cornell.med.icb.goby.methylation.MethylSimilarityScan
  • edu.cornell.med.icb.goby.xml.MethylStats
  • edu.cornell.med.icb.goby.stats.MinCombinator (implements edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator)
  • samples.ModifyAlignmentsCodeSample
  • edu.cornell.med.icb.goby.algorithmic.compression.MoveToFrontCoder
  • edu.cornell.med.icb.goby.reads.MultiReads
  • edu.cornell.med.icb.goby.util.NamedCounters
  • edu.cornell.med.icb.goby.alignments.NonAmbiguousAlignmentReader (implements edu.cornell.med.icb.goby.alignments.AlignmentReader)
  • edu.cornell.med.icb.goby.alignments.NonAmbiguousAlignmentReaderFactory (implements edu.cornell.med.icb.goby.alignments.AlignmentReaderFactory)
  • edu.cornell.med.icb.goby.alignments.perms.NoOpPermutation (implements edu.cornell.med.icb.goby.alignments.perms.QueryIndexPermutationInterface)
  • edu.cornell.med.icb.goby.alignments.perms.NoOpPermutationReader (implements edu.cornell.med.icb.goby.alignments.perms.PermutationReaderInterface)
  • edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.alignments.NoUpgradeAlignmentReaderFactory (implements edu.cornell.med.icb.goby.alignments.AlignmentReaderFactory)
  • edu.cornell.med.icb.goby.compression.NullChunkCodec (implements edu.cornell.med.icb.goby.compression.ChunkCodec)
  • edu.cornell.med.icb.goby.util.pool.NullResettableObjectPool<T> (implements edu.cornell.med.icb.goby.util.pool.ResettableObjectPoolInterface<T>)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.ObservationWriter
    • edu.cornell.med.icb.goby.stats.DummyObservationWriter
  • edu.cornell.med.icb.goby.alignments.processors.ObservedIndel (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.counts.OffsetCountsReader (implements edu.cornell.med.icb.goby.counts.CountsReaderI)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.OneBinStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.util.OutputInfo
    • edu.cornell.med.icb.goby.util.OutputInfoFromWriter
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.FilterOutputStream
      • java.util.zip.DeflaterOutputStream
        • java.util.zip.GZIPOutputStream
          • edu.cornell.med.icb.goby.compression.GzipOutputStreamWithCustomLevel
    • edu.cornell.med.icb.goby.util.LoggingOutputStream
    • edu.cornell.med.icb.goby.util.StreamSignal
  • edu.cornell.med.icb.goby.util.barcode.OverlapResult
  • samples.ParseAlignmentEntriesCodeSample
  • samples.ParseAlignmentEntriesWithIndexCodeSample
  • samples.ParseReadsCodeSample
  • edu.cornell.med.icb.goby.counts.Peak
  • edu.cornell.med.icb.goby.counts.PeakAggregator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  • edu.cornell.med.icb.goby.alignments.filters.PercentMismatchesQualityFilter (implements edu.cornell.med.icb.goby.alignments.filters.AlignmentQualityFilter)
  • edu.cornell.med.icb.goby.alignments.perms.PermutationReader (implements edu.cornell.med.icb.goby.alignments.perms.PermutationReaderInterface)
  • edu.cornell.med.icb.goby.alignments.perms.PermutationWriter (implements java.io.Closeable)
  • edu.cornell.med.icb.goby.reads.PicardFastaIndexedSequence (implements edu.cornell.med.icb.goby.reads.RandomAccessSequenceInterface)
  • edu.cornell.med.icb.goby.util.PlantIndels
  • edu.cornell.med.icb.goby.counts.PositionAdapter (implements edu.cornell.med.icb.goby.counts.CountsReaderI)
  • edu.cornell.med.icb.goby.alignments.PositionBaseInfo
  • edu.cornell.med.icb.goby.alignments.PositionFacadeAlignmentReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  • edu.cornell.med.icb.goby.alignments.PositionToBasesMap<T>
  • edu.cornell.med.icb.goby.util.PrintWeights
  • edu.cornell.med.icb.goby.algorithmic.algorithm.QFast (implements edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator)
  • edu.cornell.med.icb.goby.alignments.perms.QueryIndexPermutation (implements edu.cornell.med.icb.goby.alignments.perms.QueryIndexPermutationInterface)
    • edu.cornell.med.icb.goby.alignments.perms.ConcatenatePermutations
  • edu.cornell.med.icb.goby.util.pool.QueueResettableObjectPool<T> (implements edu.cornell.med.icb.goby.util.pool.ResettableObjectPoolInterface<T>)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.RandomAccessAnnotations
  • edu.cornell.med.icb.goby.reads.RandomAccessSequenceCache (implements edu.cornell.med.icb.goby.reads.RandomAccessSequenceInterface)
  • edu.cornell.med.icb.goby.reads.RandomAccessSequenceTestSupport (implements edu.cornell.med.icb.goby.reads.RandomAccessSequenceInterface)
  • edu.cornell.med.icb.goby.algorithmic.data.ranges.Range (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.algorithmic.data.ranges.Ranges
  • edu.cornell.med.icb.goby.algorithmic.data.Read
    • edu.cornell.med.icb.goby.algorithmic.data.ReadWithIndex
  • edu.cornell.med.icb.goby.algorithmic.data.Read.ReadSortByEnd (implements java.util.Comparator<T>, java.io.Serializable)
  • edu.cornell.med.icb.goby.algorithmic.data.Read.ReadSortByStart (implements java.util.Comparator<T>, java.io.Serializable)
  • edu.cornell.med.icb.goby.reads.ReadCodec2 (implements edu.cornell.med.icb.goby.reads.ReadCodec)
  • edu.cornell.med.icb.goby.reads.ReadCodecImpl (implements edu.cornell.med.icb.goby.reads.ReadCodec)
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.FilterReader
      • edu.cornell.med.icb.goby.util.GrepReader
  • edu.cornell.med.icb.goby.alignments.ReadGroupHelper
  • edu.cornell.med.icb.goby.alignments.ReadIndexStats
  • edu.cornell.med.icb.goby.alignments.perms.ReadNameToIndex
  • edu.cornell.med.icb.goby.alignments.ReadOriginInfo
  • edu.cornell.med.icb.goby.reads.ReadProtobuffCollectionHandler (implements edu.cornell.med.icb.goby.compression.ProtobuffCollectionHandler)
  • edu.cornell.med.icb.goby.reads.Reads
  • edu.cornell.med.icb.goby.reads.ReadSet
  • edu.cornell.med.icb.goby.reads.ReadsLoader
  • edu.cornell.med.icb.goby.reads.ReadsReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  • edu.cornell.med.icb.goby.util.ReadsToText
  • edu.cornell.med.icb.goby.reads.ReadsToTextWriter (implements edu.cornell.med.icb.goby.reads.ReadsWriter)
  • edu.cornell.med.icb.goby.reads.ReadsWriterImpl (implements edu.cornell.med.icb.goby.reads.ReadsWriter)
  • edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor (implements edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorInterface)
  • edu.cornell.med.icb.goby.alignments.ReferenceLocation (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.Release1_9_7_2
  • edu.cornell.med.icb.goby.util.RenameWeights
  • edu.cornell.med.icb.goby.stats.RpkmLikeNormalizationMethod (implements edu.cornell.med.icb.goby.stats.NormalizationMethod)
    • edu.cornell.med.icb.goby.stats.AlignedCountNormalization
    • edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization
  • edu.cornell.med.icb.goby.readers.sam.SamComparison (implements edu.cornell.med.icb.goby.readers.sam.SamComparisonInterface)
    • edu.cornell.med.icb.goby.readers.sam.SamPerPositionComparison
  • edu.cornell.med.icb.goby.modes.SamHelper (implements edu.cornell.med.icb.goby.util.pool.Resettable)
  • edu.cornell.med.icb.goby.alignments.SampleCountInfo
  • edu.cornell.med.icb.goby.stats.SamplePair
  • edu.cornell.med.icb.goby.algorithmic.data.SamplePairEnumerator
  • edu.cornell.med.icb.goby.stats.SampleStats
  • edu.cornell.med.icb.goby.algorithmic.data.xml.SampleTotalCount
  • edu.cornell.med.icb.goby.alignments.SamRecordGenomicPositionComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • edu.cornell.med.icb.goby.readers.sam.SAMRecordIterable (implements net.sf.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
  • edu.cornell.med.icb.goby.readers.sam.SamRecordParser (implements edu.cornell.med.icb.goby.util.pool.Resettable)
  • edu.cornell.med.icb.goby.alignments.ScanReferenceSequence
  • edu.cornell.med.icb.goby.algorithmic.data.Segment (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.reads.SequenceDigests
  • edu.cornell.med.icb.goby.reads.SequenceEncoder
  • edu.cornell.med.icb.goby.algorithmic.algorithm.SequenceVariationPool
  • edu.cornell.med.icb.goby.algorithmic.algorithm.SequenceVariationPool.ReadIndexInfo
  • edu.cornell.med.icb.goby.algorithmic.algorithm.SequenceVariationPool.Variation
  • edu.cornell.med.icb.goby.util.SimulateBisulfiteReads
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.SitesInFixedWindow
  • edu.cornell.med.icb.goby.alignments.processors.SkipToListIterator
  • edu.cornell.med.icb.goby.alignments.processors.SkipToSortedReader
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.SlidingCountArray
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.SmallAndLog10BinningStrategy (implements edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy)
  • edu.cornell.med.icb.goby.alignments.SomaticVariationOutputFormat (implements edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.SortedAnnotations
  • edu.cornell.med.icb.goby.modes.SplicedSamHelper
  • edu.cornell.med.icb.goby.modes.SplicedSamHelper.Limits
  • edu.cornell.med.icb.goby.stats.StatisticCalculator
    • edu.cornell.med.icb.goby.stats.AverageCalculator
    • edu.cornell.med.icb.goby.stats.AverageFisherRCalculator
    • edu.cornell.med.icb.goby.stats.ChiSquareTestCalculator
    • edu.cornell.med.icb.goby.stats.CountCalculator
    • edu.cornell.med.icb.goby.stats.CountRawSampleIdsCalculator
    • edu.cornell.med.icb.goby.stats.FisherExactRCalculator
    • edu.cornell.med.icb.goby.stats.FisherExactTestCalculator
    • edu.cornell.med.icb.goby.stats.FoldChangeCalculator
    • edu.cornell.med.icb.goby.stats.FoldChangeMagnitudeCalculator
    • edu.cornell.med.icb.goby.stats.Log2FoldChangeCalculator
    • edu.cornell.med.icb.goby.stats.SampleCountCalculator
    • edu.cornell.med.icb.goby.stats.TTestCalculator
  • edu.cornell.med.icb.goby.stats.StatisticComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • edu.cornell.med.icb.goby.util.motifs.SubSequenceMotifMatcher (implements edu.cornell.med.icb.goby.util.motifs.MotifMatcher)
  • edu.cornell.med.icb.goby.algorithmic.algorithm.SummedCombinator (implements edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator)
  • edu.cornell.med.icb.goby.util.TestSkipTo
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • edu.cornell.med.icb.goby.exception.GobyException
      • java.io.IOException
        • edu.cornell.med.icb.goby.compression.InvalidChecksumException
      • java.lang.RuntimeException
        • edu.cornell.med.icb.goby.exception.GobyRuntimeException
      • edu.cornell.med.icb.goby.readers.vcf.VCFParser.SyntaxException
  • edu.cornell.med.icb.goby.util.Timer
  • edu.cornell.med.icb.goby.stats.TSVWriter
  • edu.cornell.med.icb.goby.algorithmic.data.UnboundedFifoPool<T>
  • edu.cornell.med.icb.goby.counts.UnionAlgorithmSkeleton (implements edu.cornell.med.icb.goby.counts.CountsAggregatorI)
  • edu.cornell.med.icb.goby.counts.UnionDumpIterator (implements edu.cornell.med.icb.goby.counts.CountsAggregatorI)
  • edu.cornell.med.icb.goby.alignments.UpgradeTo1_9_6
  • edu.cornell.med.icb.goby.alignments.UpgradeTo1_9_8_2
  • edu.cornell.med.icb.goby.modes.VCFCompareMode.VCFPosition (implements java.lang.Comparable<T>)
  • edu.cornell.med.icb.goby.readers.vcf.VCFParser (implements java.io.Closeable)
  • edu.cornell.med.icb.goby.stats.VCFWriter
    • edu.cornell.med.icb.goby.stats.AnnotationAveragingWriter (implements edu.cornell.med.icb.goby.stats.RegionWriter)
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.RegionAveragingWriter (implements edu.cornell.med.icb.goby.stats.RegionWriter)
  • edu.cornell.med.icb.goby.util.WarningCounter
  • edu.cornell.med.icb.goby.modes.WeightParameters
  • edu.cornell.med.icb.goby.algorithmic.data.WeightsInfo (implements java.io.Serializable)
  • edu.cornell.med.icb.goby.counts.WiggleWindow

Interface Hierarchy

• edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorFactory
• edu.cornell.med.icb.goby.alignments.processors.AlignmentProcessorInterface
• edu.cornell.med.icb.goby.alignments.filters.AlignmentQualityFilter
• edu.cornell.med.icb.goby.alignments.AlignmentReaderFactory
• edu.cornell.med.icb.goby.algorithmic.algorithm.AnnotationCountInterface
• edu.cornell.med.icb.goby.compression.ChunkCodec
• java.io.Closeable
  • edu.cornell.med.icb.goby.alignments.AlignmentReader (also extends java.lang.Iterable<T>, java.util.Iterator<E>)
  • edu.cornell.med.icb.goby.alignments.AlignmentWriter
  • edu.cornell.med.icb.goby.counts.CountsReaderI
    • edu.cornell.med.icb.goby.counts.CountBinningAdapterI
    • edu.cornell.med.icb.goby.counts.CountsAggregatorI
  • edu.cornell.med.icb.goby.counts.CountsWriterHelperI
  • edu.cornell.med.icb.goby.counts.CountsWriterI
  • edu.cornell.med.icb.goby.reads.ReadsWriter
• edu.cornell.med.icb.goby.algorithmic.algorithm.ComputeCountInterface
• edu.cornell.med.icb.goby.alignments.CountFixerInterface
• edu.cornell.med.icb.goby.stats.DataProvider
• edu.cornell.med.icb.goby.algorithmic.data.DistinctIntValueCounterInterface
• edu.cornell.med.icb.goby.algorithmic.algorithm.EvidenceCombinator
• edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticCoderI
• edu.cornell.med.icb.goby.algorithmic.compression.FastArithmeticDecoderI
• edu.cornell.med.icb.goby.stats.InformativeDouble
• java.lang.Iterable<T>
  • edu.cornell.med.icb.goby.alignments.AlignmentReader (also extends java.io.Closeable, java.util.Iterator<E>)
• java.util.Iterator<E>
  • edu.cornell.med.icb.goby.alignments.AlignmentReader (also extends java.io.Closeable, java.lang.Iterable<T>)
• com.google.protobuf.MessageLiteOrBuilder
  • com.google.protobuf.MessageOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentCollectionOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentEntryOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeaderOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentIndexOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AlignmentTooManyHitsOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.AmbiguousLocationOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierInfoOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.IdentifierMappingOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.ReadOriginInfoOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.RelatedAlignmentEntryOrBuilder
    • edu.cornell.med.icb.goby.alignments.Alignments.SequenceVariationOrBuilder
    • edu.cornell.med.icb.goby.reads.Reads.MetaDataOrBuilder
    • edu.cornell.med.icb.goby.reads.Reads.ReadCollectionOrBuilder
    • edu.cornell.med.icb.goby.reads.Reads.ReadEntryOrBuilder
• edu.cornell.med.icb.goby.modes.MethylationFormat
• edu.cornell.med.icb.goby.stats.MethylCountProvider
• edu.cornell.med.icb.goby.util.motifs.MotifMatcher
• edu.cornell.med.icb.goby.stats.NormalizationMethod
• edu.cornell.med.icb.goby.alignments.perms.PermutationReaderInterface
• edu.cornell.med.icb.goby.compression.ProtobuffCollectionHandler
• edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.PVAlueProvider
• edu.cornell.med.icb.goby.alignments.perms.QueryIndexPermutationInterface
• edu.cornell.med.icb.goby.reads.RandomAccessSequenceInterface
• edu.cornell.med.icb.goby.reads.ReadCodec
• edu.cornell.med.icb.goby.stats.RegionWriter
• edu.cornell.med.icb.goby.util.pool.Resettable
• edu.cornell.med.icb.goby.util.pool.ResettableObjectPoolInterface<T>
• edu.cornell.med.icb.goby.readers.sam.SamComparisonInterface
• edu.cornell.med.icb.goby.modes.SequenceVariationOutputFormat
• java.io.Serializable
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.BinningStrategy
  • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.StatisticAdaptor
• edu.cornell.med.icb.goby.algorithmic.algorithm.WeightCalculator

Annotation Type Hierarchy

• edu.cornell.med.icb.goby.util.dynoptions.RegisterThis (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • edu.cornell.med.icb.goby.R.FisherExact.AlternativeHypothesis
    • edu.cornell.med.icb.goby.algorithmic.algorithm.FormulaWeightAnnotationCount.FormulaChoice
    • edu.cornell.med.icb.goby.algorithmic.algorithm.dmr.ObservationWriter.TypeOfPair
    • edu.cornell.med.icb.goby.modes.AlignmentToPileupMode.OutputFormat
    • edu.cornell.med.icb.goby.modes.CompactToFastaMode.OutputFormat
    • edu.cornell.med.icb.goby.readers.vcf.ColumnType
    • edu.cornell.med.icb.goby.reads.QualityEncoding
    • edu.cornell.med.icb.goby.stats.DifferentialExpressionCalculator.ElementType
    • edu.cornell.med.icb.goby.util.FileExtensionHelper.CompactFileType