Classes and Subpackages of org.broad.igv.sam

org.broad.igv.sam.Alignment
org.broad.igv.sam.AlignmentBlock
org.broad.igv.sam.AlignmentBlockFS
org.broad.igv.sam.AlignmentBlockTest
org.broad.igv.sam.AlignmentCounts
org.broad.igv.sam.AlignmentCounts$PositionIterator
org.broad.igv.sam.AlignmentDataManager
org.broad.igv.sam.AlignmentDataManager$DownsampleOptions
org.broad.igv.sam.AlignmentDataManagerTest
org.broad.igv.sam.AlignmentDataManagerTest$StartEndSorter
org.broad.igv.sam.AlignmentInterval
org.broad.igv.sam.AlignmentInterval$AlignmentIterator
org.broad.igv.sam.AlignmentIntervalLoaderTest
org.broad.igv.sam.AlignmentIntervalLoaderTest$RandDataIterator
org.broad.igv.sam.AlignmentPacker
org.broad.igv.sam.AlignmentPacker$BucketCollection
org.broad.igv.sam.AlignmentPacker$DenseBucketCollection
org.broad.igv.sam.AlignmentPacker$PairOrientationComparator
org.broad.igv.sam.AlignmentPacker$SparseBucketCollection
org.broad.igv.sam.AlignmentPackerTest
org.broad.igv.sam.AlignmentRenderer
org.broad.igv.sam.AlignmentTileLoader
org.broad.igv.sam.AlignmentTileLoader$AlignmentTile
org.broad.igv.sam.AlignmentTileLoader$AlignmentTile$IndexableMap
org.broad.igv.sam.AlignmentTileLoaderTest
org.broad.igv.sam.AlignmentTrack
org.broad.igv.sam.AlignmentTrack$Deselector
org.broad.igv.sam.AlignmentTrack$PopupMenu
org.broad.igv.sam.AlignmentTrack$RenderOptions
org.broad.igv.sam.AlignmentUtils
org.broad.igv.sam.AsciiLineReaderTest
org.broad.igv.sam.BAMFileReaderTest
org.broad.igv.sam.BaseAlignmentCounts
org.broad.igv.sam.BedRenderer
org.broad.igv.sam.BisulfiteBaseInfo
org.broad.igv.sam.BisulfiteBaseInfoNOMeseq
org.broad.igv.sam.BisulfiteBaseInfoTest
org.broad.igv.sam.BisulfiteBaseInfoTest$TestAlignment
org.broad.igv.sam.BisulfiteCounts
org.broad.igv.sam.BisulfiteCounts$Count
org.broad.igv.sam.CoverageTrack
org.broad.igv.sam.CoverageTrack$IntervalRenderer
org.broad.igv.sam.CoverageTrackTest
org.broad.igv.sam.DenseAlignmentCounts
org.broad.igv.sam.DenseAlignmentCountsTest
org.broad.igv.sam.DotAlignedAlignment
org.broad.igv.sam.DownsampledInterval
org.broad.igv.sam.EWigTrack
org.broad.igv.sam.EmptyAlignmentIterator
org.broad.igv.sam.FeatureRenderer
org.broad.igv.sam.FeatureWrappedAlignment
org.broad.igv.sam.FlowSignalContext
org.broad.igv.sam.FlowSignalContextBuilder
org.broad.igv.sam.FlowSignalSubContext
org.broad.igv.sam.IAlignmentDataManager
org.broad.igv.sam.MemoryAlignmentDataManager
org.broad.igv.sam.PEStats
org.broad.igv.sam.PackedAlignments
org.broad.igv.sam.PairedAlignment
org.broad.igv.sam.PicardAlignment
org.broad.igv.sam.PicardAlignmentTest
org.broad.igv.sam.PositionCache
org.broad.igv.sam.ReadMate
org.broad.igv.sam.Row
org.broad.igv.sam.SAMAlignment
org.broad.igv.sam.SAMAlignment$CigarOperator
org.broad.igv.sam.SAMWriter
org.broad.igv.sam.SAMWriter$SamAlignmentIterable
org.broad.igv.sam.SAMWriterTest
org.broad.igv.sam.SAMWriterTest$SamHeaderIterator
org.broad.igv.sam.SamIndexTest
org.broad.igv.sam.SamIndexerTest
org.broad.igv.sam.SamQueryTextReaderTest
org.broad.igv.sam.SparseAlignmentCounts
org.broad.igv.sam.SpliceJunctionFinderTrack
org.broad.igv.sam.SpliceJunctionHelper
org.broad.igv.sam.SpliceJunctionHelper$LoadOptions

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Subpackages of org.broad.igv.sam

All Classes in org.broad.igv.sam