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Package org.broad.igv.sam

Inner Packages
org.broad.igv.sam.cram
org.broad.igv.sam.lite
org.broad.igv.sam.reader
org.broad.igv.sam
Interface
Alignment
Interface
LocusScore
Interface
Feature
Interface
AlignmentBlock
Created by jrobinso on 9/22/15 .
AlignmentBlockImpl
Interface
AlignmentCounts
AlignmentDataManager
Manages data loading for a sin gle alignment file. Shared be tween alignment, coverage...
Interface
IGVEventObserver
Created by jrobinson on 6/3/16 .
AlignmentInterval
Locus
Range
Basic class to specify a genom ic interval. Coordinates are intended to be 0-based ha...
Interface
NamedFeature
AlignmentPacker
Packs alignments such that the re is no overlap
AlignmentRenderer
AlignmentTileLoader
A wrapper for an AlignmentQuer yReader that caches query res ults
AlignmentTrack
Abstract
AbstractTrack
Interface
Track
Interface
Persistable
Interface for a session persis table object.
AlignmentTrack$ColorOption
AlignmentTrack$ExperimentType
AlignmentTrack$GroupOption
AlignmentTrack$OrientationType
AlignmentTrack$SortOption
AlignmentUtils
Abstract
BaseAlignmentCounts
BisulfiteBaseInfo
BisulfiteBaseInfoNOMeseq
BisulfiteCounts
CoverageTrack
Interface
ScalableTrack
Created by jrobinson on 5/3/16 .
DenseAlignmentCounts
DotAlignedAlignment
DownsampledInterval
Genomic interval showing which areas have had reads removed (downsampled)
EWigTrack
Developmental track to explore display of conservation scor es.
EmptyAlignmentIterator
Interface
CloseableIterator
ExperimentTypeChangeEvent
Created by jrobinso on 2/10/17 .
FeatureWrappedAlignment
Some alignment formats are par sed as Features. This is all getting rather circular, ...
Gap
Created by jrobinso on 3/22/16 .
HaplotypeUtils
Experimental class for phasing alignments for high ploidy r egions.
InsertionManager
Created by jrobinso on 12/22/1 6. Experimental class to test strategies for drawing i...
InsertionMarker
Created by jrobinso on 1/13/17 .
InsertionSelectionEvent
Created by jrobinso on 1/12/17 .
LinkedAlignment
Class for experimenting with 1 0X linked reads.
PEStats
PackedAlignments
Convenience class for storing map from group -> list of ali gnments packed into rows ...
LinkedHashMap
PairedAlignment
PicardAlignment
Abstract
SAMAlignment
PositionCache
Stores objects by position so they can be looked up by inex act position (contains)
ReadMate
ReadStats
Created by jrobinso on 12/20/1 6. Some simple statistics to distinguish dna, rna, and...
ReducedMemoryAlignment
Row
A row of alignments, packed to minimize empty space
Interface
Comparable
SAMFileWriter
SAMFileWriterFactory
SAMFileWriterImpl
SAMTextWriter
SAMWriter
Write SAM/BAM Alignments to a file or stream
SparseAlignmentCounts
SpliceGap
Created by jrobinso on 3/31/16 .
SpliceJunctionHelper
A helper class for computing s plice junctions from alignmen ts. Junctions are filtere...
SpliceJunctionTrack
FeatureTrack
Track which displays features, typically showing regions of the genome in a qualitat...