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Package org.broad.igv.sam

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