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Package org.broad.igv.feature.tribble

class BCF2WrapperCodec
class CachingFeatureReader
class CodecFactory
A factory class for Tribble co decs. implements a single, st atic, public method to re...
class DGVCodec
class EMBLTableCodec
class EncodePeakCodec
Codec for UCSC / ENCDOE "broad and narrow peak" files (http ://genome.ucsc.edu/FAQ/FA...
class FeatureFileHeader
Created by IntelliJ IDEA. User : jrobinso Date: May 22, 2010 Time: 7:10:59 PM To chan...
class GFFCodec
Notes from GFF3 spec http://ww w.sequenceontology.org/gff3.s html These tags have pred...
class IGVBEDCodec
Created by IntelliJ IDEA. User : jrobinso Date: Dec 20, 2009 Time: 10:15:49 PM
Interface
interface IGVFeatureReader
Interface to replace the Tribb le equivalent. Returns plain "Iterator" rather than "C...
class IntervalListCodec
Created by jrobinso on 8/13/18 .
class Locus
A minimal representation of a Feature.
class MUTCodec
Codec for .mut and .maf mutati on files
class PAFCodec
Created by jrobinso on 10/31/1 7. reference: https://github. com/lh3/miniasm/blob/mast...
class PAFFeature
Created by jrobinso on 10/31/1 7.
class PSLCodec
class REPMaskCodec
Basically BED format with some columns rearranged Columns, from UCSC documentation 0...
class TribbleIndexNotFoundException
Thrown when an index is not fo und, but required. This class extends Exception, as op...
class TribbleReaderWrapper
Abstract
abstract class UCSCCodec
class UCSCGeneTableCodec
class UCSCSnpCodec
Created by jrobinso on 5/26/15 .
class VCFFeature
class VCFWrapperCodec
class AsciiFeatureCodec
Interface
interface IGVFeature
Interface
interface Feature
class? Exception
class AbstractFeatureCodec
Abstract
abstract class AbstractCacher
Class to handle caching data f rom any source of features Su bclasses must override qu...
Interface
interface FeatureCodec
wrappedCodecheaderheaderheaderwrappedCodec