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Package org.broad.igv.feature.tribble

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