org.broadinstitute.hellbender.utils.codecs.gtf

Class GencodeGtfSelenocysteineFeature

java.lang.Object

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfSelenocysteineFeature

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, java.lang.Comparable<GencodeGtfFeature>

public final class GencodeGtfSelenocysteineFeature
extends GencodeGtfFeature

A Gencode GTF Feature representing a selenocysteine. A GTF Feature represents one row of a GTF File. The specification of a GTF file is defined here: http://mblab.wustl.edu/GTF22.html Created by jonn on 7/25/17.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

GencodeGtfFeature.AnnotationSource, GencodeGtfFeature.FeatureTag, GencodeGtfFeature.FeatureType, GencodeGtfFeature.GeneTranscriptStatus, GencodeGtfFeature.GenomicPhase, GencodeGtfFeature.KnownGeneBiotype, GencodeGtfFeature.LocusLevel, GencodeGtfFeature.OptionalField<T>, GencodeGtfFeature.RemapStatus, GencodeGtfFeature.RemapTargetStatus, GencodeGtfFeature.TranscriptSupportLevel

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

ANNOTATION_SOURCE_ENA, ANNOTATION_SOURCE_ENSEMBL, ANNOTATION_SOURCE_HAVANA, EXTRA_FIELD_KEY_VALUE_SPLITTER, NO_EXON_NUMBER, NO_FEATURE_ORDER

Method Summary

Modifier and Type	Method and Description
static GencodeGtfFeature	create(GencodeGtfFeatureBaseData baseData)
static GencodeGtfFeature	create(java.lang.String[] gtfFields, java.lang.String gtfFileType)

Methods inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

compareTo, contains, create, equals, getAnnotationSource, getAnonymousOptionalFields, getChromosomeName, getContig, getEnd, getExonId, getExonNumber, getFeatureOrderNumber, getFeatureType, getGeneId, getGeneName, getGeneStatus, getGeneType, getGenomicEndLocation, getGenomicPhase, getGenomicPosition, getGenomicStartLocation, getGenomicStrand, getGtfSourceFileType, getLocusLevel, getOptionalField, getOptionalFields, getStart, getTranscriptId, getTranscriptName, getTranscriptStatus, getTranscriptType, getUcscGenomeVersion, hashCode, overlaps, serializeToString, setFeatureOrderNumber, setUcscGenomeVersion, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contigsMatch, getLengthOnReference, withinDistanceOf

Method Detail

create

public static GencodeGtfFeature create(java.lang.String[] gtfFields,
                                       java.lang.String gtfFileType)

create

public static GencodeGtfFeature create(GencodeGtfFeatureBaseData baseData)