Package org.broadinstitute.hellbender.utils.codecs.gtf

Class GencodeGtfUTRFeature

java.lang.Object

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

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfUTRFeature

All Implemented Interfaces:

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

public final class GencodeGtfUTRFeature
extends GencodeGtfFeature

A Gencode GTF Feature representing an untranslated region. 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	Description
static GencodeGtfFeature	create(String[] gtfFields, String gtfFileType)
static GencodeGtfFeature	create(GencodeGtfFeatureBaseData baseData)

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 Details

create

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

create

public static GencodeGtfFeature create(GencodeGtfFeatureBaseData baseData)