Uses of Class
org.snpeff.interval.GffMarker
Packages that use GffMarker
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Uses of GffMarker in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return GffMarker -
Uses of GffMarker in org.snpeff.interval
Subclasses of GffMarker in org.snpeff.interval -
Uses of GffMarker in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory with parameters of type GffMarkerModifier and TypeMethodDescriptionprotected Exon
SnpEffPredictorFactoryGff.addExon
(Transcript tr, GffMarker gffMarker, String exonId) Create a new exonCreate and add a new exonprotected Gene
protected Gene
Create and add a gene based on GffMarkerprotected IntergenicConserved
SnpEffPredictorFactoryGff.addIntergenicConserved
(GffMarker gffMarker) Add an intergenic conserved regionprotected boolean
SnpEffPredictorFactoryGff.addInterval
(GffMarker gffMarker) Add interval based on GffMarker dataprotected IntronConserved
SnpEffPredictorFactoryGff.addIntronConserved
(GffMarker gffMarker) Add an intron conserved regionCreate new UTR3primesCreate UTR5primesprotected Exon
SnpEffPredictorFactoryGff.findOrCreateExon
(String parentId, GffMarker gffMarker) Find an exon for a given parentIdprotected Gene
SnpEffPredictorFactoryGff.findOrCreateGene
(GffMarker gffMarker) Find or create a gene based on GffMarkerprotected Transcript
SnpEffPredictorFactoryGff.findOrCreateTranscript
(GffMarker gffMarker) Create and add a transcript based on GffMarker