SnpEffPredictorFactoryGtf22 (SnpEff 5.4 API)

java.lang.Object

org.snpeff.snpEffect.factory.SnpEffPredictorFactory

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22

public class SnpEffPredictorFactoryGtf22 extends SnpEffPredictorFactoryGff

This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html

Author:: pcingola

Field Summary

Fields inherited from class SnpEffPredictorFactoryGff
FASTA_DELIMITER

Fields inherited from class SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
Constructor Summary

Constructors

Constructor

Description

SnpEffPredictorFactoryGtf22(Config config)
Method Summary

Modifier and Type

Method

Description

protected boolean

parse(String line)

Parse a line

Methods inherited from class SnpEffPredictorFactoryGff
addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, readExonSequences, readExonSequencesGff, readGff

Methods inherited from class SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, getProteinByTrId, parsePosition, replaceTranscript, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SnpEffPredictorFactoryGtf22
  
  public SnpEffPredictorFactoryGtf22(Config config)
Method Details
- parse
  
  protected boolean parse(String line)
  
  Description copied from class: SnpEffPredictorFactoryGff
  
  Parse a line
  
  Overrides:
  
  parse in class SnpEffPredictorFactoryGff
  
  Returns:
  
  true if a line was parsed