Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGtf22
- java.lang.Object
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
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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
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryGtf22(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
parse(java.lang.String line)
Parse a line-
Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, readExonSequences, readExonSequencesGff, readGff
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Methods inherited from class org.snpeff.snpEffect.factory.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, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Detail
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SnpEffPredictorFactoryGtf22
public SnpEffPredictorFactoryGtf22(Config config)
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Method Detail
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parse
protected boolean parse(java.lang.String line)
Description copied from class:SnpEffPredictorFactoryGff
Parse a line- Overrides:
parse
in classSnpEffPredictorFactoryGff
- Returns:
- true if a line was parsed
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