Uses of Class
org.snpeff.interval.Genome
Packages that use Genome
Package
Description
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Uses of Genome in org.snpeff
Fields in org.snpeff declared as Genome -
Uses of Genome in org.snpeff.binseq
Constructors in org.snpeff.binseq with parameters of type Genome -
Uses of Genome in org.snpeff.codons
Methods in org.snpeff.codons with parameters of type GenomeModifier and TypeMethodDescriptionTranslate a codon into an amino acid for a given genome+chromosomeTranslate an amino acid into a codon for a given genome+chromosomeGet default genome-wide codon tableGet a codon table WARNING: It will return the standard codon table if nothing if foundvoid
CodonTables.set
(Genome genome, CodonTable codonTable) Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome tablevoid
CodonTables.set
(Genome genome, Chromosome chr, CodonTable codonTable) Set a codon table for a given genome & chromosomeConstructors in org.snpeff.codons with parameters of type Genome -
Uses of Genome in org.snpeff.fileIterator
Fields in org.snpeff.fileIterator declared as GenomeModifier and TypeFieldDescriptionprotected Genome
MarkerFileIterator.genome
protected Genome
VcfHapMapFileIterator.genome
Methods in org.snpeff.fileIterator that return GenomeConstructors in org.snpeff.fileIterator with parameters of type GenomeModifierConstructorDescriptionBedFileIterator
(String fileName, Genome genome) Gff3FileIterator
(String fileName, Genome genome) Gff3FileIterator
(String fileName, Genome genome, int inOffset) MarkerFileIterator
(String fileName, Genome genome, int inOffset) MotifFileIterator
(String fileName, Genome genome, Jaspar jaspar) RegulationBedFileIterator
(String fileName, Genome genome, String name, String cellType) RegulationFileIterator
(String fileName, Genome genome, int inOffset) RegulationGffFileIterator
(String fileName, Genome genome) VariantFileIterator
(String fileName, Genome genome) VariantTxtFileIterator
(String fileName, Genome genome) VcfFileIterator
(String fileName, Genome genome) VcfHapMapFileIterator
(String hapMapFileName, String fatsaFileName, Genome genome) -
Uses of Genome in org.snpeff.fileIterator.microCosm
Methods in org.snpeff.fileIterator.microCosm with parameters of type GenomeModifier and TypeMethodDescriptionCreate a MicroRnaBindingSite marker -
Uses of Genome in org.snpeff.interval
Methods in org.snpeff.interval that return GenomeModifier and TypeMethodDescriptionstatic Genome
Genome.createFromFaidx
(String genomeName, String faidxFile) Create a genome from a faidx file.Interval.getGenome()
Find genomeMethods in org.snpeff.interval with parameters of type GenomeModifier and TypeMethodDescriptionvoid
protected void
Parse an entry (line) from a GFF filevoid
Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"static Markers
Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positionsConstructors in org.snpeff.interval with parameters of type GenomeModifierConstructorDescriptionChromosome
(Genome parent, int start, int end, String id) ExonSpliceCharacterizer
(Genome genome) Gtf2Marker
(Genome genome, String line) -
Uses of Genome in org.snpeff.interval.tree
Methods in org.snpeff.interval.tree with parameters of type Genome -
Uses of Genome in org.snpeff.probablility
Constructors in org.snpeff.probablility with parameters of type Genome -
Uses of Genome in org.snpeff.serializer
Constructors in org.snpeff.serializer with parameters of type Genome -
Uses of Genome in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as GenomeMethods in org.snpeff.snpEffect that return GenomeConstructors in org.snpeff.snpEffect with parameters of type GenomeModifierConstructorDescriptionThis constructor is used in test casesSnpEffectPredictor
(Genome genome) -
Uses of Genome in org.snpeff.spliceSites
Constructors in org.snpeff.spliceSites with parameters of type Genome -
Uses of Genome in org.snpeff.stats
Constructors in org.snpeff.stats with parameters of type Genome