Uses of Class
org.snpeff.interval.Genome
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Uses of Genome in org.snpeff
Fields in org.snpeff declared as Genome Modifier and Type Field Description protected Genome
SnpEff. genome
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Uses of Genome in org.snpeff.binseq
Constructors in org.snpeff.binseq with parameters of type Genome Constructor Description GenomicSequences(Genome genome)
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Uses of Genome in org.snpeff.codons
Methods in org.snpeff.codons with parameters of type Genome Modifier and Type Method Description java.lang.String
CodonTables. aa(java.lang.String codon, Genome genome, java.lang.String chromosome)
Translate a codon into an amino acid for a given genome+chromosomejava.lang.String
CodonTables. codon(java.lang.String aa, Genome genome, java.lang.String chromosome)
Translate an amino acid into a codon for a given genome+chromosomeCodonTable
CodonTables. getTable(Genome genome)
Get default genome-wide codon tableCodonTable
CodonTables. getTable(Genome genome, java.lang.String chromosome)
Get 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 Constructor Description FindRareAaIntervals(Genome genome)
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Uses of Genome in org.snpeff.fileIterator
Fields in org.snpeff.fileIterator declared as Genome Modifier and Type Field Description protected Genome
MarkerFileIterator. genome
protected Genome
VcfHapMapFileIterator. genome
Methods in org.snpeff.fileIterator that return Genome Modifier and Type Method Description Genome
MarkerFileIterator. getGenome()
Constructors in org.snpeff.fileIterator with parameters of type Genome Constructor Description BedFileIterator(java.lang.String fileName, Genome genome)
Gff3FileIterator(java.lang.String fileName, Genome genome)
Gff3FileIterator(java.lang.String fileName, Genome genome, int inOffset)
MarkerFileIterator(java.lang.String fileName, Genome genome, int inOffset)
MotifFileIterator(java.lang.String fileName, Genome genome, Jaspar jaspar)
RegulationBedFileIterator(java.lang.String fileName, Genome genome, java.lang.String name, java.lang.String cellType)
RegulationFileIterator(java.lang.String fileName, Genome genome, int inOffset)
RegulationGffFileIterator(java.lang.String fileName, Genome genome)
VariantFileIterator(java.lang.String fileName, Genome genome)
VariantTxtFileIterator(java.lang.String fileName, Genome genome)
VcfFileIterator(java.lang.String fileName, Genome genome)
VcfHapMapFileIterator(java.lang.String hapMapFileName, java.lang.String fatsaFileName, Genome genome)
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Uses of Genome in org.snpeff.fileIterator.microCosm
Methods in org.snpeff.fileIterator.microCosm with parameters of type Genome Modifier and Type Method Description MicroRnaBindingSite
MicroCosmEntry. getMarker(Genome genome)
Create a MicroRnaBindingSite marker -
Uses of Genome in org.snpeff.interval
Methods in org.snpeff.interval that return Genome Modifier and Type Method Description static Genome
Genome. createFromFaidx(java.lang.String genomeName, java.lang.String faidxFile)
Create a genome from a faidx file.Genome
Interval. getGenome()
Find genomeMethods in org.snpeff.interval with parameters of type Genome Modifier and Type Method Description void
Markers. load(java.lang.String fileName, Genome genome)
protected void
GffMarker. parse(Genome genome, java.lang.String line)
Parse an entry (line) from a GFF filevoid
Marker. readTxt(java.lang.String line, int lineNum, Genome genome, int positionBase)
Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"static Markers
MarkerUtil. readTxt(java.lang.String fileName, Genome genome, int positionBase)
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 Genome Constructor Description Chromosome(Genome parent, int start, int end, java.lang.String id)
CytoBands(Genome genome)
ExonSpliceCharacterizer(Genome genome)
Genes(Genome genome)
GffMarker(Genome genome, java.lang.String line)
Gtf2Marker(Genome genome, java.lang.String line)
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Uses of Genome in org.snpeff.interval.tree
Methods in org.snpeff.interval.tree with parameters of type Genome Modifier and Type Method Description void
IntervalTree. load(java.lang.String fileName, Genome genome)
void
IntervalTreeArray. load(java.lang.String fileName, Genome genome)
void
IntervalTreeOri. load(java.lang.String fileName, Genome genome)
void
Itree. load(java.lang.String fileName, Genome genome)
Load intervals from file -
Uses of Genome in org.snpeff.probablility
Constructors in org.snpeff.probablility with parameters of type Genome Constructor Description RandMarker(Genome genome)
RandMarker(Genome genome, int seed)
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Uses of Genome in org.snpeff.serializer
Constructors in org.snpeff.serializer with parameters of type Genome Constructor Description MarkerSerializer(Genome genome)
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Uses of Genome in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as Genome Modifier and Type Field Description protected Genome
Hgvs. genome
Methods in org.snpeff.snpEffect that return Genome Modifier and Type Method Description Genome
Config. getGenome()
Genome
Config. getGenome(java.lang.String genomeId)
Genome
SnpEffectPredictor. getGenome()
Constructors in org.snpeff.snpEffect with parameters of type Genome Constructor Description SnpEffectPredictor(Genome genome)
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Uses of Genome in org.snpeff.snpEffect.testCases.integration
Methods in org.snpeff.snpEffect.testCases.integration with parameters of type Genome Modifier and Type Method Description java.lang.String
TestCasesIntegrationBase. showTranscripts(Genome genome)
java.lang.String
TestCasesIntegrationBase. showTranscripts(Genome genome, boolean hideProtein)
Show a genome in a 'standard' way -
Uses of Genome in org.snpeff.snpEffect.testCases.unity
Fields in org.snpeff.snpEffect.testCases.unity declared as Genome Modifier and Type Field Description protected Genome
TestCasesBase. genome
protected Genome
TestCasesIntervalTree. genome
protected Genome
TestCasesVariantDecompose. genome
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Genome Modifier and Type Method Description java.lang.String
TestCasesBase. showTranscripts(Genome genome)
Show a genome in a 'standard' way -
Uses of Genome in org.snpeff.spliceSites
Constructors in org.snpeff.spliceSites with parameters of type Genome Constructor Description TranscriptSet(Genome genome)
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Uses of Genome in org.snpeff.stats
Constructors in org.snpeff.stats with parameters of type Genome Constructor Description VariantEffectStats(Genome genome)
VariantStats(Genome genome)
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