Constant Field Values
Contents
org.snpeff.*
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org.snpeff.Fastq2Fastq
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org.snpeff.Pcingola
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org.snpeff.Qseq2Fastq
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org.snpeff.SnpEffModifier and TypeConstant FieldValue
public static final String
"2023-11-28 15:56"
public static final String
"2023-11-28 15:56"
public static final int
40
public static final String
"ann"
public static final String
"b"
public static final String
"SnpEff"
public static final String
"SnpEff 5.2b (build 2023-11-28 15:56), by Pablo Cingolani"
public static final String
"5.2b (build 2023-11-28 15:56), by Pablo Cingolani"
public static final String
"5.2b (build 2023-11-28 15:56)"
public static final String
"5.2"
public static final String
"5.2b"
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org.snpeff.align.VariantRealignModifier and TypeConstant FieldValue
public static final int
10
public static final int
3
public static final int
100
public static final int
1
public static final int
2
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org.snpeff.align.VcfRefAltAlign
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org.snpeff.binseq.DnaSequenceByteModifier and TypeConstant FieldValue
public static final int
4
public static final int
2
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org.snpeff.binseq.GenomicSequencesModifier and TypeConstant FieldValue
public static final int
1000000
public static final int
1000000
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org.snpeff.binseq.coder.CoderModifier and TypeConstant FieldValue
public static final int
64
public static final int
8
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org.snpeff.binseq.coder.DnaCoderModifier and TypeConstant FieldValue
protected static final int
32
protected static final int
2
protected static final int
31
public static final long
-1L
protected static final long
3L
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org.snpeff.binseq.coder.DnaQualityCoderModifier and TypeConstant FieldValue
public static final int
63
public static final int
0
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org.snpeff.codons.CodonTable
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org.snpeff.codons.CodonTablesModifier and TypeConstant FieldValue
public static final String
"TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G"
public static final String
"Standard"
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org.snpeff.codons.FindRareAaIntervals
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org.snpeff.collections.HashLongLongArray
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org.snpeff.coverage.CountReadsOnMarkersModifier and TypeConstant FieldValue
public static final int
10
public static final int
10000
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org.snpeff.fastq.FastqSplit
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org.snpeff.fileIterator.LineClassFileIterator<T>
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org.snpeff.fileIterator.MotifFileIterator
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org.snpeff.fileIterator.RegulationBedFileIterator
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org.snpeff.fileIterator.RegulationGffFileIterator
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org.snpeff.fileIterator.TableFile
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org.snpeff.fileIterator.VcfFileIterator
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org.snpeff.genBank.EmblModifier and TypeConstant FieldValue
public static final int
5
public static final int
15
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org.snpeff.genBank.Feature
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org.snpeff.genBank.Features
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org.snpeff.genBank.GenBank
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org.snpeff.geneSets.algorithm.EnrichmentAlgorithmModifier and TypeConstant FieldValue
public static final String
"cccccc"
public static final int
40
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org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
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org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithmModifier and TypeConstant FieldValue
public static final double
0.05
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org.snpeff.gsa.ScoreList
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org.snpeff.gtex.Gtex
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org.snpeff.interval.CytoBands
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org.snpeff.interval.ExonSpliceCharacterizerModifier and TypeConstant FieldValue
public static final int
1000
public static final int
1000
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org.snpeff.interval.Gene
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org.snpeff.interval.GffMarkerModifier and TypeConstant FieldValue
public static final String
"biotype"
public static final String
"db_xref"
public static final String
"exon_id"
public static final String
"gene"
public static final String
"gene_biotype"
public static final String
"gene_id"
public static final String
"gene_name"
public static final String
"gene_type"
public static final String
"ID"
public static final String
"name"
public static final String
"Name"
public static final String
"Parent"
public static final String
"protein_id"
public static final String
"tag"
public static final String
"transcript_id"
public static final String
"transcript_support_level"
public static final String
"transcript_version"
public static final String
";"
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org.snpeff.interval.Intergenic
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org.snpeff.interval.MotifModifier and TypeConstant FieldValue
public static final boolean
false
public static final double
0.01
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org.snpeff.interval.ProteinInteractionLocus
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org.snpeff.interval.SpliceSiteModifier and TypeConstant FieldValue
public static final int
2
public static final int
3
public static final int
8
public static final int
3
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org.snpeff.interval.TranscriptSupportLevel
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org.snpeff.interval.VariantModifier and TypeConstant FieldValue
public static final double
0.01
public static final int
1000000
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org.snpeff.interval.codonChange.CodonChange
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org.snpeff.interval.tree.IntervalTreeArrayModifier and TypeConstant FieldValue
public static final int
1024
public static final int
4
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org.snpeff.logStatsServer.LogStatsModifier and TypeConstant FieldValue
public static final int
1000
public static final int
5
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org.snpeff.logStatsServer.VersionCheckModifier and TypeConstant FieldValue
public static final int
1000
public static final int
3
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org.snpeff.motif.Pwm
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org.snpeff.nextProt.NextProtSequenceConservationModifier and TypeConstant FieldValue
public static final int
5
public static final double
0.99
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org.snpeff.nmer.Nmer
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org.snpeff.outputFormatter.VcfOutputFormatter
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org.snpeff.pdb.PdbFile
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org.snpeff.pdb.ProteinInteractionsModifier and TypeConstant FieldValue
public static final double
3.0
public static final double
0.05
public static final String
"db/pdb"
public static final int
20
public static final String
"HUMAN"
public static final String
"HOMO SAPIENS"
public static final double
3.0
public static final String
"interactions.bin"
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org.snpeff.ped.TfamEntryModifier and TypeConstant FieldValue
public static final int
2
public static final int
1
public static final int
-9
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org.snpeff.probablility.NormalDistribution
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org.snpeff.probablility.RankSumPdfModifier and TypeConstant FieldValue
public static final int
40
public static final int
40
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org.snpeff.reactome.ReactomeModifier and TypeConstant FieldValue
public static final double
1.0E-6
public static final double
0.001
public static final int
1000
public static final int
10000
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org.snpeff.reactome.events.Reaction
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org.snpeff.snpEffect.ConfigModifier and TypeConstant FieldValue
public static final String
"snpEff.config"
public static final String
"./data"
public static final String
"/etc/snpeff/snpEff.config"
public static final String
".bundle"
public static final String
"codon."
public static final String
".codonTable"
public static final String
"coordinates"
public static final String
"data.dir"
public static final String
"database"
public static final String
"database.repository"
public static final String
"database.repositoryKey"
public static final String
"dbnsfp.fields"
public static final String
".genome"
public static final String
"lof.deleteProteinCodingBases"
public static final String
"lof.ignoreProteinCodingAfter"
public static final String
"lof.ignoreProteinCodingBefore"
public static final String
".reference"
public static final String
"versions.url"
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org.snpeff.snpEffect.Hgvs
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org.snpeff.snpEffect.LossOfFunction
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org.snpeff.snpEffect.PurityChangeModifier and TypeConstant FieldValue
public static final int
5
public static final int
3
public static final boolean
false
public static final String
"\t"
public static final int
2
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org.snpeff.snpEffect.SnpEffectPredictorModifier and TypeConstant FieldValue
public static final int
5000
public static final int
10
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org.snpeff.snpEffect.VariantEffect
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org.snpeff.snpEffect.commandLine.SnpEffCmdAcatModifier and TypeConstant FieldValue
public static final String
"ACAT"
public static final double
0.99
public static final String
"NCACTIVITY"
public static final String
"NCCAT"
public static final String
"NCCONS"
public static final String
"NCELEMENT"
public static final String
"NCFACTOR"
public static final String
"NCMARK"
public static final String
"T2D_GENES"
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org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
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org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
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org.snpeff.snpEffect.commandLine.SnpEffCmdEffModifier and TypeConstant FieldValue
public static final String
"snpEff_summary.csv"
public static final String
"snpEff_genes.txt"
public static final String
"snpEff_summary.html"
public static final int
10000
public static final String
"snpEff_csv_summary.ftl"
public static final String
"snpEff_genes.ftl"
public static final String
"snpEff_summary.ftl"
public static final String
"src/main/resources"
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org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
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org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
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org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
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org.snpeff.spliceSites.AcgtTreeModifier and TypeConstant FieldValue
public static final int
1
public static final double
2.0
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org.snpeff.spliceSites.SnpEffCmdSpliceAnalysisModifier and TypeConstant FieldValue
public static final double
0.95
public static final int
100
public static final double
0.05
public static final double
0.95
public static final double
5.0
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org.snpeff.spliceSites.SpliceTypesModifier and TypeConstant FieldValue
public static final int
100
public static final double
0.05
public static final double
0.95
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org.snpeff.spliceSites.TranscriptSet
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org.snpeff.stats.AlleleCountStats
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org.snpeff.stats.CountByType
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org.snpeff.stats.PosStats
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org.snpeff.stats.VariantEffectStats
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org.snpeff.stats.VariantStats
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org.snpeff.stats.VariantTypeStats
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org.snpeff.stats.plot.GooglePlot
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org.snpeff.stats.plot.GooglePlotInt
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org.snpeff.svg.SvgModifier and TypeConstant FieldValue
public static final int
10
public static final int
1000
public static final int
1000
public static final String
"#000000"
public static final int
1
public static final String
"#FFFFFF"
public static final String
"#000000"
public static final int
20
public static final int
1
public static final int
10
public static final String
"font-family: Arial; font-size:10;"
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org.snpeff.svg.SvgBnd
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org.snpeff.svg.SvgIntron
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org.snpeff.svg.SvgScaleModifier and TypeConstant FieldValue
public static final int
30
public static final int
20
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org.snpeff.util.Download
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org.snpeff.util.Gpr
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org.snpeff.util.GprSeqModifier and TypeConstant FieldValue
public static final char
'!'
public static final byte
0xff
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org.snpeff.util.IubString
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org.snpeff.util.LogModifier and TypeConstant FieldValue
public static final int
10
public static final int
25
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org.snpeff.vcf.EffFormatVersion
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org.snpeff.vcf.FileIndexChrPos
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org.snpeff.vcf.VcfConsequence
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org.snpeff.vcf.VcfEntryModifier and TypeConstant FieldValue
public static final double
0.05
public static final double
0.01
public static final String
"PASS"
public static final String
";"
public static final String
"*"
public static final String
"<*>"
public static final String
"<NON_REF>"
public static final String
"END"
public static final String
"HE"
public static final String
"HO"
public static final String
"NA"
public static final String
"Private"
public static final char
','
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org.snpeff.vcf.VcfGenotype
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org.snpeff.vcf.VcfHeader