# Serialized Form

## Package org.snpeff.binseq

### Class org.snpeff.binseq.BinarySequence

class BinarySequence extends Object implements Serializable

serialVersionUID:
  2349094116844619569L

### Class org.snpeff.binseq.DnaAndQualitySequence

class DnaAndQualitySequence extends BinarySequence implements Serializable

serialVersionUID:
  4523047567848438494L

#### Serialized Fields

##### codes

    byte[] codes

### Class org.snpeff.binseq.DnaAndQualitySequenceWithId

class DnaAndQualitySequenceWithId extends DnaAndQualitySequence implements Serializable

serialVersionUID:
  4523294567844568494L

#### Serialized Fields

##### id

    long id

### Class org.snpeff.binseq.DnaNSequence

class DnaNSequence extends DnaSequence implements Serializable

serialVersionUID:
  843945646419836582L

#### Serialized Fields

##### hasN

    OpenBitSet hasN

### Class org.snpeff.binseq.DnaSequence

class DnaSequence extends BinarySequence implements Serializable

serialVersionUID:
  4523047339848048494L

#### Serialized Fields

##### coder

    DnaCoder coder

##### codes

    long[] codes

##### length

    int length

### Class org.snpeff.binseq.DnaSequenceId

class DnaSequenceId extends DnaSequence implements Serializable

serialVersionUID:
  452657339854548494L

#### Serialized Fields

##### id

    long id

### Class org.snpeff.binseq.DnaSequencePe

class DnaSequencePe extends BinarySequence implements Serializable

serialVersionUID:
  -7267466011654235050L

#### Serialized Fields

##### gap

    int gap

##### seq1

    DnaSequence seq1

##### seq2

    DnaSequence seq2

### Class org.snpeff.binseq.GenomicSequences

class GenomicSequences extends Object implements Serializable

serialVersionUID:
  2339867422366567569L

#### Serialized Fields

##### allSmallLoaded

    boolean allSmallLoaded

##### debug

    boolean debug

##### disableLoad

    boolean disableLoad

##### genome

    Genome genome

##### intervalForest

    IntervalForest intervalForest

##### verbose

    boolean verbose

## Package org.snpeff.binseq.coder

### Class org.snpeff.binseq.coder.Coder

class Coder extends Object implements Serializable

### Class org.snpeff.binseq.coder.DnaCoder

class DnaCoder extends Coder implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### COUNT_DIFFS

    int[] COUNT_DIFFS

##### MASK_BASE

    long[] MASK_BASE

##### MASK_HIGH

    long[] MASK_HIGH

##### MASK_LOW

    long[] MASK_LOW

### Class org.snpeff.binseq.coder.DnaQualityCoder

class DnaQualityCoder extends DnaCoder implements Serializable

## Package org.snpeff.collections

### Class org.snpeff.collections.AutoHashMap

class AutoHashMap extends HashMap<K,V> implements Serializable

serialVersionUID:
  255818677257868365L

#### Serialized Fields

##### instance

    V instance

### Class org.snpeff.collections.MultivalueHashMap

class MultivalueHashMap extends HashMap<K,LinkedList<V>> implements Serializable

serialVersionUID:
  -8860279543165990227L

### Class org.snpeff.collections.OpenBitSet

class OpenBitSet extends Object implements Serializable

#### Serialized Fields

##### bits

    long[] bits

##### wlen

    int wlen

## Package org.snpeff.coverage

### Class org.snpeff.coverage.CountFragments

class CountFragments extends Object implements Serializable

serialVersionUID:
  1150158182247576450L

#### Serialized Fields

##### coverageByName

    HashMap<String,CoverageChr> coverageByName

### Class org.snpeff.coverage.Coverage

class Coverage extends Object implements Serializable

serialVersionUID:
  1150158182247576450L

#### Serialized Fields

##### coverageByName

    HashMap<String,CoverageChr> coverageByName

### Class org.snpeff.coverage.CoverageChr

class CoverageChr extends Object implements Serializable

serialVersionUID:
  -5620938926858131251L

#### Serialized Fields

##### count

    short[] count

## Package org.snpeff.fileIterator

### Class org.snpeff.fileIterator.TableFile

class TableFile extends Object implements Serializable

serialVersionUID:
  9180460090637138107L

#### Serialized Fields

##### fieldByName

    HashMap<String,Field> fieldByName

##### fieldNames

    String[] fieldNames

##### fieldStr

    String fieldStr

##### fileName

    String fileName

##### hasTitle

    boolean hasTitle

##### separator

    String separator

##### size

    int size

##### verbose

    boolean verbose

## Package org.snpeff.geneOntology

### Class org.snpeff.geneOntology.GoTerm

class GoTerm extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### acc

    String acc

##### childs

    HashSet<GoTerm> childs

##### description

    String description

##### goTerms

    GoTerms goTerms

##### interestingSymbolIdSet

    HashSet<String> interestingSymbolIdSet

##### level

    int level

##### maxRank

    int maxRank

##### nameSpace

    String nameSpace

##### parents

    HashSet<GoTerm> parents

##### rankedSymbols

    int rankedSymbols

##### rankSum

    long rankSum

##### symbolIdSet

    HashSet<String> symbolIdSet

### Class org.snpeff.geneOntology.GoTerms

class GoTerms extends Object implements Serializable

#### Serialized Fields

##### goTermsByGoTermAcc

    HashMap<String,GoTerm> goTermsByGoTermAcc

##### goTermsBySymbolId

    HashMap<String,Set<GoTerm>> goTermsBySymbolId

##### interestingSymbolIdsSet

    HashSet<String> interestingSymbolIdsSet

##### label

    String label

##### maxRank

    int maxRank

##### nameSpace

    String nameSpace

##### rankSymbolId

    HashMap<String,Integer> rankSymbolId

## Package org.snpeff.geneSets

### Class org.snpeff.geneSets.GeneSet

class GeneSet extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### description

    String description

##### genes

    HashSet<String> genes

##### geneSets

    GeneSets geneSets

##### interestingGenesCount

    int interestingGenesCount

##### maxRank

    int maxRank

##### name

    String name

##### rankedGenesCount

    int rankedGenesCount

##### rankSum

    long rankSum

### Class org.snpeff.geneSets.GeneSets

class GeneSets extends Object implements Serializable

serialVersionUID:
  -359594418467719013L

#### Serialized Fields

##### doNotAddIfNotInGeneSet

    boolean doNotAddIfNotInGeneSet

##### genes

    HashSet<String> genes

##### geneSetsByGene

    HashMap<String,HashSet<GeneSet>> geneSetsByGene

##### geneSetsByName

    HashMap<String,GeneSet> geneSetsByName

##### interestingGenes

    HashSet<String> interestingGenes

##### label

    String label

##### valueByGene

    HashMap<String,Double> valueByGene

##### verbose

    boolean verbose

### Class org.snpeff.geneSets.GeneSetsRanked

class GeneSetsRanked extends GeneSets implements Serializable

serialVersionUID:
  -7922357470081599803L

#### Serialized Fields

##### maxRank

    int maxRank

##### rankByGene

    HashMap<String,Integer> rankByGene

## Package org.snpeff.genotypes

### Class org.snpeff.genotypes.Genotypes

class Genotypes extends Object implements Serializable

serialVersionUID:
  5417498450863908076L

#### Serialized Fields

##### genotypeVectors

    GenotypeVector[] genotypeVectors

##### vcfFileName

    String vcfFileName

### Class org.snpeff.genotypes.GenotypeVector

class GenotypeVector extends Object implements Serializable

serialVersionUID:
  4734574592894281057L

#### Serialized Fields

##### genotype

    byte[] genotype

##### size

    int size

## Package org.snpeff.interval

### Class org.snpeff.interval.Cds

class Cds extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

#### Serialized Fields

##### frame

    byte frame

### Class org.snpeff.interval.Chromosome

class Chromosome extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

#### Serialized Fields

##### chromosomeNum

    double chromosomeNum

##### circular

    boolean circular

##### sequence

    DnaSequence sequence

### Class org.snpeff.interval.Custom

class Custom extends Marker implements Serializable

serialVersionUID:
  -6843535415295857726L

#### Serialized Fields

##### label

    String label

##### score

    double score

### Class org.snpeff.interval.Downstream

class Downstream extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

### Class org.snpeff.interval.Exon

class Exon extends MarkerSeq implements Serializable

serialVersionUID:
  5324352193278472543L

#### Serialized Fields

##### aaIdxEnd

    int aaIdxEnd

##### aaIdxStart

    int aaIdxStart

##### frame

    byte frame

##### rank

    int rank

##### spliceSites

    ArrayList<SpliceSite> spliceSites

##### spliceType

    Exon.ExonSpliceType spliceType

### Class org.snpeff.interval.Gene

class Gene extends IntervalAndSubIntervals<Transcript> implements Serializable

serialVersionUID:
  8419206759034068147L

#### Serialized Fields

##### bioType

    BioType bioType

##### geneName

    String geneName

##### intervalTreeGene

    Itree intervalTreeGene

### Class org.snpeff.interval.GenericMarker

class GenericMarker extends Marker implements Serializable

serialVersionUID:
  -1645062778820144533L

#### Serialized Fields

##### line

    String line

### Class org.snpeff.interval.Genes

class Genes extends Object implements Serializable

serialVersionUID:
  9022385501946879197L

#### Serialized Fields

##### debug

    boolean debug

##### genesById

    HashMap<String,Gene> genesById

##### genome

    Genome genome

### Class org.snpeff.interval.Genome

class Genome extends Marker implements Serializable

serialVersionUID:
  -330362012383572257L

#### Serialized Fields

##### chromoFastaFiles

    String[] chromoFastaFiles

##### chromosomeNamesSorted

    List<String> chromosomeNamesSorted

##### chromosomes

    HashMap<String,Chromosome> chromosomes

##### codingInfo

    Boolean codingInfo

##### cytoBands

    CytoBands cytoBands

##### fastaDir

    String fastaDir

##### genes

    Genes genes

##### genomeId

    int genomeId

##### genomicSequences

    GenomicSequences genomicSequences

##### length

    long length

##### species

    String species

##### transcriptSupportLevelInfo

    Boolean transcriptSupportLevelInfo

##### version

    String version

### Class org.snpeff.interval.GffMarker

class GffMarker extends Custom implements Serializable

serialVersionUID:
  -164502778854644537L

#### Serialized Fields

##### frame

    int frame

##### gffType

    GffType gffType

##### gffTypeStr

    String gffTypeStr

##### keys

    Set<String> keys

##### keyValues

    Map<String,String> keyValues

##### source

    String source

### Class org.snpeff.interval.Gtf2Marker

class Gtf2Marker extends GffMarker implements Serializable

serialVersionUID:
  5416962964309837838L

### Class org.snpeff.interval.Intergenic

class Intergenic extends Marker implements Serializable

serialVersionUID:
  -2487664381262354896L

#### Serialized Fields

##### name

    String name

### Class org.snpeff.interval.IntergenicConserved

class IntergenicConserved extends Marker implements Serializable

serialVersionUID:
  -1816568396090993792L

### Class org.snpeff.interval.Interval

class Interval extends Object implements Serializable

serialVersionUID:
  -3547434510230920403L

#### Serialized Fields

##### chromosomeNameOri

    String chromosomeNameOri

##### end

    int end

##### id

    String id

##### parent

    Interval parent

##### start

    int start

##### strandMinus

    boolean strandMinus

### Class org.snpeff.interval.IntervalAndSubIntervals

class IntervalAndSubIntervals extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

#### Serialized Fields

##### sorted

    List<T extends Marker> sorted

##### sortedStrand

    List<T extends Marker> sortedStrand

##### subIntervals

    Map<String,T extends Marker> subIntervals

### Class org.snpeff.interval.Intron

class Intron extends Marker implements Serializable

serialVersionUID:
  -8283322526157264389L

#### Serialized Fields

##### exonAfter

    Exon exonAfter

##### exonBefore

    Exon exonBefore

##### rank

    int rank

##### spliceSites

    ArrayList<SpliceSite> spliceSites

### Class org.snpeff.interval.IntronConserved

class IntronConserved extends Marker implements Serializable

serialVersionUID:
  -3148108162409498012L

### Class org.snpeff.interval.Marker

class Marker extends Interval implements Serializable

serialVersionUID:
  7878886900660027549L

#### Serialized Fields

##### type

    EffectType type

### Class org.snpeff.interval.MarkerParentId

class MarkerParentId extends Marker implements Serializable

#### Serialized Fields

##### parentId

    int parentId

### Class org.snpeff.interval.Markers

class Markers extends Object implements Serializable

serialVersionUID:
  259791388087691277L

#### Serialized Fields

##### markers

    ArrayList<Marker> markers

##### name

    String name

### Class org.snpeff.interval.MarkerSeq

class MarkerSeq extends Marker implements Serializable

serialVersionUID:
  -8794533547221460207L

#### Serialized Fields

##### sequence

    DnaSequence sequence

### Class org.snpeff.interval.MicroRnaBindingSite

class MicroRnaBindingSite extends Marker implements Serializable

serialVersionUID:
  -9089500641817245554L

#### Serialized Fields

##### pValue

    double pValue

### Class org.snpeff.interval.Motif

class Motif extends Marker implements Serializable

serialVersionUID:
  8464487883781181867L

#### Serialized Fields

##### pwm

    Pwm pwm

##### pwmId

    String pwmId

##### pwmName

    String pwmName

### Class org.snpeff.interval.NextProt

class NextProt extends Marker implements Serializable

serialVersionUID:
  8939301304881007289L

#### Serialized Fields

##### highlyConservedAaSequence

    boolean highlyConservedAaSequence

##### name

    String name

##### transcriptId

    String transcriptId

### Class org.snpeff.interval.ProteinInteractionLocus

class ProteinInteractionLocus extends Marker implements Serializable

serialVersionUID:
  1L

### Class org.snpeff.interval.ProteinProteinInteractionLocus

class ProteinProteinInteractionLocus extends ProteinInteractionLocus implements Serializable

serialVersionUID:
  -2111056845758378137L

#### Serialized Fields

##### trInteract

    Transcript trInteract

### Class org.snpeff.interval.ProteinStructuralInteractionLocus

class ProteinStructuralInteractionLocus extends ProteinInteractionLocus implements Serializable

serialVersionUID:
  1416019843839053485L

### Class org.snpeff.interval.RareAminoAcid

class RareAminoAcid extends Marker implements Serializable

serialVersionUID:
  -1926572865764543849L

### Class org.snpeff.interval.Regulation

class Regulation extends Marker implements Serializable

serialVersionUID:
  -5607588295343642199L

#### Serialized Fields

##### name

    String name

##### regulationType

    String regulationType

### Class org.snpeff.interval.SpliceSite

class SpliceSite extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

### Class org.snpeff.interval.SpliceSiteAcceptor

class SpliceSiteAcceptor extends SpliceSite implements Serializable

serialVersionUID:
  -7416687954435361328L

### Class org.snpeff.interval.SpliceSiteBranch

class SpliceSiteBranch extends SpliceSite implements Serializable

serialVersionUID:
  7903892379174750342L

### Class org.snpeff.interval.SpliceSiteBranchU12

class SpliceSiteBranchU12 extends SpliceSiteBranch implements Serializable

serialVersionUID:
  7903892379174750342L

### Class org.snpeff.interval.SpliceSiteDonor

class SpliceSiteDonor extends SpliceSite implements Serializable

serialVersionUID:
  -2117470153797320999L

### Class org.snpeff.interval.SpliceSiteRegion

class SpliceSiteRegion extends SpliceSite implements Serializable

serialVersionUID:
  -7416687954435361328L

### Class org.snpeff.interval.Transcript

class Transcript extends IntervalAndSubIntervals<Exon> implements Serializable

serialVersionUID:
  -2665025617916107311L

#### Serialized Fields

##### aa2pos

    int[] aa2pos

##### aaCheck

    boolean aaCheck

##### bioType

    BioType bioType

##### canonical

    boolean canonical

##### cds

    String cds

##### cds2pos

    int[] cds2pos

##### cdsEnd

    int cdsEnd

##### cdss

    List<Cds> cdss

##### cdsStart

    int cdsStart

##### corrected

    boolean corrected

##### dnaCheck

    boolean dnaCheck

##### downstream

    Downstream downstream

##### firstCodingExon

    Exon firstCodingExon

##### introns

    List<Intron> introns

##### mRna

    String mRna

##### protein

    String protein

##### proteinCoding

    boolean proteinCoding

##### proteinId

    String proteinId

##### ribosomalSlippage

    boolean ribosomalSlippage

##### spliceRegionExonSize

    int spliceRegionExonSize

##### spliceRegionIntronMax

    int spliceRegionIntronMax

##### spliceRegionIntronMin

    int spliceRegionIntronMin

##### spliceSiteSize

    int spliceSiteSize

##### tags

    String tags

##### transcriptSupportLevel

    TranscriptSupportLevel transcriptSupportLevel

##### upDownLength

    int upDownLength

##### upstream

    Upstream upstream

##### utrs

    List<Utr> utrs

##### version

    String version

### Class org.snpeff.interval.Upstream

class Upstream extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

### Class org.snpeff.interval.Utr

class Utr extends Marker implements Serializable

serialVersionUID:
  1636197649250882952L

### Class org.snpeff.interval.Utr3prime

class Utr3prime extends Utr implements Serializable

serialVersionUID:
  5688641008301281991L

### Class org.snpeff.interval.Utr5prime

class Utr5prime extends Utr implements Serializable

serialVersionUID:
  3710420226746056364L

#### Serialized Fields

##### utrs

    List<Utr5prime> utrs

### Class org.snpeff.interval.Variant

class Variant extends Marker implements Serializable

serialVersionUID:
  -2928105165111400441L

#### Serialized Fields

##### alt

    String alt

##### genotype

    String genotype

##### imprecise

    boolean imprecise

##### ref

    String ref

##### variantType

    Variant.VariantType variantType

### Class org.snpeff.interval.VariantBnd

class VariantBnd extends Variant implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### before

    boolean before

##### endPoint

    Marker endPoint

##### left

    boolean left

### Class org.snpeff.interval.VariantNonRef

class VariantNonRef extends Variant implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### variantRef

    Variant variantRef

### Class org.snpeff.interval.VariantWithScore

class VariantWithScore extends Variant implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### score

    double score

## Package org.snpeff.interval.tree

### Class org.snpeff.interval.tree.IntervalForest

class IntervalForest extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### debug

    boolean debug

##### forest

    HashMap<String,Itree> forest

##### name

    String name

### Class org.snpeff.interval.tree.IntervalNode

class IntervalNode extends Object implements Serializable

serialVersionUID:
  -444656480302906048L

#### Serialized Fields

##### center

    int center

##### intervalsCenter

    Marker[] intervalsCenter

##### leftNode

    IntervalNode leftNode

##### rightNode

    IntervalNode rightNode

### Class org.snpeff.interval.tree.IntervalNodeOri

class IntervalNodeOri extends Object implements Serializable

serialVersionUID:
  -444656480302906048L

#### Serialized Fields

##### center

    Integer center

##### intervals

    SortedMap<Marker,List<Marker>> intervals

##### leftNode

    IntervalNodeOri leftNode

##### rightNode

    IntervalNodeOri rightNode

### Class org.snpeff.interval.tree.IntervalTree

class IntervalTree extends Object implements Serializable

serialVersionUID:
  1808077263026999072L

#### Serialized Fields

##### head

    IntervalNode head

##### inSync

    boolean inSync

##### intervals

    Markers intervals

### Class org.snpeff.interval.tree.IntervalTreeOri

class IntervalTreeOri extends Object implements Serializable

serialVersionUID:
  1808077263026999072L

#### Serialized Fields

##### head

    IntervalNodeOri head

##### inSync

    boolean inSync

##### intervals

    Markers intervals

## Package org.snpeff.nmer

### Class org.snpeff.nmer.NmerCount

class NmerCount extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### hash

    gnu.trove.map.hash.TLongIntHashMap hash

##### nmerSize

    int nmerSize

### Class org.snpeff.nmer.NmerCountWc

class NmerCountWc extends NmerCount implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### nmerMin

    Nmer nmerMin

##### nmerWc

    Nmer nmerWc

## Package org.snpeff.snpEffect

### Class org.snpeff.snpEffect.Config

class Config extends Object implements Serializable

serialVersionUID:
  877453207407217465L

#### Serialized Fields

##### bundleByGenomeId

    HashMap<String,String> bundleByGenomeId

##### configDirPath

    String configDirPath

##### configFileCanonicaPath

    String configFileCanonicaPath

##### configFileName

    String configFileName

##### databaseRepository

    String databaseRepository

##### databaseRepositoryKey

    String databaseRepositoryKey

##### dataDir

    String dataDir

##### debug

    boolean debug

##### errorChromoHit

    boolean errorChromoHit

##### errorOnMissingChromo

    boolean errorOnMissingChromo

##### expandIub

    boolean expandIub

##### genome

    Genome genome

##### genomeById

    HashMap<String,Genome> genomeById

##### genomeVersion

    String genomeVersion

##### hgvs

    boolean hgvs

##### hgvsOld

    boolean hgvsOld

##### hgvsOneLetterAa

    boolean hgvsOneLetterAa

##### hgvsShift

    boolean hgvsShift

##### hgvsTrId

    boolean hgvsTrId

##### lofDeleteProteinCodingBases

    double lofDeleteProteinCodingBases

##### lofIgnoreProteinCodingAfter

    double lofIgnoreProteinCodingAfter

##### lofIgnoreProteinCodingBefore

    double lofIgnoreProteinCodingBefore

##### nameById

    HashMap<String,String> nameById

##### onlyRegulation

    boolean onlyRegulation

##### properties

    Properties properties

##### quiet

    boolean quiet

##### referenceById

    HashMap<String,String> referenceById

##### snpEffectPredictor

    SnpEffectPredictor snpEffectPredictor

##### treatAllAsProteinCoding

    boolean treatAllAsProteinCoding

##### verbose

    boolean verbose

##### versionsUrl

    String versionsUrl

### Class org.snpeff.snpEffect.SnpEffectPredictor

class SnpEffectPredictor extends Object implements Serializable

serialVersionUID:
  4519418862303325081L

#### Serialized Fields

##### debug

    boolean debug

##### genome

    Genome genome

##### intervalForest

    IntervalForest intervalForest

##### markers

    Markers markers

##### spliceRegionExonSize

    int spliceRegionExonSize

##### spliceRegionIntronMax

    int spliceRegionIntronMax

##### spliceRegionIntronMin

    int spliceRegionIntronMin

##### spliceSiteSize

    int spliceSiteSize

##### upDownStreamLength

    int upDownStreamLength

##### useChromosomes

    boolean useChromosomes

## Package org.snpeff.stats

### Class org.snpeff.stats.CountByKey

class CountByKey extends Object implements Serializable

#### Serialized Fields

##### countByKey

    HashMap<T,Long> countByKey

### Class org.snpeff.stats.CountByType

class CountByType extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### countByType

    HashMap<String,Long> countByType

##### scoreByType

    HashMap<String,Double> scoreByType

### Class org.snpeff.stats.CoverageByType

class CoverageByType extends AutoHashMap<String,PosStats> implements Serializable

serialVersionUID:
  6365021779756255154L

### Class org.snpeff.stats.GeneCountByTypeTable

class GeneCountByTypeTable extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### bioType

    HashMap<String,String> bioType

##### countersByType

    HashMap<String,CountByType> countersByType

##### counterSizeByType

    HashMap<String,CountByType> counterSizeByType

##### keys

    HashSet<String> keys

##### sizeByType

    HashMap<String,Integer> sizeByType

##### types

    HashSet<String> types

### Class org.snpeff.stats.IntStats

class IntStats extends Object implements Serializable

#### Serialized Fields

##### counters

    gnu.trove.map.hash.TIntIntHashMap counters

##### maxBins

    int maxBins

##### needUpdate

    boolean needUpdate

##### statsProcedure

    org.snpeff.stats.StatsProcedure statsProcedure

## Package org.snpeff.vcf

### Class org.snpeff.vcf.VariantVcfEntry

class VariantVcfEntry extends Variant implements Serializable

serialVersionUID:
  2589022632388179932L

#### Serialized Fields

##### vcfEntry

    VcfEntry vcfEntry

### Class org.snpeff.vcf.VcfEntry

class VcfEntry extends Marker implements Serializable

serialVersionUID:
  4226374412681243433L

#### Serialized Fields

##### alts

    String[] alts

##### altStr

    String altStr

##### chromosomeName

    String chromosomeName

##### filter

    String filter

##### format

    String format

##### formatFields

    String[] formatFields

##### genotypeFields

    String[] genotypeFields

##### genotypeFieldsStr

    String genotypeFieldsStr

##### genotypeScores

    byte[] genotypeScores

##### info

    HashMap<String,String> info

##### infoStr

    String infoStr

##### line

    String line

##### lineNum

    int lineNum

##### quality

    Double quality

##### ref

    String ref

##### variants

    LinkedList<Variant> variants

##### vcfEffects

    List<VcfEffect> vcfEffects

##### vcfFileIterator

    VcfFileIterator vcfFileIterator

##### vcfGenotypes

    ArrayList<VcfGenotype> vcfGenotypes

### Class org.snpeff.vcf.VcfHeader

class VcfHeader extends Object implements Serializable

#### Serialized Fields

##### chromLine

    boolean chromLine

##### header

    StringBuffer header

##### numberOfSamples

    int numberOfSamples

##### sampleName2Num

    Map<String,Integer> sampleName2Num

##### sampleNames

    ArrayList<String> sampleNames

##### vcfFormatById

    Map<String,VcfHeaderFormat> vcfFormatById

##### vcfInfoById

    Map<String,VcfHeaderInfo> vcfInfoById

### Class org.snpeff.vcf.VcfHeaderEntry

class VcfHeaderEntry extends Object implements Serializable

serialVersionUID:
  2024092601L

#### Serialized Fields

##### id

    String id

##### line

    String line

### Class org.snpeff.vcf.VcfHeaderFormat

class VcfHeaderFormat extends VcfHeaderInfo implements Serializable

### Class org.snpeff.vcf.VcfHeaderInfo

class VcfHeaderInfo extends VcfHeaderEntry implements Serializable

serialVersionUID:
  2024092501L

#### Serialized Fields

##### description

    String description

##### implicit

    boolean implicit

##### number

    int number

##### vcfInfoNumber

    VcfHeaderInfo.VcfInfoNumber vcfInfoNumber

##### vcfInfoType

    VcfInfoType vcfInfoType