# Serialized Form

## Package htsjdk.beta.exception

### Exception Class htsjdk.beta.exception.HtsjdkException

class HtsjdkException extends RuntimeException implements Serializable

serialVersionUID:
  1L

### Exception Class htsjdk.beta.exception.HtsjdkIOException

class HtsjdkIOException extends HtsjdkException implements Serializable

serialVersionUID:
  1L

### Exception Class htsjdk.beta.exception.HtsjdkPluginException

class HtsjdkPluginException extends HtsjdkException implements Serializable

serialVersionUID:
  1L

### Exception Class htsjdk.beta.exception.HtsjdkUnsupportedOperationException

class HtsjdkUnsupportedOperationException extends HtsjdkPluginException implements Serializable

## Package htsjdk.beta.io.bundle

### Class htsjdk.beta.io.bundle.Bundle

class Bundle extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### primaryContentType

    String primaryContentType

##### resources

    Map<String, BundleResource> resources

### Class htsjdk.beta.io.bundle.BundleResourceBase

class BundleResourceBase extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### contentType

    String contentType

##### displayName

    String displayName

##### format

    String format

### Class htsjdk.beta.io.bundle.InputStreamResource

class InputStreamResource extends BundleResourceBase implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### bufferedInputStream

    BufferedInputStream bufferedInputStream

##### rawInputStream

    InputStream rawInputStream

### Class htsjdk.beta.io.bundle.IOPathResource

class IOPathResource extends BundleResourceBase implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### ioPath

    IOPath ioPath

### Class htsjdk.beta.io.bundle.OutputStreamResource

class OutputStreamResource extends BundleResourceBase implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### outputStream

    OutputStream outputStream

### Class htsjdk.beta.io.bundle.SeekableStreamResource

class SeekableStreamResource extends InputStreamResource implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### seekableStream

    SeekableStream seekableStream

## Package htsjdk.beta.plugin.reads

### Class htsjdk.beta.plugin.reads.ReadsBundle

class ReadsBundle extends Bundle implements Serializable

serialVersionUID:
  1L

## Package htsjdk.beta.plugin.variants

### Class htsjdk.beta.plugin.variants.VariantsBundle

class VariantsBundle extends Bundle implements Serializable

serialVersionUID:
  1L

## Package htsjdk.io

### Class htsjdk.io.HtsPath

class HtsPath extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### rawInputString

    String rawInputString

##### uri

    URI uri

## Package htsjdk.samtools

### Class htsjdk.samtools.AbstractSAMHeaderRecord

class AbstractSAMHeaderRecord extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mAttributes

    Map<String,String> mAttributes

### Class htsjdk.samtools.AlignmentBlock

class AlignmentBlock extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### length

    int length

##### readStart

    int readStart

##### referenceStart

    int referenceStart

### Class htsjdk.samtools.BAMFileSpan

class BAMFileSpan extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### chunks

    List<Chunk> chunks

The constituent chunks of this list.

### Class htsjdk.samtools.BAMRecord

class BAMRecord extends SAMRecord implements Serializable

#### Serialized Fields

##### mAttributesDecoded

    boolean mAttributesDecoded

##### mBinaryDataStale

    boolean mBinaryDataStale

If any of the properties set from mRestOfBinaryData have been overridden by calls to setters, this is set to true, indicating that mRestOfBinaryData cannot be used to write this record to disk.

##### mCigarDecoded

    boolean mCigarDecoded

##### mCigarLength

    int mCigarLength

##### mCigarLengthValid

    boolean mCigarLengthValid

##### mReadLength

    int mReadLength

##### mReadLengthValid

    boolean mReadLengthValid

##### mReadNameLength

    short mReadNameLength

##### mReadNameLengthValid

    boolean mReadNameLengthValid

##### mRestOfBinaryData

    byte[] mRestOfBinaryData

Variable-length part of BAMRecord. Lazily decoded.

### Class htsjdk.samtools.Chunk

class Chunk extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mChunkEnd

    long mChunkEnd

A pointer to the end of a region in a SAM/BAM file. The end is exclusive: this pointer points to one byte past the end of the region of interest inside the file.

##### mChunkStart

    long mChunkStart

A pointer to the start of a region in a SAM/BAM file. The start is inclusive: start reading from this point.

### Class htsjdk.samtools.Cigar

class Cigar extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### cigarElements

    List<CigarElement> cigarElements

### Class htsjdk.samtools.CigarElement

class CigarElement extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### length

    int length

##### operator

    CigarOperator operator

### Exception Class htsjdk.samtools.FileTruncatedException

class FileTruncatedException extends SAMException implements Serializable

### Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue

class SAMBinaryTagAndUnsignedArrayValue extends SAMBinaryTagAndValue implements Serializable

### Class htsjdk.samtools.SAMBinaryTagAndValue

class SAMBinaryTagAndValue extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### next

    SAMBinaryTagAndValue next

##### tag

    short tag

##### value

    Object value

### Exception Class htsjdk.samtools.SAMException

class SAMException extends RuntimeException implements Serializable

### Class htsjdk.samtools.SAMFileHeader

class SAMFileHeader extends AbstractSAMHeaderRecord implements Serializable

#### Serialized Fields

##### groupOrder

    SAMFileHeader.GroupOrder groupOrder

##### mComments

    List<String> mComments

##### mProgramRecordMap

    Map<String, SAMProgramRecord> mProgramRecordMap

##### mProgramRecords

    List<SAMProgramRecord> mProgramRecords

##### mReadGroupMap

    Map<String, SAMReadGroupRecord> mReadGroupMap

##### mReadGroups

    List<SAMReadGroupRecord> mReadGroups

##### mSequenceDictionary

    SAMSequenceDictionary mSequenceDictionary

##### mValidationErrors

    List<SAMValidationError> mValidationErrors

##### sortOrder

    SAMFileHeader.SortOrder sortOrder

### Exception Class htsjdk.samtools.SAMFormatException

class SAMFormatException extends SAMException implements Serializable

### Class htsjdk.samtools.SAMHeaderRecordComparator

class SAMHeaderRecordComparator extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### attributes

    String[] attributes

### Class htsjdk.samtools.SAMProgramRecord

class SAMProgramRecord extends AbstractSAMHeaderRecord implements Serializable

#### Serialized Fields

##### mProgramGroupId

    String mProgramGroupId

### Class htsjdk.samtools.SAMReadGroupRecord

class SAMReadGroupRecord extends AbstractSAMHeaderRecord implements Serializable

#### Serialized Fields

##### mReadGroupId

    String mReadGroupId

### Class htsjdk.samtools.SAMRecord

class SAMRecord extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mAlignmentBlocks

    List<AlignmentBlock> mAlignmentBlocks

##### mAlignmentStart

    int mAlignmentStart

##### mAttributes

    SAMBinaryTagAndValue mAttributes

##### mBaseQualities

    byte[] mBaseQualities

##### mCigar

    Cigar mCigar

##### mCigarString

    String mCigarString

##### mFlags

    int mFlags

##### mHeader

    SAMFileHeader mHeader

##### mInferredInsertSize

    int mInferredInsertSize

##### mMappingQuality

    int mMappingQuality

##### mMateAlignmentStart

    int mMateAlignmentStart

##### mMateReferenceIndex

    Integer mMateReferenceIndex

##### mMateReferenceName

    String mMateReferenceName

##### mReadBases

    byte[] mReadBases

##### mReadName

    String mReadName

##### mReferenceIndex

    Integer mReferenceIndex

##### mReferenceName

    String mReferenceName

##### mValidationStringency

    ValidationStringency mValidationStringency

Some attributes (e.g. CIGAR) are not decoded immediately. Use this to decide how to validate when decoded.

### Class htsjdk.samtools.SAMRecordCoordinateComparator

class SAMRecordCoordinateComparator extends Object implements Serializable

serialVersionUID:
  1L

### Class htsjdk.samtools.SAMRecordDuplicateComparator

class SAMRecordDuplicateComparator extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### libraryIds

    Map<String,Short> libraryIds

##### nextLibraryId

    short nextLibraryId

##### scoringStrategy

    DuplicateScoringStrategy.ScoringStrategy scoringStrategy

### Class htsjdk.samtools.SAMRecordQueryHashComparator

class SAMRecordQueryHashComparator extends SAMRecordQueryNameComparator implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### hasher

    Murmur3 hasher

### Class htsjdk.samtools.SAMRecordQueryNameComparator

class SAMRecordQueryNameComparator extends Object implements Serializable

serialVersionUID:
  1L

### Class htsjdk.samtools.SAMSequenceDictionary

class SAMSequenceDictionary extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mSequenceMap

    Map<String, SAMSequenceRecord> mSequenceMap

##### mSequences

    List<SAMSequenceRecord> mSequences

### Class htsjdk.samtools.SAMSequenceRecord

class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mAlternativeSequenceName

    Set<String> mAlternativeSequenceName

##### mSequenceIndex

    int mSequenceIndex

##### mSequenceLength

    int mSequenceLength

##### mSequenceName

    String mSequenceName

### Exception Class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException

class SanityCheckFailedException extends RuntimeException implements Serializable

### Class htsjdk.samtools.SAMValidationError

class SAMValidationError extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### message

    String message

##### readName

    String readName

##### recordNumber

    long recordNumber

##### source

    String source

##### type

    SAMValidationError.Type type

### Class htsjdk.samtools.SBIIndex

class SBIIndex extends Object implements Serializable

#### Serialized Fields

##### header

    SBIIndex.Header header

##### virtualOffsets

    long[] virtualOffsets

### Class htsjdk.samtools.SBIIndex.Header

class Header extends Object implements Serializable

#### Serialized Fields

##### fileLength

    long fileLength

##### granularity

    long granularity

##### md5

    byte[] md5

##### totalNumberOfRecords

    long totalNumberOfRecords

##### uuid

    byte[] uuid

## Package htsjdk.samtools.cram

### Exception Class htsjdk.samtools.cram.CRAMException

class CRAMException extends SAMException implements Serializable

## Package htsjdk.samtools.cram.encoding.readfeatures

### Class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore

class BaseQualityScore extends Object implements Serializable

#### Serialized Fields

##### position

    int position

##### qualityScore

    byte qualityScore

### Class htsjdk.samtools.cram.encoding.readfeatures.Bases

class Bases extends Object implements Serializable

#### Serialized Fields

##### bases

    byte[] bases

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.Deletion

class Deletion extends Object implements Serializable

#### Serialized Fields

##### length

    int length

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.HardClip

class HardClip extends Object implements Serializable

#### Serialized Fields

##### length

    int length

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.InsertBase

class InsertBase extends Object implements Serializable

#### Serialized Fields

##### base

    byte base

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.Insertion

class Insertion extends Object implements Serializable

#### Serialized Fields

##### position

    int position

##### sequence

    byte[] sequence

### Class htsjdk.samtools.cram.encoding.readfeatures.Padding

class Padding extends Object implements Serializable

#### Serialized Fields

##### length

    int length

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.ReadBase

class ReadBase extends Object implements Serializable

#### Serialized Fields

##### base

    byte base

##### position

    int position

##### qualityScore

    byte qualityScore

### Class htsjdk.samtools.cram.encoding.readfeatures.RefSkip

class RefSkip extends Object implements Serializable

#### Serialized Fields

##### length

    int length

##### position

    int position

### Class htsjdk.samtools.cram.encoding.readfeatures.Scores

class Scores extends Object implements Serializable

#### Serialized Fields

##### position

    int position

##### scores

    byte[] scores

### Class htsjdk.samtools.cram.encoding.readfeatures.SoftClip

class SoftClip extends Object implements Serializable

#### Serialized Fields

##### position

    int position

##### sequence

    byte[] sequence

### Class htsjdk.samtools.cram.encoding.readfeatures.Substitution

class Substitution extends Object implements Serializable

#### Serialized Fields

##### base

    byte base

The read base, allowed values are ACGTN.

##### code

    byte code

A byte value denoting combination of the read base and the reference base.

##### position

    int position

zero-based position in read

##### referenceBase

    byte referenceBase

The reference sequence base matching the position of this substitution, allowed values are ACGTN.

## Package htsjdk.samtools.cram.ref

### Exception Class htsjdk.samtools.cram.ref.GaveUpException

class GaveUpException extends RuntimeException implements Serializable

serialVersionUID:
  -8997576068346912410L

#### Serialized Fields

##### md5

    String md5

## Package htsjdk.samtools.fastq

### Class htsjdk.samtools.fastq.FastqRecord

class FastqRecord extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### baseQualityString

    String baseQualityString

##### qualityHeader

    String qualityHeader

##### readName

    String readName

##### readString

    String readString

## Package htsjdk.samtools.metrics

### Class htsjdk.samtools.metrics.MetricsFile

class MetricsFile extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### columnLabels

    Set<String> columnLabels

##### headers

    List<Header> headers

##### histograms

    List<Histogram<HKEY extends Comparable>> histograms

##### metrics

    List<BEAN extends MetricBase> metrics

### Class htsjdk.samtools.metrics.StringHeader

class StringHeader extends Object implements Serializable

#### Serialized Fields

##### value

    String value

### Class htsjdk.samtools.metrics.VersionHeader

class VersionHeader extends Object implements Serializable

#### Serialized Fields

##### versionedItem

    String versionedItem

##### versionString

    String versionString

## Package htsjdk.samtools.util

### Class htsjdk.samtools.util.CollectionUtil.DefaultingMap

class DefaultingMap extends HashMap<K,V> implements Serializable

#### Serialized Fields

##### defaultGenerator

    CollectionUtil.DefaultingMap.Factory<V,K> defaultGenerator

##### injectValueOnDefault

    boolean injectValueOnDefault

### Class htsjdk.samtools.util.CollectionUtil.MultiMap

class MultiMap extends HashMap<K, Collection<V>> implements Serializable

### Exception Class htsjdk.samtools.util.DateParser.InvalidDateException

class InvalidDateException extends SAMException implements Serializable

### Class htsjdk.samtools.util.Histogram

class Histogram extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### binLabel

    String binLabel

##### map

    NavigableMap<K extends Comparable, Histogram.Bin<K extends Comparable>> map

##### valueLabel

    String valueLabel

### Class htsjdk.samtools.util.Histogram.Bin

class Bin extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### id

    K extends Comparable id

##### value

    double value

### Class htsjdk.samtools.util.IntervalCoordinateComparator

class IntervalCoordinateComparator extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### header

    SAMFileHeader header

### Class htsjdk.samtools.util.Iso8601Date

class Iso8601Date extends Date implements Serializable

### Class htsjdk.samtools.util.ListMap

class ListMap extends HashMap<K,List<V>> implements Serializable

### Class htsjdk.samtools.util.LocusComparator

class LocusComparator extends Object implements Serializable

serialVersionUID:
  1L

### Class htsjdk.samtools.util.Murmur3

class Murmur3 extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### seed

    int seed

### Class htsjdk.samtools.util.RelativeIso8601Date

class RelativeIso8601Date extends Iso8601Date implements Serializable

#### Serialized Fields

##### doSetTimeNextQuery

    boolean doSetTimeNextQuery

Flag that indicates this instance is lazy and has not yet been queried (and so its value should be updated at the next query).

### Exception Class htsjdk.samtools.util.RuntimeEOFException

class RuntimeEOFException extends SAMException implements Serializable

### Exception Class htsjdk.samtools.util.RuntimeIOException

class RuntimeIOException extends SAMException implements Serializable

### Exception Class htsjdk.samtools.util.RuntimeScriptException

class RuntimeScriptException extends RuntimeException implements Serializable

### Exception Class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException

class SequenceListsDifferException extends SAMException implements Serializable

## Package htsjdk.samtools.util.htsget

### Exception Class htsjdk.samtools.util.htsget.HtsgetMalformedResponseException

class HtsgetMalformedResponseException extends RuntimeException implements Serializable

## Package htsjdk.tribble

### Exception Class htsjdk.tribble.TribbleException

class TribbleException extends RuntimeException implements Serializable

#### Serialized Fields

##### source

    String source

### Exception Class htsjdk.tribble.TribbleException.CorruptedIndexFile

class CorruptedIndexFile extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.FeatureFileDoesntExist

class FeatureFileDoesntExist extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.InternalCodecException

class InternalCodecException extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.InvalidDecodeLine

class InvalidDecodeLine extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.InvalidHeader

class InvalidHeader extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.MalformedFeatureFile

class MalformedFeatureFile extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.TabixReaderFailure

class TabixReaderFailure extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType

class UnableToCreateCorrectIndexType extends TribbleException implements Serializable

### Exception Class htsjdk.tribble.TribbleException.UnableToReadIndexFile

class UnableToReadIndexFile extends TribbleException implements Serializable

## Package htsjdk.tribble.exception

### Exception Class htsjdk.tribble.exception.CodecLineParsingException

class CodecLineParsingException extends RuntimeException implements Serializable

### Exception Class htsjdk.tribble.exception.UnsortedFileException

class UnsortedFileException extends RuntimeException implements Serializable

## Package htsjdk.variant.variantcontext

### Class htsjdk.variant.variantcontext.CommonInfo

class CommonInfo extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### attributes

    Map<String,Object> attributes

##### filters

    Set<String> filters

##### log10PError

    double log10PError

##### name

    String name

### Class htsjdk.variant.variantcontext.FastGenotype

class FastGenotype extends Genotype implements Serializable

#### Serialized Fields

##### AD

    int[] AD

##### alleles

    List<Allele> alleles

##### DP

    int DP

##### extendedAttributes

    Map<String,Object> extendedAttributes

##### GQ

    int GQ

##### isPhased

    boolean isPhased

##### PL

    int[] PL

### Class htsjdk.variant.variantcontext.Genotype

class Genotype extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### filters

    String filters

##### sampleName

    String sampleName

##### type

    GenotypeType type

### Class htsjdk.variant.variantcontext.GenotypesContext

class GenotypesContext extends Object implements Serializable

serialVersionUID:
  1L

#### Serialization Methods

##### writeObject

private void writeObject(ObjectOutputStream out) throws IOException
Custom serialization routine. Needed to ensure that we decode any lazily-decoded data before serialization.

Parameters:
  `out` - stream to which to serialize this object
Throws:
  `IOException`

#### Serialized Fields

##### immutable

    boolean immutable

Are we allowing users to modify the list?

##### maxPloidy

    int maxPloidy

Cached value of the maximum ploidy observed among all samples

##### notToBeDirectlyAccessedGenotypes

    ArrayList<Genotype> notToBeDirectlyAccessedGenotypes

An ArrayList of genotypes contained in this context WARNING: TO ENABLE THE LAZY VERSION OF THIS CLASS, NO METHODS SHOULD DIRECTLY ACCESS THIS VARIABLE. USE getGenotypes() INSTEAD.

##### sampleNamesInOrder

    List<String> sampleNamesInOrder

sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order

##### sampleNameToOffset

    Map<String,Integer> sampleNameToOffset

a map optimized for efficient lookup. Each genotype in genotypes must have its sample name in sampleNameToOffset, with a corresponding integer value that indicates the offset of that genotype in the vector of genotypes

### Class htsjdk.variant.variantcontext.LazyGenotypesContext

class LazyGenotypesContext extends GenotypesContext implements Serializable

#### Serialization Methods

##### readObject

private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
Custom de-serialization routine to ensure that all LazyGenotypesContexts we de-serialize are fully decoded. Throws an IllegalStateException if that is not the case. Necessary because the LazyParser required to decode the lazy context is transient. Note that the custom writeObject() companion to this method is implemented in the superclass (GenotypesContext), since decoding lazy data writes to superclass fields.

Parameters:
  `in` - stream from which to de-serialize the LazyGenotypesContext
Throws:
  `IOException`
  `ClassNotFoundException`

#### Serialized Fields

##### loaded

    boolean loaded

True if we've already decoded the values in unparsedGenotypeData

##### nUnparsedGenotypes

    int nUnparsedGenotypes

nUnparsedGenotypes the number of genotypes contained in the unparsedGenotypes data (known already in the parser). Useful for isEmpty and size() optimizations

### Class htsjdk.variant.variantcontext.SimpleAllele

class SimpleAllele extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### bases

    byte[] bases

##### isNoCall

    boolean isNoCall

##### isRef

    boolean isRef

##### isSymbolic

    boolean isSymbolic

### Class htsjdk.variant.variantcontext.VariantContext

class VariantContext extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### alleles

    List<Allele> alleles

A set of the alleles segregating in this context

##### ALT

    Allele ALT

##### commonInfo

    CommonInfo commonInfo

##### contig

    String contig

The location of this VariantContext

##### fullyDecoded

    boolean fullyDecoded

##### genotypeCounts

    int[] genotypeCounts

Counts for each of the possible Genotype types in this context

##### genotypes

    GenotypesContext genotypes

A mapping from sampleName -> genotype objects for all genotypes associated with this context

##### ID

    String ID

##### monomorphic

    Boolean monomorphic

##### REF

    Allele REF

##### start

    long start

##### stop

    long stop

##### type

    VariantContext.Type type

The type (cached for performance reasons) of this context

##### typeIgnoringNonRef

    VariantContext.Type typeIgnoringNonRef

The type of this context, cached separately if ignoreNonRef is true

### Class htsjdk.variant.variantcontext.VariantContextComparator

class VariantContextComparator extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### contigIndexLookup

    Map<String,Integer> contigIndexLookup

## Package htsjdk.variant.variantcontext.filter

### Class htsjdk.variant.variantcontext.filter.CompoundFilter

class CompoundFilter extends ArrayList<VariantContextFilter> implements Serializable

#### Serialized Fields

##### requireAll

    boolean requireAll

## Package htsjdk.variant.vcf

### Class htsjdk.variant.vcf.VCFAltHeaderLine

class VCFAltHeaderLine extends VCFSimpleHeaderLine implements Serializable

serialVersionUID:
  1L

### Class htsjdk.variant.vcf.VCFCompoundHeaderLine

class VCFCompoundHeaderLine extends VCFHeaderLine implements Serializable

#### Serialized Fields

##### count

    int count

##### countType

    VCFHeaderLineCount countType

##### description

    String description

##### lineType

    VCFCompoundHeaderLine.SupportedHeaderLineType lineType

##### name

    String name

##### source

    String source

##### type

    VCFHeaderLineType type

##### version

    String version

### Class htsjdk.variant.vcf.VCFContigHeaderLine

class VCFContigHeaderLine extends VCFSimpleHeaderLine implements Serializable

#### Serialized Fields

##### contigIndex

    Integer contigIndex

### Class htsjdk.variant.vcf.VCFFilterHeaderLine

class VCFFilterHeaderLine extends VCFSimpleHeaderLine implements Serializable

serialVersionUID:
  1L

### Class htsjdk.variant.vcf.VCFFormatHeaderLine

class VCFFormatHeaderLine extends VCFCompoundHeaderLine implements Serializable

### Class htsjdk.variant.vcf.VCFHeader

class VCFHeader extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### contigMetaData

    Map<String, VCFContigHeaderLine> contigMetaData

##### mFilterMetaData

    Map<String, VCFFilterHeaderLine> mFilterMetaData

##### mFormatMetaData

    Map<String, VCFFormatHeaderLine> mFormatMetaData

##### mGenotypeSampleNames

    List<String> mGenotypeSampleNames

##### mInfoMetaData

    Map<String, VCFInfoHeaderLine> mInfoMetaData

##### mMetaData

    Set<VCFHeaderLine> mMetaData

##### mOtherMetaData

    Map<String, VCFHeaderLine> mOtherMetaData

##### sampleNamesInOrder

    ArrayList<String> sampleNamesInOrder

##### sampleNameToOffset

    HashMap<String,Integer> sampleNameToOffset

##### samplesWereAlreadySorted

    boolean samplesWereAlreadySorted

##### vcfHeaderVersion

    VCFHeaderVersion vcfHeaderVersion

The VCF version for this header; once a header version is established, it can only be changed subject to version transition rules defined by `VCFHeader.validateVersionTransition(VCFHeaderVersion, VCFHeaderVersion)`

##### writeCommandLine

    boolean writeCommandLine

##### writeEngineHeaders

    boolean writeEngineHeaders

### Class htsjdk.variant.vcf.VCFHeaderLine

class VCFHeaderLine extends Object implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### mKey

    String mKey

##### mValue

    String mValue

### Class htsjdk.variant.vcf.VCFInfoHeaderLine

class VCFInfoHeaderLine extends VCFCompoundHeaderLine implements Serializable

### Class htsjdk.variant.vcf.VCFMetaHeaderLine

class VCFMetaHeaderLine extends VCFSimpleHeaderLine implements Serializable

serialVersionUID:
  1L

### Class htsjdk.variant.vcf.VCFPedigreeHeaderLine

class VCFPedigreeHeaderLine extends VCFSimpleHeaderLine implements Serializable

serialVersionUID:
  1L

### Class htsjdk.variant.vcf.VCFSampleHeaderLine

class VCFSampleHeaderLine extends VCFSimpleHeaderLine implements Serializable

serialVersionUID:
  1L

### Class htsjdk.variant.vcf.VCFSimpleHeaderLine

class VCFSimpleHeaderLine extends VCFHeaderLine implements Serializable

#### Serialized Fields

##### genericFields

    Map<String,String> genericFields

##### name

    String name