Serialized Form

Package htsjdk.beta.exception

Exception htsjdk.beta.exception.HtsjdkException

class HtsjdkException extends RuntimeException implements Serializable

serialVersionUID:

1L

Exception htsjdk.beta.exception.HtsjdkIOException

class HtsjdkIOException extends HtsjdkException implements Serializable

serialVersionUID:

1L

Exception htsjdk.beta.exception.HtsjdkPluginException

class HtsjdkPluginException extends HtsjdkException implements Serializable

serialVersionUID:

1L

Exception 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.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 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 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 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 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 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 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.sra

Class htsjdk.samtools.sra.SRAAccession

class SRAAccession extends Object implements Serializable

Serialized Fields

acc

String acc

Class htsjdk.samtools.sra.SRALazyRecord

class SRALazyRecord extends SAMRecord implements Serializable

Serialized Fields

accession

SRAAccession accession

initializedAttributes

Set<htsjdk.samtools.sra.SRALazyRecord.LazyAttribute> initializedAttributes

initializedFields

Set<htsjdk.samtools.sra.SRALazyRecord.LazyField> initializedFields

initializedFlags

Set<htsjdk.samtools.sra.SRALazyRecord.LazyFlag> initializedFlags

isAligned

boolean isAligned

sraAlignmentId

String sraAlignmentId

sraReadId

String sraReadId

unalignedReadFragmentIndex

int unalignedReadFragmentIndex

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 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 htsjdk.samtools.util.RuntimeEOFException

class RuntimeEOFException extends SAMException implements Serializable

Exception htsjdk.samtools.util.RuntimeIOException

class RuntimeIOException extends SAMException implements Serializable

Exception htsjdk.samtools.util.RuntimeScriptException

class RuntimeScriptException extends RuntimeException implements Serializable

Exception htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException

class SequenceListsDifferException extends SAMException implements Serializable

Package htsjdk.samtools.util.htsget

Exception htsjdk.samtools.util.htsget.HtsgetMalformedResponseException

class HtsgetMalformedResponseException extends RuntimeException implements Serializable

Package htsjdk.tribble

Exception htsjdk.tribble.TribbleException

class TribbleException extends RuntimeException implements Serializable

Serialized Fields

source

String source

Exception htsjdk.tribble.TribbleException.CorruptedIndexFile

class CorruptedIndexFile extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.FeatureFileDoesntExist

class FeatureFileDoesntExist extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.InternalCodecException

class InternalCodecException extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.InvalidDecodeLine

class InvalidDecodeLine extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.InvalidHeader

class InvalidHeader extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.MalformedFeatureFile

class MalformedFeatureFile extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.TabixReaderFailure

class TabixReaderFailure extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType

class UnableToCreateCorrectIndexType extends TribbleException implements Serializable

Exception htsjdk.tribble.TribbleException.UnableToReadIndexFile

class UnableToReadIndexFile extends TribbleException implements Serializable

Package htsjdk.tribble.exception

Exception htsjdk.tribble.exception.CodecLineParsingException

class CodecLineParsingException extends RuntimeException implements Serializable

Exception 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