Serialized Form

Package htsjdk.samtools
- Class htsjdk.samtools.AbstractSAMHeaderRecord extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mAttributes
```
java.util.Map<K,V> mAttributes
```
- Class htsjdk.samtools.AlignmentBlock extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - readStart
```
int readStart
```
    - referenceStart
```
int referenceStart
```
    - length
```
int length
```
- Class htsjdk.samtools.BAMRecord extends SAMRecord implements Serializable
  - Serialized Fields
    - mRestOfBinaryData
```
byte[] mRestOfBinaryData
```
      Variable-length part of BAMRecord. Lazily decoded.
    - mReadLength
```
int mReadLength
```
    - mReadLengthValid
```
boolean mReadLengthValid
```
    - mReadNameLength
```
short mReadNameLength
```
    - mReadNameLengthValid
```
boolean mReadNameLengthValid
```
    - mCigarLength
```
int mCigarLength
```
    - mCigarLengthValid
```
boolean mCigarLengthValid
```
    - mAttributesDecoded
```
boolean mAttributesDecoded
```
    - mCigarDecoded
```
boolean mCigarDecoded
```
    - 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.
- Class htsjdk.samtools.Chunk extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - 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.
    - 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.
- Class htsjdk.samtools.Cigar extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cigarElements
```
java.util.List<E> cigarElements
```
- Class htsjdk.samtools.CigarElement extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - length
```
int length
```
    - operator
```
CigarOperator operator
```
- Class htsjdk.samtools.FileTruncatedException extends SAMException implements Serializable
- Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue extends SAMBinaryTagAndValue implements Serializable
- Class htsjdk.samtools.SAMBinaryTagAndValue extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tag
```
short tag
```
    - value
```
java.lang.Object value
```
    - next
```
SAMBinaryTagAndValue next
```
- Class htsjdk.samtools.SAMException extends java.lang.RuntimeException implements Serializable
- Class htsjdk.samtools.SAMFileHeader extends AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mReadGroups
```
java.util.List<E> mReadGroups
```
    - mProgramRecords
```
java.util.List<E> mProgramRecords
```
    - mReadGroupMap
```
java.util.Map<K,V> mReadGroupMap
```
    - mProgramRecordMap
```
java.util.Map<K,V> mProgramRecordMap
```
    - mSequenceDictionary
```
SAMSequenceDictionary mSequenceDictionary
```
    - mComments
```
java.util.List<E> mComments
```
    - textHeader
```
java.lang.String textHeader
```
    - mValidationErrors
```
java.util.List<E> mValidationErrors
```
- Class htsjdk.samtools.SAMFormatException extends SAMException implements Serializable
- Class htsjdk.samtools.SAMProgramRecord extends AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mProgramGroupId
```
java.lang.String mProgramGroupId
```
- Class htsjdk.samtools.SAMReadGroupRecord extends AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mReadGroupId
```
java.lang.String mReadGroupId
```
- Class htsjdk.samtools.SAMRecord extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mReadName
```
java.lang.String mReadName
```
    - mReadBases
```
byte[] mReadBases
```
    - mBaseQualities
```
byte[] mBaseQualities
```
    - mReferenceName
```
java.lang.String mReferenceName
```
    - mAlignmentStart
```
int mAlignmentStart
```
    - mMappingQuality
```
int mMappingQuality
```
    - mCigarString
```
java.lang.String mCigarString
```
    - mCigar
```
Cigar mCigar
```
    - mAlignmentBlocks
```
java.util.List<E> mAlignmentBlocks
```
    - mFlags
```
int mFlags
```
    - mMateReferenceName
```
java.lang.String mMateReferenceName
```
    - mMateAlignmentStart
```
int mMateAlignmentStart
```
    - mInferredInsertSize
```
int mInferredInsertSize
```
    - mAttributes
```
SAMBinaryTagAndValue mAttributes
```
    - mReferenceIndex
```
java.lang.Integer mReferenceIndex
```
    - mMateReferenceIndex
```
java.lang.Integer mMateReferenceIndex
```
    - mIndexingBin
```
java.lang.Integer mIndexingBin
```
    - mValidationStringency
```
ValidationStringency mValidationStringency
```
      Some attributes (e.g. CIGAR) are not decoded immediately. Use this to decide how to validate when decoded.
    - mHeader
```
SAMFileHeader mHeader
```
- Class htsjdk.samtools.SAMSequenceDictionary extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mSequences
```
java.util.List<E> mSequences
```
    - mSequenceMap
```
java.util.Map<K,V> mSequenceMap
```
- Class htsjdk.samtools.SAMSequenceRecord extends AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mSequenceName
```
java.lang.String mSequenceName
```
    - mSequenceIndex
```
int mSequenceIndex
```
    - mSequenceLength
```
int mSequenceLength
```
- Class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException extends java.lang.RuntimeException implements Serializable
- Class htsjdk.samtools.SAMValidationError extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - type
```
SAMValidationError.Type type
```
    - message
```
java.lang.String message
```
    - readName
```
java.lang.String readName
```
    - recordNumber
```
long recordNumber
```
    - source
```
java.lang.String source
```
Package htsjdk.samtools.cram.common
- Class htsjdk.samtools.cram.common.NonforgivingPrintStream.PrintStreamError extends java.lang.RuntimeException implements Serializable
Package htsjdk.samtools.cram.encoding.read_features
- Class htsjdk.samtools.cram.encoding.read_features.BaseChange extends java.lang.Object implements Serializable
  - Serialized Fields
    - change
```
int change
```
- Class htsjdk.samtools.cram.encoding.read_features.BaseQualityScore extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - qualityScore
```
byte qualityScore
```
- Class htsjdk.samtools.cram.encoding.read_features.Deletion extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - length
```
int length
```
- Class htsjdk.samtools.cram.encoding.read_features.HardClip extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - length
```
int length
```
- Class htsjdk.samtools.cram.encoding.read_features.InsertBase extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - base
```
byte base
```
- Class htsjdk.samtools.cram.encoding.read_features.Insertion extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - sequence
```
byte[] sequence
```
- Class htsjdk.samtools.cram.encoding.read_features.Padding extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - length
```
int length
```
- Class htsjdk.samtools.cram.encoding.read_features.ReadBase extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - base
```
byte base
```
    - qualityScore
```
byte qualityScore
```
- Class htsjdk.samtools.cram.encoding.read_features.RefSkip extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - length
```
int length
```
- Class htsjdk.samtools.cram.encoding.read_features.SoftClip extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - sequence
```
byte[] sequence
```
- Class htsjdk.samtools.cram.encoding.read_features.Substitution extends java.lang.Object implements Serializable
  - Serialized Fields
    - position
```
int position
```
    - base
```
byte base
```
    - refernceBase
```
byte refernceBase
```
    - baseChange
```
BaseChange baseChange
```
    - code
```
byte code
```
Package htsjdk.samtools.cram.mask
- Class htsjdk.samtools.cram.mask.ReadMaskException extends java.lang.Exception implements Serializable
- Class htsjdk.samtools.cram.mask.ReadMaskFormatException extends ReadMaskException implements Serializable
Package htsjdk.samtools.util
- Class htsjdk.samtools.util.CollectionUtil.DefaultingMap extends java.util.HashMap<K,V> implements Serializable
  - Serialized Fields
    - defaultGenerator
```
CollectionUtil.DefaultingMap.Factory<V,K> defaultGenerator
```
    - injectValueOnDefault
```
boolean injectValueOnDefault
```
- Class htsjdk.samtools.util.CollectionUtil.MultiMap extends java.util.HashMap<K,java.util.Collection<V>> implements Serializable
- Class htsjdk.samtools.util.DateParser.InvalidDateException extends SAMException implements Serializable
- Class htsjdk.samtools.util.Histogram extends java.util.TreeMap<K extends java.lang.Comparable,Histogram.Bin> implements Serializable
  - Serialized Fields
    - binLabel
```
java.lang.String binLabel
```
    - valueLabel
```
java.lang.String valueLabel
```
    - mean
```
java.lang.Double mean
```
- Class htsjdk.samtools.util.Iso8601Date extends java.util.Date implements Serializable
- Class htsjdk.samtools.util.ListMap extends java.util.HashMap<K,java.util.List<V>> implements Serializable
- Class htsjdk.samtools.util.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).
- Class htsjdk.samtools.util.RuntimeEOFException extends SAMException implements Serializable
- Class htsjdk.samtools.util.RuntimeIOException extends SAMException implements Serializable
- Class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException extends SAMException implements Serializable
Package htsjdk.tribble
- Class htsjdk.tribble.TribbleException extends java.lang.RuntimeException implements Serializable
  - Serialized Fields
    - source
```
java.lang.String source
```
- Class htsjdk.tribble.TribbleException.FeatureFileDoesntExist extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.InternalCodecException extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.InvalidDecodeLine extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.InvalidHeader extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.MalformedFeatureFile extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.TabixReaderFailure extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType extends TribbleException implements Serializable
- Class htsjdk.tribble.TribbleException.UnableToReadIndexFile extends TribbleException implements Serializable
Package htsjdk.tribble.exception
- Class htsjdk.tribble.exception.CodecLineParsingException extends java.lang.RuntimeException implements Serializable
- Class htsjdk.tribble.exception.UnsortedFileException extends java.lang.RuntimeException implements Serializable
Package htsjdk.variant.variantcontext
- Class htsjdk.variant.variantcontext.Allele extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isRef
```
boolean isRef
```
    - isNoCall
```
boolean isNoCall
```
    - isSymbolic
```
boolean isSymbolic
```
    - bases
```
byte[] bases
```
- Class htsjdk.variant.variantcontext.CommonInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - log10PError
```
double log10PError
```
    - name
```
java.lang.String name
```
    - filters
```
java.util.Set<E> filters
```
    - attributes
```
java.util.Map<K,V> attributes
```
- Class htsjdk.variant.variantcontext.FastGenotype extends Genotype implements Serializable
  - Serialized Fields
    - alleles
```
java.util.List<E> alleles
```
    - isPhased
```
boolean isPhased
```
    - GQ
```
int GQ
```
    - DP
```
int DP
```
    - AD
```
int[] AD
```
    - PL
```
int[] PL
```
    - extendedAttributes
```
java.util.Map<K,V> extendedAttributes
```
- Class htsjdk.variant.variantcontext.Genotype extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sampleName
```
java.lang.String sampleName
```
    - type
```
GenotypeType type
```
    - filters
```
java.lang.String filters
```
- Class htsjdk.variant.variantcontext.GenotypesContext extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      Custom serialization routine. Needed to ensure that we decode any lazily-decoded data before serialization.
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - sampleNamesInOrder
```
java.util.List<E> sampleNamesInOrder
```
      sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order
    - sampleNameToOffset
```
java.util.Map<K,V> 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
    - notToBeDirectlyAccessedGenotypes
```
java.util.ArrayList<E> 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.
    - maxPloidy
```
int maxPloidy
```
      Cached value of the maximum ploidy observed among all samples
    - immutable
```
boolean immutable
```
      Are we allowing users to modify the list?
- Class htsjdk.variant.variantcontext.LazyGenotypesContext extends GenotypesContext implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.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.
      
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
  - Serialized Fields
    - nUnparsedGenotypes
```
int nUnparsedGenotypes
```
      nUnparsedGenotypes the number of genotypes contained in the unparsedGenotypes data (known already in the parser). Useful for isEmpty and size() optimizations
    - loaded
```
boolean loaded
```
      True if we've already decoded the values in unparsedGenotypeData
- Class htsjdk.variant.variantcontext.VariantContext extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fullyDecoded
```
boolean fullyDecoded
```
    - commonInfo
```
CommonInfo commonInfo
```
    - contig
```
java.lang.String contig
```
      The location of this VariantContext
    - start
```
long start
```
    - stop
```
long stop
```
    - ID
```
java.lang.String ID
```
    - type
```
VariantContext.Type type
```
      The type (cached for performance reasons) of this context
    - alleles
```
java.util.List<E> alleles
```
      A set of the alleles segregating in this context
    - genotypes
```
GenotypesContext genotypes
```
      A mapping from sampleName -> genotype objects for all genotypes associated with this context
    - genotypeCounts
```
int[] genotypeCounts
```
      Counts for each of the possible Genotype types in this context
    - REF
```
Allele REF
```
    - ALT
```
Allele ALT
```
    - monomorphic
```
java.lang.Boolean monomorphic
```
Package htsjdk.variant.vcf
- Class htsjdk.variant.vcf.VCFCompoundHeaderLine extends VCFHeaderLine implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
    - count
```
int count
```
    - countType
```
VCFHeaderLineCount countType
```
    - description
```
java.lang.String description
```
    - type
```
VCFHeaderLineType type
```
    - lineType
```
VCFCompoundHeaderLine.SupportedHeaderLineType lineType
```
- Class htsjdk.variant.vcf.VCFContigHeaderLine extends VCFSimpleHeaderLine implements Serializable
  - Serialized Fields
    - contigIndex
```
java.lang.Integer contigIndex
```
- Class htsjdk.variant.vcf.VCFFilterHeaderLine extends VCFSimpleHeaderLine implements Serializable
- Class htsjdk.variant.vcf.VCFFormatHeaderLine extends VCFCompoundHeaderLine implements Serializable
- Class htsjdk.variant.vcf.VCFHeader extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mMetaData
```
java.util.Set<E> mMetaData
```
    - mInfoMetaData
```
java.util.Map<K,V> mInfoMetaData
```
    - mFormatMetaData
```
java.util.Map<K,V> mFormatMetaData
```
    - mFilterMetaData
```
java.util.Map<K,V> mFilterMetaData
```
    - mOtherMetaData
```
java.util.Map<K,V> mOtherMetaData
```
    - contigMetaData
```
java.util.List<E> contigMetaData
```
    - mGenotypeSampleNames
```
java.util.List<E> mGenotypeSampleNames
```
    - samplesWereAlreadySorted
```
boolean samplesWereAlreadySorted
```
    - sampleNamesInOrder
```
java.util.ArrayList<E> sampleNamesInOrder
```
    - sampleNameToOffset
```
java.util.HashMap<K,V> sampleNameToOffset
```
    - writeEngineHeaders
```
boolean writeEngineHeaders
```
    - writeCommandLine
```
boolean writeCommandLine
```
- Class htsjdk.variant.vcf.VCFHeaderLine extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mKey
```
java.lang.String mKey
```
    - mValue
```
java.lang.String mValue
```
- Class htsjdk.variant.vcf.VCFInfoHeaderLine extends VCFCompoundHeaderLine implements Serializable
- Class htsjdk.variant.vcf.VCFSimpleHeaderLine extends VCFHeaderLine implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
    - genericFields
```
java.util.Map<K,V> genericFields
```

Serialized Form

Package htsjdk.samtools

Class htsjdk.samtools.AbstractSAMHeaderRecord extends java.lang.Object implements Serializable

Serialized Fields

mAttributes

Class htsjdk.samtools.AlignmentBlock extends java.lang.Object implements Serializable

Serialized Fields

readStart

referenceStart

length

Class htsjdk.samtools.BAMRecord extends SAMRecord implements Serializable

Serialized Fields

mRestOfBinaryData

mReadLength

mReadLengthValid

mReadNameLength

mReadNameLengthValid

mCigarLength

mCigarLengthValid

mAttributesDecoded

mCigarDecoded

mBinaryDataStale

Class htsjdk.samtools.Chunk extends java.lang.Object implements Serializable

Serialized Fields

mChunkStart

mChunkEnd

Class htsjdk.samtools.Cigar extends java.lang.Object implements Serializable

Serialized Fields

cigarElements

Class htsjdk.samtools.CigarElement extends java.lang.Object implements Serializable

Serialized Fields

length

operator

Class htsjdk.samtools.FileTruncatedException extends SAMException implements Serializable

Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue extends SAMBinaryTagAndValue implements Serializable

Class htsjdk.samtools.SAMBinaryTagAndValue extends java.lang.Object implements Serializable

Serialized Fields

tag

value

next

Class htsjdk.samtools.SAMException extends java.lang.RuntimeException implements Serializable

Class htsjdk.samtools.SAMFileHeader extends AbstractSAMHeaderRecord implements Serializable

Serialized Fields

mReadGroups

mProgramRecords

mReadGroupMap

mProgramRecordMap

mSequenceDictionary

mComments

textHeader

mValidationErrors

Class htsjdk.samtools.SAMFormatException extends SAMException implements Serializable

Class htsjdk.samtools.SAMProgramRecord extends AbstractSAMHeaderRecord implements Serializable

Serialized Fields

mProgramGroupId

Class htsjdk.samtools.SAMReadGroupRecord extends AbstractSAMHeaderRecord implements Serializable

Serialized Fields

mReadGroupId

Class htsjdk.samtools.SAMRecord extends java.lang.Object implements Serializable

Serialized Fields

mReadName

mReadBases

mBaseQualities

mReferenceName

mAlignmentStart

mMappingQuality

mCigarString

mCigar

mAlignmentBlocks

mFlags

mMateReferenceName

mMateAlignmentStart

mInferredInsertSize

mAttributes

mReferenceIndex

mMateReferenceIndex

mIndexingBin

mValidationStringency

mHeader

Class htsjdk.samtools.SAMSequenceDictionary extends java.lang.Object implements Serializable