int readStart
int referenceStart
int length
byte[] mRestOfBinaryData
int mReadLength
boolean mReadLengthValid
short mReadNameLength
boolean mReadNameLengthValid
int mCigarLength
boolean mCigarLengthValid
boolean mAttributesDecoded
boolean mCigarDecoded
boolean mBinaryDataStale
long mChunkStart
long mChunkEnd
int length
CigarOperator operator
short tag
Object value
SAMBinaryTagAndValue next
List<E> mReadGroups
List<E> mProgramRecords
Map<K,V> mReadGroupMap
Map<K,V> mProgramRecordMap
SAMSequenceDictionary mSequenceDictionary
List<E> mComments
String textHeader
List<E> mValidationErrors
String[] attributes
String mProgramGroupId
String mReadGroupId
String mReadName
byte[] mReadBases
byte[] mBaseQualities
String mReferenceName
int mAlignmentStart
int mMappingQuality
String mCigarString
Cigar mCigar
List<E> mAlignmentBlocks
int mFlags
String mMateReferenceName
int mMateAlignmentStart
int mInferredInsertSize
SAMBinaryTagAndValue mAttributes
Integer mReferenceIndex
Integer mMateReferenceIndex
Integer mIndexingBin
ValidationStringency mValidationStringency
SAMFileHeader mHeader
Map<K,V> libraryIds
short nextLibraryId
DuplicateScoringStrategy.ScoringStrategy scoringStrategy
Murmur3 hasher
String mSequenceName
int mSequenceIndex
int mSequenceLength
SAMValidationError.Type type
String message
String readName
long recordNumber
String source
int position
byte qualityScore
int position
byte[] bases
int position
int length
int position
int length
int position
byte base
int position
byte[] sequence
int position
int length
int position
byte base
byte qualityScore
int position
int length
int position
byte[] scores
int position
byte[] sequence
int position
byte base
byte referenceBase
byte code
String md5
String value
String acc
SRAAccession accession
boolean isAligned
String sraReadId
String sraAlignmentId
int unalignedReadFragmentIndex
Set<E> initializedFields
Set<E> initializedFlags
Set<E> initializedAttributes
CollectionUtil.DefaultingMap.Factory<V,K> defaultGenerator
boolean injectValueOnDefault
Comparable<T> id
double value
int seed
boolean doSetTimeNextQuery
String source
boolean isRef
boolean isNoCall
boolean isSymbolic
byte[] bases
String sampleName
GenotypeType type
String filters
private void writeObject(ObjectOutputStream out) throws IOException
IOException
List<E> sampleNamesInOrder
Map<K,V> sampleNameToOffset
ArrayList<E> notToBeDirectlyAccessedGenotypes
int maxPloidy
boolean immutable
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
int nUnparsedGenotypes
boolean loaded
boolean fullyDecoded
CommonInfo commonInfo
String contig
long start
long stop
String ID
VariantContext.Type type
List<E> alleles
GenotypesContext genotypes
int[] genotypeCounts
Allele REF
Allele ALT
Boolean monomorphic
boolean requireAll
String name
int count
VCFHeaderLineCount countType
String description
VCFHeaderLineType type
VCFCompoundHeaderLine.SupportedHeaderLineType lineType
Integer contigIndex
Set<E> mMetaData
Map<K,V> mInfoMetaData
Map<K,V> mFormatMetaData
Map<K,V> mFilterMetaData
Map<K,V> mOtherMetaData
List<E> contigMetaData
List<E> mGenotypeSampleNames
boolean samplesWereAlreadySorted
ArrayList<E> sampleNamesInOrder
HashMap<K,V> sampleNameToOffset
boolean writeEngineHeaders
boolean writeCommandLine