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