Serialized Form (Hadoop-BAM 7.9.1 API)

Package htsjdk.samtools
- Class htsjdk.samtools.AbstractSAMHeaderRecord extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mAttributes
```
Map<K,V> mAttributes
```
- Class htsjdk.samtools.AlignmentBlock extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - readStart
```
int readStart
```
    - referenceStart
```
int referenceStart
```
    - length
```
int length
```
- Class htsjdk.samtools.BAMFileSpan extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - chunks
```
List<E> chunks
```
- Class htsjdk.samtools.BAMRecord extends htsjdk.samtools.SAMRecord implements Serializable
  - Serialized Fields
    - mRestOfBinaryData
```
byte[] mRestOfBinaryData
```
    - 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
```
- Class htsjdk.samtools.Chunk extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mChunkStart
```
long mChunkStart
```
    - mChunkEnd
```
long mChunkEnd
```
- Class htsjdk.samtools.Cigar extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cigarElements
```
List<E> cigarElements
```
- Class htsjdk.samtools.CigarElement extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - length
```
int length
```
    - operator
```
htsjdk.samtools.CigarOperator operator
```
- Class htsjdk.samtools.FileTruncatedException extends htsjdk.samtools.SAMException implements Serializable
- Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue extends htsjdk.samtools.SAMBinaryTagAndValue implements Serializable
- Class htsjdk.samtools.SAMBinaryTagAndValue extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tag
```
short tag
```
    - value
```
Object value
```
    - next
```
htsjdk.samtools.SAMBinaryTagAndValue next
```
- Class htsjdk.samtools.SAMException extends RuntimeException implements Serializable
- Class htsjdk.samtools.SAMFileHeader extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - sortOrder
```
htsjdk.samtools.SAMFileHeader.SortOrder sortOrder
```
    - groupOrder
```
htsjdk.samtools.SAMFileHeader.GroupOrder groupOrder
```
    - mReadGroups
```
List<E> mReadGroups
```
    - mProgramRecords
```
List<E> mProgramRecords
```
    - mReadGroupMap
```
Map<K,V> mReadGroupMap
```
    - mProgramRecordMap
```
Map<K,V> mProgramRecordMap
```
    - mSequenceDictionary
```
htsjdk.samtools.SAMSequenceDictionary mSequenceDictionary
```
    - mComments
```
List<E> mComments
```
    - textHeader
```
String textHeader
```
    - mValidationErrors
```
List<E> mValidationErrors
```
- Class htsjdk.samtools.SAMFormatException extends htsjdk.samtools.SAMException implements Serializable
- Class htsjdk.samtools.SAMHeaderRecordComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - attributes
```
String[] attributes
```
- Class htsjdk.samtools.SAMProgramRecord extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mProgramGroupId
```
String mProgramGroupId
```
- Class htsjdk.samtools.SAMReadGroupRecord extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable
  - Serialized Fields
    - mReadGroupId
```
String mReadGroupId
```
- Class htsjdk.samtools.SAMRecord extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mReadName
```
String mReadName
```
    - mReadBases
```
byte[] mReadBases
```
    - mBaseQualities
```
byte[] mBaseQualities
```
    - mReferenceName
```
String mReferenceName
```
    - mAlignmentStart
```
int mAlignmentStart
```
    - mMappingQuality
```
int mMappingQuality
```
    - mCigarString
```
String mCigarString
```
    - mCigar
```
htsjdk.samtools.Cigar mCigar
```
    - mAlignmentBlocks
```
List<E> mAlignmentBlocks
```
    - mFlags
```
int mFlags
```
    - mMateReferenceName
```
String mMateReferenceName
```
    - mMateAlignmentStart
```
int mMateAlignmentStart
```
    - mInferredInsertSize
```
int mInferredInsertSize
```
    - mAttributes
```
htsjdk.samtools.SAMBinaryTagAndValue mAttributes
```
    - mReferenceIndex
```
Integer mReferenceIndex
```
    - mMateReferenceIndex
```
Integer mMateReferenceIndex
```
    - mIndexingBin
```
Integer mIndexingBin
```
    - mValidationStringency
```
htsjdk.samtools.ValidationStringency mValidationStringency
```
    - mHeader
```
htsjdk.samtools.SAMFileHeader mHeader
```
- Class htsjdk.samtools.SAMRecordCoordinateComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class htsjdk.samtools.SAMRecordDuplicateComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - libraryIds
```
Map<K,V> libraryIds
```
    - nextLibraryId
```
short nextLibraryId
```
    - scoringStrategy
```
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy scoringStrategy
```
- Class htsjdk.samtools.SAMRecordQueryHashComparator extends htsjdk.samtools.SAMRecordQueryNameComparator implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - hasher
```
htsjdk.samtools.util.Murmur3 hasher
```
- Class htsjdk.samtools.SAMRecordQueryNameComparator extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class htsjdk.samtools.SAMSequenceDictionary extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mSequences
```
List<E> mSequences
```
    - mSequenceMap
```
Map<K,V> mSequenceMap
```
- Class htsjdk.samtools.SAMSequenceRecord extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mSequenceName
```
String mSequenceName
```
    - mSequenceIndex
```
int mSequenceIndex
```
    - mSequenceLength
```
int mSequenceLength
```
- Class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException extends RuntimeException implements Serializable
- Class htsjdk.samtools.SAMValidationError extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - type
```
htsjdk.samtools.SAMValidationError.Type type
```
    - message
```
String message
```
    - readName
```
String readName
```
    - recordNumber
```
long recordNumber
```
    - source
```
String source
```
Package org.seqdoop.hadoop_bam
- Class org.seqdoop.hadoop_bam.FormatException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext extends LazyParsingGenotypesContext implements Serializable
- Class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext extends htsjdk.variant.variantcontext.LazyGenotypesContext implements Serializable
  - Serialized Fields
    - parserCopy
```
LazyParsingGenotypesContext.Parser parserCopy
```
- Class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext extends LazyParsingGenotypesContext implements Serializable
- Class org.seqdoop.hadoop_bam.VariantContextWithHeader extends htsjdk.variant.variantcontext.VariantContext implements Serializable
  - Serialized Fields
    - header
```
htsjdk.variant.vcf.VCFHeader header
```

Serialized Form

Package htsjdk.samtools

Class htsjdk.samtools.AbstractSAMHeaderRecord extends Object implements Serializable

Serialized Fields

mAttributes

Class htsjdk.samtools.AlignmentBlock extends Object implements Serializable

Serialized Fields

readStart

referenceStart

length

Class htsjdk.samtools.BAMFileSpan extends Object implements Serializable

Serialized Fields

chunks

Class htsjdk.samtools.BAMRecord extends htsjdk.samtools.SAMRecord implements Serializable

Serialized Fields

mRestOfBinaryData

mReadLength

mReadLengthValid

mReadNameLength

mReadNameLengthValid

mCigarLength

mCigarLengthValid

mAttributesDecoded

mCigarDecoded

mBinaryDataStale

Class htsjdk.samtools.Chunk extends Object implements Serializable

Serialized Fields

mChunkStart

mChunkEnd

Class htsjdk.samtools.Cigar extends Object implements Serializable

Serialized Fields

cigarElements

Class htsjdk.samtools.CigarElement extends Object implements Serializable

Serialized Fields

length

operator

Class htsjdk.samtools.FileTruncatedException extends htsjdk.samtools.SAMException implements Serializable

Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue extends htsjdk.samtools.SAMBinaryTagAndValue implements Serializable

Class htsjdk.samtools.SAMBinaryTagAndValue extends Object implements Serializable

Serialized Fields

tag

value

next

Class htsjdk.samtools.SAMException extends RuntimeException implements Serializable

Class htsjdk.samtools.SAMFileHeader extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable

Serialized Fields

sortOrder

groupOrder

mReadGroups

mProgramRecords

mReadGroupMap

mProgramRecordMap

mSequenceDictionary

mComments

textHeader

mValidationErrors

Class htsjdk.samtools.SAMFormatException extends htsjdk.samtools.SAMException implements Serializable

Class htsjdk.samtools.SAMHeaderRecordComparator extends Object implements Serializable

Serialized Fields

attributes

Class htsjdk.samtools.SAMProgramRecord extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable

Serialized Fields

mProgramGroupId

Class htsjdk.samtools.SAMReadGroupRecord extends htsjdk.samtools.AbstractSAMHeaderRecord implements Serializable

Serialized Fields

mReadGroupId

Class htsjdk.samtools.SAMRecord extends Object implements Serializable

Serialized Fields

mReadName

mReadBases

mBaseQualities

mReferenceName

mAlignmentStart

mMappingQuality

mCigarString

mCigar

mAlignmentBlocks

mFlags

mMateReferenceName

mMateAlignmentStart