Serialized Form
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Package htsjdk.samtools
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Class htsjdk.samtools.AbstractSAMHeaderRecord extends Object implements Serializable
- serialVersionUID:
- 1L
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Class htsjdk.samtools.AlignmentBlock extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
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length
int length
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readStart
int readStart
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referenceStart
int referenceStart
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Class htsjdk.samtools.BAMFileSpan extends Object implements Serializable
- serialVersionUID:
- 1L
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Class htsjdk.samtools.BAMRecord extends SAMRecord implements Serializable
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Serialized Fields
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mAttributesDecoded
boolean mAttributesDecoded
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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
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mCigarLength
int mCigarLength
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mCigarLengthValid
boolean mCigarLengthValid
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mReadLength
int mReadLength
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mReadLengthValid
boolean mReadLengthValid
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mReadNameLength
short mReadNameLength
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mReadNameLengthValid
boolean mReadNameLengthValid
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mRestOfBinaryData
byte[] mRestOfBinaryData
Variable-length part of BAMRecord. Lazily decoded.
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-
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Class htsjdk.samtools.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.
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Class htsjdk.samtools.Cigar extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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cigarElements
List<CigarElement> cigarElements
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-
Class htsjdk.samtools.CigarElement extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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length
int length
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operator
CigarOperator operator
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Class htsjdk.samtools.FileTruncatedException extends SAMException implements Serializable
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Class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue extends SAMBinaryTagAndValue implements Serializable
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Class htsjdk.samtools.SAMBinaryTagAndValue extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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next
SAMBinaryTagAndValue next
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tag
short tag
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value
Object value
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-
Class htsjdk.samtools.SAMException extends RuntimeException implements Serializable
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Class htsjdk.samtools.SAMFileHeader extends AbstractSAMHeaderRecord implements Serializable
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Serialized Fields
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groupOrder
SAMFileHeader.GroupOrder groupOrder
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mComments
List<String> mComments
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mProgramRecordMap
Map<String,SAMProgramRecord> mProgramRecordMap
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mProgramRecords
List<SAMProgramRecord> mProgramRecords
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mReadGroupMap
Map<String,SAMReadGroupRecord> mReadGroupMap
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mReadGroups
List<SAMReadGroupRecord> mReadGroups
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mSequenceDictionary
SAMSequenceDictionary mSequenceDictionary
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mValidationErrors
List<SAMValidationError> mValidationErrors
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sortOrder
SAMFileHeader.SortOrder sortOrder
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-
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Class htsjdk.samtools.SAMFormatException extends SAMException implements Serializable
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Class htsjdk.samtools.SAMHeaderRecordComparator extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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attributes
String[] attributes
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Class htsjdk.samtools.SAMProgramRecord extends AbstractSAMHeaderRecord implements Serializable
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Serialized Fields
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mProgramGroupId
String mProgramGroupId
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-
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Class htsjdk.samtools.SAMReadGroupRecord extends AbstractSAMHeaderRecord implements Serializable
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Serialized Fields
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mReadGroupId
String mReadGroupId
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-
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Class htsjdk.samtools.SAMRecord extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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mAlignmentBlocks
List<AlignmentBlock> mAlignmentBlocks
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mAlignmentStart
int mAlignmentStart
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mAttributes
SAMBinaryTagAndValue mAttributes
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mBaseQualities
byte[] mBaseQualities
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mCigar
Cigar mCigar
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mCigarString
String mCigarString
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mFlags
int mFlags
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mHeader
SAMFileHeader mHeader
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mInferredInsertSize
int mInferredInsertSize
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mMappingQuality
int mMappingQuality
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mMateAlignmentStart
int mMateAlignmentStart
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mMateReferenceIndex
Integer mMateReferenceIndex
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mMateReferenceName
String mMateReferenceName
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mReadBases
byte[] mReadBases
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mReadName
String mReadName
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mReferenceIndex
Integer mReferenceIndex
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mReferenceName
String mReferenceName
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mValidationStringency
ValidationStringency mValidationStringency
Some attributes (e.g. CIGAR) are not decoded immediately. Use this to decide how to validate when decoded.
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Class htsjdk.samtools.SAMRecordCoordinateComparator extends Object implements Serializable
- serialVersionUID:
- 1L
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Class htsjdk.samtools.SAMRecordDuplicateComparator extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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libraryIds
Map<String,Short> libraryIds
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nextLibraryId
short nextLibraryId
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scoringStrategy
DuplicateScoringStrategy.ScoringStrategy scoringStrategy
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Class htsjdk.samtools.SAMRecordQueryHashComparator extends SAMRecordQueryNameComparator implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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hasher
Murmur3 hasher
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Class htsjdk.samtools.SAMRecordQueryNameComparator extends Object implements Serializable
- serialVersionUID:
- 1L
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Class htsjdk.samtools.SAMSequenceDictionary extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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mSequenceMap
Map<String,SAMSequenceRecord> mSequenceMap
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mSequences
List<SAMSequenceRecord> mSequences
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Class htsjdk.samtools.SAMSequenceRecord extends AbstractSAMHeaderRecord implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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mSequenceIndex
int mSequenceIndex
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mSequenceLength
int mSequenceLength
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mSequenceName
String mSequenceName
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Class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException extends RuntimeException implements Serializable
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Class htsjdk.samtools.SAMValidationError extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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message
String message
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readName
String readName
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recordNumber
long recordNumber
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source
String source
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type
SAMValidationError.Type type
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Class htsjdk.samtools.SBIIndex extends Object implements Serializable
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Serialized Fields
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header
SBIIndex.Header header
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virtualOffsets
long[] virtualOffsets
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-
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Class htsjdk.samtools.SBIIndex.Header extends Object implements Serializable
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Serialized Fields
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fileLength
long fileLength
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granularity
long granularity
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md5
byte[] md5
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totalNumberOfRecords
long totalNumberOfRecords
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uuid
byte[] uuid
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-
-
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Package htsjdk.samtools.cram
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Class htsjdk.samtools.cram.CRAMException extends SAMException implements Serializable
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Package htsjdk.samtools.cram.encoding.readfeatures
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Class htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore extends Object implements Serializable
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Serialized Fields
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position
int position
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qualityScore
byte qualityScore
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.Bases extends Object implements Serializable
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Serialized Fields
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bases
byte[] bases
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position
int position
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.Deletion extends Object implements Serializable
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Serialized Fields
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length
int length
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position
int position
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.HardClip extends Object implements Serializable
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Serialized Fields
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length
int length
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position
int position
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.InsertBase extends Object implements Serializable
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Serialized Fields
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base
byte base
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position
int position
-
-
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Class htsjdk.samtools.cram.encoding.readfeatures.Insertion extends Object implements Serializable
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Serialized Fields
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position
int position
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sequence
byte[] sequence
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.Padding extends Object implements Serializable
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Serialized Fields
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length
int length
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position
int position
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.ReadBase extends Object implements Serializable
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Serialized Fields
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base
byte base
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position
int position
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qualityScore
byte qualityScore
-
-
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Class htsjdk.samtools.cram.encoding.readfeatures.RefSkip extends Object implements Serializable
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Serialized Fields
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length
int length
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position
int position
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.Scores extends Object implements Serializable
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Serialized Fields
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position
int position
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scores
byte[] scores
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-
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Class htsjdk.samtools.cram.encoding.readfeatures.SoftClip extends Object implements Serializable
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Serialized Fields
-
position
int position
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sequence
byte[] sequence
-
-
-
Class htsjdk.samtools.cram.encoding.readfeatures.Substitution extends Object implements Serializable
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Serialized Fields
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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.
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-
-
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Package htsjdk.samtools.cram.ref
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Class htsjdk.samtools.cram.ref.GaveUpException extends RuntimeException implements Serializable
- serialVersionUID:
- -8997576068346912410L
-
Serialized Fields
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md5
String md5
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-
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Package htsjdk.samtools.fastq
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Package htsjdk.samtools.metrics
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Class htsjdk.samtools.metrics.MetricsFile extends Object implements Serializable
- serialVersionUID:
- 1L
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Class htsjdk.samtools.metrics.StringHeader extends Object implements Serializable
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Serialized Fields
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value
String value
-
-
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Class htsjdk.samtools.metrics.VersionHeader extends Object implements Serializable
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-
Package htsjdk.samtools.sra
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Class htsjdk.samtools.sra.SRAAccession extends Object implements Serializable
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Serialized Fields
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acc
String acc
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-
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Class htsjdk.samtools.sra.SRALazyRecord extends SAMRecord implements Serializable
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Serialized Fields
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accession
SRAAccession accession
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initializedAttributes
Set<htsjdk.samtools.sra.SRALazyRecord.LazyAttribute> initializedAttributes
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initializedFields
Set<htsjdk.samtools.sra.SRALazyRecord.LazyField> initializedFields
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initializedFlags
Set<htsjdk.samtools.sra.SRALazyRecord.LazyFlag> initializedFlags
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isAligned
boolean isAligned
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sraAlignmentId
String sraAlignmentId
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sraReadId
String sraReadId
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unalignedReadFragmentIndex
int unalignedReadFragmentIndex
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-
-
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Package htsjdk.samtools.util
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Class htsjdk.samtools.util.CollectionUtil.DefaultingMap extends HashMap<K,V> implements Serializable
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Serialized Fields
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defaultGenerator
CollectionUtil.DefaultingMap.Factory<V,K> defaultGenerator
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injectValueOnDefault
boolean injectValueOnDefault
-
-
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Class htsjdk.samtools.util.CollectionUtil.MultiMap extends HashMap<K,Collection<V>> implements Serializable
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Class htsjdk.samtools.util.DateParser.InvalidDateException extends SAMException implements Serializable
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Class htsjdk.samtools.util.Histogram extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
binLabel
String binLabel
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map
NavigableMap<K extends Comparable,Histogram.Bin<K extends Comparable>> map
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valueLabel
String valueLabel
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-
Class htsjdk.samtools.util.Histogram.Bin extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
id
K extends Comparable id
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value
double value
-
-
Class htsjdk.samtools.util.IntervalCoordinateComparator extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
header
SAMFileHeader header
-
-
Class htsjdk.samtools.util.Iso8601Date extends Date implements Serializable
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Class htsjdk.samtools.util.ListMap extends HashMap<K,List<V>> implements Serializable
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Class htsjdk.samtools.util.LocusComparator extends Object implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.samtools.util.Murmur3 extends Object implements Serializable
- serialVersionUID:
- 1L
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Serialized Fields
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seed
int seed
-
-
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).
-
-
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Class htsjdk.samtools.util.RuntimeEOFException extends SAMException implements Serializable
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Class htsjdk.samtools.util.RuntimeIOException extends SAMException implements Serializable
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Class htsjdk.samtools.util.RuntimeScriptException extends RuntimeException implements Serializable
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Class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException extends SAMException implements Serializable
-
-
Package htsjdk.tribble
-
Class htsjdk.tribble.TribbleException extends RuntimeException implements Serializable
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Serialized Fields
-
source
String source
-
-
-
Class htsjdk.tribble.TribbleException.CorruptedIndexFile extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.FeatureFileDoesntExist extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.InternalCodecException extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.InvalidDecodeLine extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.InvalidHeader extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.MalformedFeatureFile extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.TabixReaderFailure extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType extends TribbleException implements Serializable
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Class htsjdk.tribble.TribbleException.UnableToReadIndexFile extends TribbleException implements Serializable
-
-
Package htsjdk.tribble.exception
-
Class htsjdk.tribble.exception.CodecLineParsingException extends RuntimeException implements Serializable
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Class htsjdk.tribble.exception.UnsortedFileException extends RuntimeException implements Serializable
-
-
Package htsjdk.variant.variantcontext
-
Class htsjdk.variant.variantcontext.Allele extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
bases
byte[] bases
-
isNoCall
boolean isNoCall
-
isRef
boolean isRef
-
isSymbolic
boolean isSymbolic
-
-
Class htsjdk.variant.variantcontext.CommonInfo extends Object implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.variantcontext.FastGenotype extends Genotype implements Serializable
-
Class htsjdk.variant.variantcontext.Genotype extends Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
filters
String filters
-
sampleName
String sampleName
-
type
GenotypeType type
-
-
Class htsjdk.variant.variantcontext.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.- 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 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.- 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.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
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start
long start
-
stop
long stop
-
type
VariantContext.Type type
The type (cached for performance reasons) of this context
-
-
Class htsjdk.variant.variantcontext.VariantContextComparator extends Object implements Serializable
- serialVersionUID:
- 1L
-
-
Package htsjdk.variant.variantcontext.filter
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Class htsjdk.variant.variantcontext.filter.CompoundFilter extends ArrayList<VariantContextFilter> implements Serializable
-
Serialized Fields
-
requireAll
boolean requireAll
-
-
-
-
Package htsjdk.variant.vcf
-
Class htsjdk.variant.vcf.VCFAltHeaderLine extends VCFSimpleHeaderLine implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.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 extends VCFSimpleHeaderLine implements Serializable
-
Serialized Fields
-
contigIndex
Integer contigIndex
-
-
-
Class htsjdk.variant.vcf.VCFFilterHeaderLine extends VCFSimpleHeaderLine implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.VCFFormatHeaderLine extends VCFCompoundHeaderLine implements Serializable
-
Class htsjdk.variant.vcf.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 byVCFHeader.validateVersionTransition(VCFHeaderVersion, VCFHeaderVersion)
-
writeCommandLine
boolean writeCommandLine
-
writeEngineHeaders
boolean writeEngineHeaders
-
-
Class htsjdk.variant.vcf.VCFHeaderLine extends Object implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.VCFInfoHeaderLine extends VCFCompoundHeaderLine implements Serializable
-
Class htsjdk.variant.vcf.VCFMetaHeaderLine extends VCFSimpleHeaderLine implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.VCFPedigreeHeaderLine extends VCFSimpleHeaderLine implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.VCFSampleHeaderLine extends VCFSimpleHeaderLine implements Serializable
- serialVersionUID:
- 1L
-
Class htsjdk.variant.vcf.VCFSimpleHeaderLine extends VCFHeaderLine implements Serializable
-