Package htsjdk.samtools

Class BAMRecord

java.lang.Object

htsjdk.samtools.SAMRecord

htsjdk.samtools.BAMRecord

All Implemented Interfaces:

HtsRecord, Locatable, Serializable, Cloneable

public class BAMRecord
extends SAMRecord

Wrapper class for binary BAM records. Delays unpacking all data binary until requested.

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.samtools.SAMRecord

SAMRecord.SAMTagAndValue

Field Summary

Fields

Modifier and Type	Field	Description
static final short	CIGAR_SIZE_MULTIPLIER	Constant for converting between the number of operators in a Cigar and the length of the int[] array needed to represent it in the BAM format
static final int	MAX_CIGAR_ELEMENT_LENGTH
static final int	MAX_CIGAR_OPERATORS	Maximal number of cigar operators that can be represented normally in the cigar part of the bam record.

Fields inherited from class htsjdk.samtools.SAMRecord

MAX_INSERT_SIZE, mMateReferenceIndex, mReferenceIndex, NO_ALIGNMENT_CIGAR, NO_ALIGNMENT_REFERENCE_INDEX, NO_ALIGNMENT_REFERENCE_NAME, NO_ALIGNMENT_START, NO_MAPPING_QUALITY, NULL_QUALS, NULL_QUALS_STRING, NULL_SEQUENCE, NULL_SEQUENCE_STRING, serialVersionUID, TAGS_TO_REVERSE, TAGS_TO_REVERSE_COMPLEMENT, UNKNOWN_MAPPING_QUALITY

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	BAMRecord(SAMFileHeader header, int referenceID, int coordinate, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceID, int mateCoordinate, int insertSize, byte[] restOfData)	Create a new BAM Record.

Method Summary

Modifier and Type	Method	Description
void	clearAttributes()	Removes all attributes.
protected void	eagerDecode()	Force all the lazily-initialized attributes to be decoded.
Object	getAttribute(short tag)
int	getAttributesBinarySize()	Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.
byte[]	getBaseQualities()	Do not modify the value returned by this method.
protected SAMBinaryTagAndValue	getBinaryAttributes()
Cigar	getCigar()	Do not modify the value returned by this method.
int	getCigarLength()	Avoids decoding CIGAR in order to get length.
byte[]	getReadBases()	Do not modify the value returned by this method.
int	getReadLength()	Avoids decoding binary block to get read length.
String	getReadName()
int	getReadNameLength()	Avoids decoding read name to get read name length.
byte[]	getVariableBinaryRepresentation()	If this record has a valid binary representation of the variable-length portion of a binary record stored, return that byte array, otherwise return null.
protected void	setAttribute(short tag, Object value, boolean isUnsignedArray)
void	setBaseQualities(byte[] value)
void	setCigar(Cigar cigar)	For setting the Cigar string when changed.
void	setCigarString(String value)
void	setReadBases(byte[] value)
void	setReadName(String value)

Methods inherited from class htsjdk.samtools.SAMRecord

clone, computeIndexingBinIfAbsent, deepCopy, equals, format, getAlignmentBlocks, getAlignmentEnd, getAlignmentStart, getAttribute, getAttribute, getAttributes, getBaseQualityString, getByteArrayAttribute, getByteArrayAttribute, getByteAttribute, getByteAttribute, getCharacterAttribute, getCharacterAttribute, getCigarString, getContig, getDuplicateReadFlag, getEnd, getFileSource, getFirstOfPairFlag, getFlags, getFloatArrayAttribute, getFloatArrayAttribute, getFloatAttribute, getFloatAttribute, getHeader, getInferredInsertSize, getIntegerAttribute, getIntegerAttribute, getMappingQuality, getMateAlignmentStart, getMateNegativeStrandFlag, getMateReferenceIndex, getMateReferenceName, getMateUnmappedFlag, getNotPrimaryAlignmentFlag, getOriginalBaseQualities, getPairedReadName, getProperPairFlag, getReadFailsVendorQualityCheckFlag, getReadGroup, getReadNegativeStrandFlag, getReadPairedFlag, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadString, getReadUnmappedFlag, getReferenceIndex, getReferenceName, getReferencePositionAtReadPosition, getReferencePositionAtReadPosition, getSAMFlags, getSAMString, getSecondOfPairFlag, getShortAttribute, getShortAttribute, getSignedByteArrayAttribute, getSignedByteArrayAttribute, getSignedIntArrayAttribute, getSignedIntArrayAttribute, getSignedShortArrayAttribute, getSignedShortArrayAttribute, getStart, getStringAttribute, getStringAttribute, getSupplementaryAlignmentFlag, getTransientAttribute, getUnclippedEnd, getUnclippedStart, getUnsignedByteArrayAttribute, getUnsignedByteArrayAttribute, getUnsignedIntArrayAttribute, getUnsignedIntArrayAttribute, getUnsignedIntegerAttribute, getUnsignedIntegerAttribute, getUnsignedIntegerAttribute, getUnsignedShortArrayAttribute, getUnsignedShortArrayAttribute, getValidationStringency, hasAttribute, hasAttribute, hashCode, initializeCigar, isAllowedAttributeValue, isSecondaryAlignment, isSecondaryOrSupplementary, isUnsignedArrayAttribute, isValid, isValid, removeTransientAttribute, resolveIndexFromName, resolveNameFromIndex, reverseComplement, reverseComplement, reverseComplement, setAlignmentStart, setAttribute, setAttribute, setAttribute, setAttribute, setAttributes, setBaseQualityString, setDuplicateReadFlag, setFileSource, setFirstOfPairFlag, setFlags, setHeader, setHeaderStrict, setInferredInsertSize, setMappingQuality, setMateAlignmentStart, setMateNegativeStrandFlag, setMateReferenceIndex, setMateReferenceName, setMateUnmappedFlag, setNotPrimaryAlignmentFlag, setOriginalBaseQualities, setProperPairFlag, setReadFailsVendorQualityCheckFlag, setReadNegativeStrandFlag, setReadPairedFlag, setReadString, setReadUmappedFlag, setReadUnmappedFlag, setReferenceIndex, setReferenceName, setSecondaryAlignment, setSecondOfPairFlag, setSupplementaryAlignmentFlag, setTransientAttribute, setUnsignedArrayAttribute, setValidationStringency, toString, validateCigar

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Field Details

CIGAR_SIZE_MULTIPLIER

public static final short CIGAR_SIZE_MULTIPLIER

Constant for converting between the number of operators in a Cigar and the length of the int[] array needed to represent it in the BAM format

See Also:

• Constant Field Values

MAX_CIGAR_OPERATORS

public static final int MAX_CIGAR_OPERATORS

Maximal number of cigar operators that can be represented normally in the cigar part of the bam record. Records that have larger cigars will have their Cigars encoded to int[] and placed in the CG tag in the attributes (BAM only) This should happen upon encoding. In place of the Cigar a sentinel value will be placed SN

When a BAM record is decoded, the sentinel cigar informs of the existance of the CG tag, which is decoded and removed. The sentinel value is then replaced with the actual cigar (in memory).

See Also:

• Constant Field Values

MAX_CIGAR_ELEMENT_LENGTH

public static final int MAX_CIGAR_ELEMENT_LENGTH

See Also:

• Constant Field Values

Constructor Details

BAMRecord

protected BAMRecord(SAMFileHeader header,
 int referenceID,
 int coordinate,
 short readNameLength,
 short mappingQuality,
 int indexingBin,
 int cigarLen,
 int flags,
 int readLen,
 int mateReferenceID,
 int mateCoordinate,
 int insertSize,
 byte[] restOfData)

Create a new BAM Record. If the reference sequence index or mate reference sequence index are any value other than NO_ALIGNMENT_REFERENCE_INDEX (-1), then the specified index values must exist in the sequence dictionary in the header argument.

Method Details

eagerDecode

protected void eagerDecode()

Force all the lazily-initialized attributes to be decoded.

Overrides:

eagerDecode in class SAMRecord

getVariableBinaryRepresentation

public byte[] getVariableBinaryRepresentation()

If this record has a valid binary representation of the variable-length portion of a binary record stored, return that byte array, otherwise return null. This will never be true for SAMRecords. It will be true for BAMRecords that have not been eagerDecoded(), and for which none of the data in the variable-length portion has been changed.

Overrides:

getVariableBinaryRepresentation in class SAMRecord

getAttributesBinarySize

public int getAttributesBinarySize()

Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.

Overrides:

getAttributesBinarySize in class SAMRecord

Returns:

binary file size of attribute, if known, else -1.

setReadName

public void setReadName(String value)

Overrides:

setReadName in class SAMRecord

setCigar

public void setCigar(Cigar cigar)

Description copied from class: SAMRecord

For setting the Cigar string when changed. Note that this nulls the indexing bin, which would need to be recomputed on write (if needed). To avoid clobbering the indexing bin, use SAMRecord.initializeCigar(htsjdk.samtools.Cigar)

Overrides:

setCigar in class SAMRecord

setCigarString

public void setCigarString(String value)

Overrides:

setCigarString in class SAMRecord

setReadBases

public void setReadBases(byte[] value)

Overrides:

setReadBases in class SAMRecord

setBaseQualities

public void setBaseQualities(byte[] value)

Overrides:

setBaseQualities in class SAMRecord

setAttribute

protected void setAttribute(short tag,
 Object value,
 boolean isUnsignedArray)

Overrides:

setAttribute in class SAMRecord

clearAttributes

public void clearAttributes()

Removes all attributes.

Overrides:

clearAttributes in class SAMRecord

getReadLength

public int getReadLength()

Avoids decoding binary block to get read length.

Overrides:

getReadLength in class SAMRecord

Returns:

number of bases in the read.

getReadName

public String getReadName()

Overrides:

getReadName in class SAMRecord

getReadNameLength

public int getReadNameLength()

Avoids decoding read name to get read name length. Do not include null terminator.

Overrides:

getReadNameLength in class SAMRecord

Returns:

length not including a null terminator.

getCigar

public Cigar getCigar()

Description copied from class: SAMRecord

Do not modify the value returned by this method. If you want to change the Cigar, create a new Cigar and call setCigar() or call setCigarString()

Overrides:

getCigar in class SAMRecord

Returns:

Cigar object for the read, or null if there is none.

getCigarLength

public int getCigarLength()

Avoids decoding CIGAR in order to get length.

Overrides:

getCigarLength in class SAMRecord

Returns:

number of cigar elements (number + operator) in the cigar string.

getReadBases

public byte[] getReadBases()

Description copied from class: SAMRecord

Do not modify the value returned by this method. If you want to change the bases, create a new byte[] and call setReadBases() or call setReadString().

Overrides:

getReadBases in class SAMRecord

Returns:

read sequence as ASCII bytes ACGTN=.

getBaseQualities

public byte[] getBaseQualities()

Description copied from class: SAMRecord

Do not modify the value returned by this method. If you want to change the qualities, create a new byte[] and call setBaseQualities() or call setBaseQualityString().

Overrides:

getBaseQualities in class SAMRecord

Returns:

Base qualities, as binary phred scores (not ASCII).

getAttribute

public Object getAttribute(short tag)

Overrides:

getAttribute in class SAMRecord

Parameters:

tag - Binary representation of a 2-char String tag as created by SAMTagUtil.

See Also:

• SAMRecord.getAttribute(java.lang.String)

getBinaryAttributes

protected SAMBinaryTagAndValue getBinaryAttributes()

Overrides:

getBinaryAttributes in class SAMRecord

Returns:

Pointer to the first of the tags. Returns null if there are no tags.