public class BAMRecord extends SAMRecord
SAMRecord.SAMTagAndValue
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
Modifier | Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
void |
clearAttributes()
Removes all attributes.
|
protected void |
eagerDecode()
Force all the lazily-initialized attributes to be decoded.
|
java.lang.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.
|
java.lang.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,
java.lang.Object value,
boolean isUnsignedArray) |
void |
setBaseQualities(byte[] value) |
void |
setCigar(Cigar cigar) |
void |
setCigarString(java.lang.String value) |
void |
setReadBases(byte[] value) |
void |
setReadName(java.lang.String value) |
clone, deepCopy, equals, format, getAlignmentBlocks, getAlignmentEnd, getAlignmentStart, getAttribute, getAttributes, getBaseQualityString, getByteArrayAttribute, getByteAttribute, getCharacterAttribute, getCigarString, getContig, getDuplicateReadFlag, getEnd, getFileSource, getFirstOfPairFlag, getFlags, getFloatArrayAttribute, getFloatAttribute, getHeader, getInferredInsertSize, 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, getSignedByteArrayAttribute, getSignedIntArrayAttribute, getSignedShortArrayAttribute, getStart, getStringAttribute, getSupplementaryAlignmentFlag, getTransientAttribute, getUnclippedEnd, getUnclippedStart, getUnsignedByteArrayAttribute, getUnsignedIntArrayAttribute, getUnsignedIntegerAttribute, getUnsignedIntegerAttribute, getUnsignedShortArrayAttribute, getValidationStringency, hasAttribute, hashCode, initializeCigar, isAllowedAttributeValue, isSecondaryAlignment, isSecondaryOrSupplementary, isUnsignedArrayAttribute, isValid, isValid, removeTransientAttribute, resolveIndexFromName, resolveNameFromIndex, reverseComplement, reverseComplement, reverseComplement, setAlignmentStart, 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
finalize, getClass, notify, notifyAll, wait, wait, wait
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf
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)
protected void eagerDecode()
eagerDecode
in class SAMRecord
public byte[] getVariableBinaryRepresentation()
getVariableBinaryRepresentation
in class SAMRecord
public int getAttributesBinarySize()
getAttributesBinarySize
in class SAMRecord
public void setReadName(java.lang.String value)
setReadName
in class SAMRecord
public void setCigarString(java.lang.String value)
setCigarString
in class SAMRecord
public void setReadBases(byte[] value)
setReadBases
in class SAMRecord
public void setBaseQualities(byte[] value)
setBaseQualities
in class SAMRecord
protected void setAttribute(short tag, java.lang.Object value, boolean isUnsignedArray)
setAttribute
in class SAMRecord
public void clearAttributes()
clearAttributes
in class SAMRecord
public int getReadLength()
getReadLength
in class SAMRecord
public java.lang.String getReadName()
getReadName
in class SAMRecord
public int getReadNameLength()
getReadNameLength
in class SAMRecord
public Cigar getCigar()
SAMRecord
public int getCigarLength()
getCigarLength
in class SAMRecord
public byte[] getReadBases()
SAMRecord
getReadBases
in class SAMRecord
public byte[] getBaseQualities()
SAMRecord
getBaseQualities
in class SAMRecord
public java.lang.Object getAttribute(short tag)
getAttribute
in class SAMRecord
tag
- Binary representation of a 2-char String tag as created by SAMTagUtil.SAMRecord.getAttribute(java.lang.String)
protected SAMBinaryTagAndValue getBinaryAttributes()
getBinaryAttributes
in class SAMRecord