public class SRALazyRecord 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, UNKNOWN_MAPPING_QUALITY
Modifier | Constructor and Description |
---|---|
|
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.AlignmentIterator alignmentIterator,
java.lang.String readId,
java.lang.String alignmentId) |
|
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.ReadIterator unalignmentIterator,
java.lang.String readId,
int unalignedReadFragmentIndex) |
protected |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
java.lang.String readId,
int unalignedReadFragmentIndex) |
protected |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
java.lang.String readId,
java.lang.String alignmentId) |
Modifier and Type | Method and Description |
---|---|
void |
clearAttributes()
Removes all attributes.
|
java.lang.Object |
clone()
Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator
|
void |
detachFromIterator()
Is being called when original NGS iterator is being moved to the next object.
|
boolean |
equals(java.lang.Object o)
For records equality, we should only compare read id, reference and position on the reference.
|
java.lang.String |
format() |
int |
getAlignmentStart() |
java.lang.Object |
getAttribute(short tag) |
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.
|
java.lang.String |
getCigarString() |
boolean |
getFirstOfPairFlag()
the read is the first read in a pair.
|
int |
getFlags()
It is preferable to use the get*Flag() methods that handle the flag word symbolically.
|
int |
getInferredInsertSize() |
int |
getMappingQuality() |
int |
getMateAlignmentStart() |
boolean |
getMateNegativeStrandFlag()
strand of the mate (false for forward; true for reverse strand).
|
java.lang.Integer |
getMateReferenceIndex()
Returns the mate reference index for this record.
|
java.lang.String |
getMateReferenceName() |
boolean |
getMateUnmappedFlag()
the mate is unmapped.
|
boolean |
getNotPrimaryAlignmentFlag()
the alignment is not primary (a read having split hits may have multiple primary alignment records).
|
boolean |
getProperPairFlag()
the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
|
byte[] |
getReadBases()
Do not modify the value returned by this method.
|
boolean |
getReadNegativeStrandFlag()
strand of the query (false for forward; true for reverse strand).
|
boolean |
getReadPairedFlag()
the read is paired in sequencing, no matter whether it is mapped in a pair.
|
java.lang.Integer |
getReferenceIndex()
Returns the reference index for this record.
|
java.lang.String |
getReferenceName() |
boolean |
getSecondOfPairFlag()
the read is the second read in a pair.
|
int |
hashCode()
The same approach as with 'equals' method.
|
boolean |
isUnsignedArrayAttribute(java.lang.String tag) |
java.util.List<SAMValidationError> |
isValid(boolean firstOnly)
Perform various validations of SAMRecord.
|
void |
setAlignmentStart(int value) |
void |
setAttribute(short tag,
java.lang.Object value) |
protected void |
setAttribute(short tag,
java.lang.Object value,
boolean isUnsignedArray) |
protected void |
setAttributes(SAMBinaryTagAndValue attributes)
Replace any existing attributes with the given linked item.
|
void |
setBaseQualities(byte[] value) |
void |
setCigar(Cigar value) |
void |
setCigarString(java.lang.String value) |
void |
setFirstOfPairFlag(boolean flag)
the read is the first read in a pair.
|
void |
setFlags(int value) |
void |
setInferredInsertSize(int value) |
void |
setMappingQuality(int value) |
void |
setMateAlignmentStart(int value) |
void |
setMateNegativeStrandFlag(boolean flag)
strand of the mate (false for forward; true for reverse strand).
|
void |
setMateReferenceIndex(int value)
Updates the mate reference index.
|
void |
setMateReferenceName(java.lang.String value)
Sets the mate reference name for this record.
|
void |
setMateUnmappedFlag(boolean flag)
the mate is unmapped.
|
void |
setNotPrimaryAlignmentFlag(boolean flag)
the alignment is not primary (a read having split hits may have multiple primary alignment records).
|
void |
setProperPairFlag(boolean flag)
the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
|
void |
setReadBases(byte[] value) |
void |
setReadNegativeStrandFlag(boolean flag)
strand of the query (false for forward; true for reverse strand).
|
void |
setReadPairedFlag(boolean flag)
the read is paired in sequencing, no matter whether it is mapped in a pair.
|
void |
setReferenceIndex(int value)
Updates the reference index.
|
void |
setReferenceName(java.lang.String value)
Sets the reference name for this record.
|
void |
setSecondOfPairFlag(boolean flag)
the read is the second read in a pair.
|
deepCopy, eagerDecode, getAlignmentBlocks, getAlignmentEnd, getAttribute, getAttributes, getAttributesBinarySize, getBaseQualityString, getByteArrayAttribute, getByteAttribute, getCharacterAttribute, getCigarLength, getContig, getDuplicateReadFlag, getEnd, getFileSource, getFloatArrayAttribute, getFloatAttribute, getHeader, getIntegerAttribute, getOriginalBaseQualities, getPairedReadName, getReadFailsVendorQualityCheckFlag, getReadGroup, getReadLength, getReadName, getReadNameLength, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadString, getReadUnmappedFlag, getReferencePositionAtReadPosition, getReferencePositionAtReadPosition, getSAMFlags, getSAMString, getShortAttribute, getSignedByteArrayAttribute, getSignedIntArrayAttribute, getSignedShortArrayAttribute, getStart, getStringAttribute, getSupplementaryAlignmentFlag, getTransientAttribute, getUnclippedEnd, getUnclippedStart, getUnsignedByteArrayAttribute, getUnsignedIntArrayAttribute, getUnsignedIntegerAttribute, getUnsignedIntegerAttribute, getUnsignedShortArrayAttribute, getValidationStringency, getVariableBinaryRepresentation, initializeCigar, isAllowedAttributeValue, isSecondaryOrSupplementary, isValid, removeTransientAttribute, resolveIndexFromName, resolveNameFromIndex, setAttribute, setBaseQualityString, setDuplicateReadFlag, setFileSource, setHeader, setHeaderStrict, setOriginalBaseQualities, setReadFailsVendorQualityCheckFlag, setReadName, setReadString, setReadUmappedFlag, setReadUnmappedFlag, setSupplementaryAlignmentFlag, setTransientAttribute, setUnsignedArrayAttribute, setValidationStringency, toString, validateCigar
public SRALazyRecord(SAMFileHeader header, SRAAccession accession, ngs.ReadCollection run, ngs.AlignmentIterator alignmentIterator, java.lang.String readId, java.lang.String alignmentId)
public SRALazyRecord(SAMFileHeader header, SRAAccession accession, ngs.ReadCollection run, ngs.ReadIterator unalignmentIterator, java.lang.String readId, int unalignedReadFragmentIndex)
protected SRALazyRecord(SAMFileHeader header, SRAAccession accession, java.lang.String readId, java.lang.String alignmentId)
protected SRALazyRecord(SAMFileHeader header, SRAAccession accession, java.lang.String readId, int unalignedReadFragmentIndex)
public void detachFromIterator()
public int getAlignmentStart()
getAlignmentStart
in class SAMRecord
public void setAlignmentStart(int value)
setAlignmentStart
in class SAMRecord
value
- 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.public int getMappingQuality()
getMappingQuality
in class SAMRecord
public void setMappingQuality(int value)
setMappingQuality
in class SAMRecord
public java.lang.String getReferenceName()
getReferenceName
in class SAMRecord
public void setReferenceName(java.lang.String value)
SAMRecord
setReferenceName
in class SAMRecord
value
- - must not be nullpublic java.lang.Integer getReferenceIndex()
SAMRecord
getReferenceIndex
in class SAMRecord
public void setReferenceIndex(int value)
SAMRecord
setReferenceIndex
in class SAMRecord
value
- Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the
record must have a SAMFileHeader and the index must exist in the associated sequence
dictionary.public java.lang.String getCigarString()
getCigarString
in class SAMRecord
public void setCigarString(java.lang.String value)
setCigarString
in class SAMRecord
public Cigar getCigar()
SAMRecord
public byte[] getReadBases()
SAMRecord
getReadBases
in class SAMRecord
public void setReadBases(byte[] value)
setReadBases
in class SAMRecord
public byte[] getBaseQualities()
SAMRecord
getBaseQualities
in class SAMRecord
public void setBaseQualities(byte[] value)
setBaseQualities
in class SAMRecord
public int getMateAlignmentStart()
getMateAlignmentStart
in class SAMRecord
public void setMateAlignmentStart(int value)
setMateAlignmentStart
in class SAMRecord
public java.lang.String getMateReferenceName()
getMateReferenceName
in class SAMRecord
public void setMateReferenceName(java.lang.String value)
SAMRecord
setMateReferenceName
in class SAMRecord
value
- - must not be nullpublic java.lang.Integer getMateReferenceIndex()
SAMRecord
getMateReferenceIndex
in class SAMRecord
public void setMateReferenceIndex(int value)
SAMRecord
setMateReferenceIndex
in class SAMRecord
value
- Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the
record must have a SAMFileHeader and the index must exist in the associated sequence
dictionary.public int getInferredInsertSize()
getInferredInsertSize
in class SAMRecord
public void setInferredInsertSize(int value)
setInferredInsertSize
in class SAMRecord
public int getFlags()
SAMRecord
public boolean getReadNegativeStrandFlag()
SAMRecord
getReadNegativeStrandFlag
in class SAMRecord
public void setReadNegativeStrandFlag(boolean flag)
SAMRecord
setReadNegativeStrandFlag
in class SAMRecord
public boolean getReadPairedFlag()
SAMRecord
getReadPairedFlag
in class SAMRecord
public void setReadPairedFlag(boolean flag)
SAMRecord
setReadPairedFlag
in class SAMRecord
public boolean getProperPairFlag()
SAMRecord
getProperPairFlag
in class SAMRecord
public void setProperPairFlag(boolean flag)
SAMRecord
setProperPairFlag
in class SAMRecord
public boolean getNotPrimaryAlignmentFlag()
SAMRecord
getNotPrimaryAlignmentFlag
in class SAMRecord
public void setNotPrimaryAlignmentFlag(boolean flag)
SAMRecord
setNotPrimaryAlignmentFlag
in class SAMRecord
public boolean getMateNegativeStrandFlag()
SAMRecord
getMateNegativeStrandFlag
in class SAMRecord
public void setMateNegativeStrandFlag(boolean flag)
SAMRecord
setMateNegativeStrandFlag
in class SAMRecord
public boolean getMateUnmappedFlag()
SAMRecord
getMateUnmappedFlag
in class SAMRecord
public void setMateUnmappedFlag(boolean flag)
SAMRecord
setMateUnmappedFlag
in class SAMRecord
public boolean getFirstOfPairFlag()
SAMRecord
getFirstOfPairFlag
in class SAMRecord
public void setFirstOfPairFlag(boolean flag)
SAMRecord
setFirstOfPairFlag
in class SAMRecord
public boolean getSecondOfPairFlag()
SAMRecord
getSecondOfPairFlag
in class SAMRecord
public void setSecondOfPairFlag(boolean flag)
SAMRecord
setSecondOfPairFlag
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)
public void setAttribute(short tag, java.lang.Object value)
setAttribute
in class SAMRecord
tag
- Binary representation of a 2-char String tag as created by SAMTagUtil.SAMRecord.setAttribute(java.lang.String, java.lang.Object)
protected void setAttribute(short tag, java.lang.Object value, boolean isUnsignedArray)
setAttribute
in class SAMRecord
public void clearAttributes()
SAMRecord
clearAttributes
in class SAMRecord
protected void setAttributes(SAMBinaryTagAndValue attributes)
SAMRecord
setAttributes
in class SAMRecord
protected SAMBinaryTagAndValue getBinaryAttributes()
getBinaryAttributes
in class SAMRecord
public boolean isUnsignedArrayAttribute(java.lang.String tag)
isUnsignedArrayAttribute
in class SAMRecord
public boolean equals(java.lang.Object o)
public int hashCode()
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
public java.lang.String format()
public java.util.List<SAMValidationError> isValid(boolean firstOnly)
SAMRecord