SAMRecord

java.lang.Object
- htsjdk.samtools.SAMRecord

All Implemented Interfaces:

Locatable, java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

BAMRecord
```
public class SAMRecord
extends java.lang.Object
implements java.lang.Cloneable, Locatable, java.io.Serializable
```
See Also:
Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SAMRecord.SAMTagAndValue
Tag name and value of an attribute, for getAttributes() method.

Nested Classes
Modifier and Type	Class and Description
`static class`	`SAMRecord.SAMTagAndValue` Tag name and value of an attribute, for getAttributes() method.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`MAX_INSERT_SIZE` abs(insertSize) must be <= this
`protected java.lang.Integer`	`mMateReferenceIndex`
`protected java.lang.Integer`	`mReferenceIndex`
`static java.lang.String`	`NO_ALIGNMENT_CIGAR` Cigar string for an unaligned read.
`static int`	`NO_ALIGNMENT_REFERENCE_INDEX` If a read has this reference index, it is unaligned, but not all unaligned reads have this reference index (see above).
`static java.lang.String`	`NO_ALIGNMENT_REFERENCE_NAME` If a read has this reference name, it is unaligned, but not all unaligned reads have this reference name (see above).
`static int`	`NO_ALIGNMENT_START` If a read has reference name "*", it will have this value for position.
`static int`	`NO_MAPPING_QUALITY` Alignment score for an unaligned read.
`static byte[]`	`NULL_QUALS` This should rarely be used, since all reads should have quality scores.
`static java.lang.String`	`NULL_QUALS_STRING`
`static byte[]`	`NULL_SEQUENCE` This should rarely be used, since a read with no sequence doesn't make much sense.
`static java.lang.String`	`NULL_SEQUENCE_STRING`
`static long`	`serialVersionUID`
`static int`	`UNKNOWN_MAPPING_QUALITY` Alignment score for a good alignment, but where computing a Phred-score is not feasible.

Constructor Summary

Constructors
Constructor and Description

SAMRecord(SAMFileHeader header)

Constructors
Constructor and Description
`SAMRecord(SAMFileHeader header)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`clearAttributes()` Removes all attributes.
`java.lang.Object`	`clone()` Note that this does a shallow copy of everything, except for the attribute list, for which a copy of the list is made, but the attributes themselves are copied by reference.
`protected void`	`eagerDecode()` Force all lazily-initialized data members to be initialized.
`boolean`	`equals(java.lang.Object o)`
`java.lang.String`	`format()` Deprecated. This method is not guaranteed to return a valid SAM text representation of the SAMRecord. To get standard SAM text representation, use htsjdk.samtools.SAMRecord#getSAMString().
`java.util.List<AlignmentBlock>`	`getAlignmentBlocks()` Returns blocks of the read sequence that have been aligned directly to the reference sequence.
`int`	`getAlignmentEnd()`
`int`	`getAlignmentStart()`
`java.lang.Object`	`getAttribute(short tag)`
`java.lang.Object`	`getAttribute(java.lang.String tag)` Get the value for a SAM tag.
`java.util.List<SAMRecord.SAMTagAndValue>`	`getAttributes()`
`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.
`java.lang.String`	`getBaseQualityString()`
`protected SAMBinaryTagAndValue`	`getBinaryAttributes()`
`byte[]`	`getByteArrayAttribute(java.lang.String tag)` Will work for signed byte array, unsigned byte array, or old-style hex array
`java.lang.Byte`	`getByteAttribute(java.lang.String tag)` Get the tag value and attempt to coerce it into the requested type.
`java.lang.Character`	`getCharacterAttribute(java.lang.String tag)`
`Cigar`	`getCigar()` Do not modify the value returned by this method.
`int`	`getCigarLength()` This method is preferred over getCigar().getNumElements(), because for BAMRecord it may be faster.
`java.lang.String`	`getCigarString()`
`java.lang.String`	`getContig()` Gets the contig name for the contig this is mapped to.
`boolean`	`getDuplicateReadFlag()` the read is either a PCR duplicate or an optical duplicate.
`int`	`getEnd()` an alias of `getAlignmentEnd()`
`SAMFileSource`	`getFileSource()` Gets the source of this SAM record -- both the reader that retrieved the record and the position on disk from whence it came.
`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.
`float[]`	`getFloatArrayAttribute(java.lang.String tag)`
`java.lang.Float`	`getFloatAttribute(java.lang.String tag)`
`SAMFileHeader`	`getHeader()`
`int`	`getInferredInsertSize()`
`java.lang.Integer`	`getIntegerAttribute(java.lang.String tag)` Get the tag value and attempt to coerce it into the requested type.
`int`	`getMappingQuality()`
`int`	`getMateAlignmentStart()`
`boolean`	`getMateNegativeStrandFlag()` strand of the mate (false for forward; true for reverse strand).
`java.lang.Integer`	`getMateReferenceIndex()`
`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).
`byte[]`	`getOriginalBaseQualities()` If the original base quality scores have been store in the "OQ" tag will return the numeric score as a byte[]
`java.lang.String`	`getPairedReadName()`
`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`	`getReadFailsVendorQualityCheckFlag()` the read fails platform/vendor quality checks.
`SAMReadGroupRecord`	`getReadGroup()` Get the SAMReadGroupRecord for this SAMRecord.
`int`	`getReadLength()` This method is preferred over getReadBases().length, because for BAMRecord it may be faster.
`java.lang.String`	`getReadName()`
`int`	`getReadNameLength()` This method is preferred over getReadName().length(), because for BAMRecord it may be faster.
`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.String`	`getReadString()`
`boolean`	`getReadUnmappedFlag()` the query sequence itself is unmapped.
`java.lang.Integer`	`getReferenceIndex()`
`java.lang.String`	`getReferenceName()`
`int`	`getReferencePositionAtReadPosition(int offset)`
`java.lang.String`	`getSAMString()` Returns the record in the SAM line-based text format.
`boolean`	`getSecondOfPairFlag()` the read is the second read in a pair.
`java.lang.Short`	`getShortAttribute(java.lang.String tag)` Get the tag value and attempt to coerce it into the requested type.
`byte[]`	`getSignedByteArrayAttribute(java.lang.String tag)` Will work for signed byte array or old-style hex array
`int[]`	`getSignedIntArrayAttribute(java.lang.String tag)`
`short[]`	`getSignedShortArrayAttribute(java.lang.String tag)`
`int`	`getStart()` an alias of {@link #getAlignmentStart()
`java.lang.String`	`getStringAttribute(java.lang.String tag)`
`boolean`	`getSupplementaryAlignmentFlag()` the alignment is supplementary (TODO: further explanation?).
`int`	`getUnclippedEnd()`
`int`	`getUnclippedStart()`
`byte[]`	`getUnsignedByteArrayAttribute(java.lang.String tag)`
`int[]`	`getUnsignedIntArrayAttribute(java.lang.String tag)`
`short[]`	`getUnsignedShortArrayAttribute(java.lang.String tag)`
`ValidationStringency`	`getValidationStringency()`
`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.
`int`	`hashCode()`
`protected void`	`initializeCigar(Cigar cigar)` For setting the Cigar string when BAMRecord has decoded it.
`boolean`	`isSecondaryOrSupplementary()` Tests if this record is either a secondary and/or supplementary alignment; equivalent to `(getNotPrimaryAlignmentFlag() \|\| getSupplementaryAlignmentFlag())`.
`boolean`	`isUnsignedArrayAttribute(java.lang.String tag)`
`java.util.List<SAMValidationError>`	`isValid()` Perform various validations of SAMRecord.
`java.util.List<SAMValidationError>`	`isValid(boolean firstOnly)` Perform various validations of SAMRecord.
`void`	`setAlignmentStart(int value)`
`protected void`	`setAttribute(short tag, java.lang.Object value)`
`protected void`	`setAttribute(short tag, java.lang.Object value, boolean isUnsignedArray)`
`void`	`setAttribute(java.lang.String tag, java.lang.Object value)` Set a named attribute onto the SAMRecord.
`protected void`	`setAttributes(SAMBinaryTagAndValue attributes)` Replace any existing attributes with the given linked item.
`void`	`setBaseQualities(byte[] value)`
`void`	`setBaseQualityString(java.lang.String value)`
`void`	`setCigar(Cigar cigar)`
`void`	`setCigarString(java.lang.String value)`
`void`	`setDuplicateReadFlag(boolean flag)` the read is either a PCR duplicate or an optical duplicate.
`protected void`	`setFileSource(SAMFileSource fileSource)` Sets a marker providing the source reader for this file and the position in the file from which the read originated.
`void`	`setFirstOfPairFlag(boolean flag)` the read is the first read in a pair.
`void`	`setFlags(int value)`
`void`	`setHeader(SAMFileHeader header)` Setting header into SAMRecord facilitates conversion btw reference sequence names and indices
`void`	`setInferredInsertSize(int inferredInsertSize)`
`void`	`setMappingQuality(int value)`
`void`	`setMateAlignmentStart(int mateAlignmentStart)`
`void`	`setMateNegativeStrandFlag(boolean flag)` strand of the mate (false for forward; true for reverse strand).
`void`	`setMateReferenceIndex(int referenceIndex)`
`void`	`setMateReferenceName(java.lang.String mateReferenceName)`
`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`	`setOriginalBaseQualities(byte[] oq)` Sets the original base quality scores into the "OQ" tag as a String.
`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`	`setReadFailsVendorQualityCheckFlag(boolean flag)` the read fails platform/vendor quality checks.
`void`	`setReadName(java.lang.String 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`	`setReadString(java.lang.String value)`
`void`	`setReadUmappedFlag(boolean flag)` Deprecated.
`void`	`setReadUnmappedFlag(boolean flag)` the query sequence itself is unmapped.
`void`	`setReferenceIndex(int referenceIndex)`
`void`	`setReferenceName(java.lang.String value)`
`void`	`setSecondOfPairFlag(boolean flag)` the read is the second read in a pair.
`void`	`setSupplementaryAlignmentFlag(boolean flag)` the alignment is supplementary (TODO: further explanation?).
`void`	`setUnsignedArrayAttribute(java.lang.String tag, java.lang.Object value)` Because Java does not support unsigned integer types, we think it is a bad idea to encode them in SAM files.
`void`	`setValidationStringency(ValidationStringency validationStringency)` Control validation of lazily-decoded elements.
`java.lang.String`	`toString()` Simple toString() that gives a little bit of useful info about the read.
`java.util.List<SAMValidationError>`	`validateCigar(long recordNumber)` Run all validations of CIGAR.

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - serialVersionUID
```
public static final long serialVersionUID
```
    See Also:
    Constant Field Values
  - UNKNOWN_MAPPING_QUALITY
```
public static final int UNKNOWN_MAPPING_QUALITY
```
    Alignment score for a good alignment, but where computing a Phred-score is not feasible.
    
    See Also:
    Constant Field Values
  - NO_MAPPING_QUALITY
```
public static final int NO_MAPPING_QUALITY
```
    Alignment score for an unaligned read.
    
    See Also:
    Constant Field Values
  - NO_ALIGNMENT_REFERENCE_NAME
```
public static final java.lang.String NO_ALIGNMENT_REFERENCE_NAME
```
    If a read has this reference name, it is unaligned, but not all unaligned reads have this reference name (see above).
    
    See Also:
    Constant Field Values
  - NO_ALIGNMENT_REFERENCE_INDEX
```
public static final int NO_ALIGNMENT_REFERENCE_INDEX
```
    If a read has this reference index, it is unaligned, but not all unaligned reads have this reference index (see above).
    
    See Also:
    Constant Field Values
  - NO_ALIGNMENT_CIGAR
```
public static final java.lang.String NO_ALIGNMENT_CIGAR
```
    Cigar string for an unaligned read.
    
    See Also:
    Constant Field Values
  - NO_ALIGNMENT_START
```
public static final int NO_ALIGNMENT_START
```
    If a read has reference name "*", it will have this value for position.
    
    See Also:
    Constant Field Values
  - NULL_SEQUENCE
```
public static final byte[] NULL_SEQUENCE
```
    This should rarely be used, since a read with no sequence doesn't make much sense.
  - NULL_SEQUENCE_STRING
```
public static final java.lang.String NULL_SEQUENCE_STRING
```
    See Also:
    Constant Field Values
  - NULL_QUALS
```
public static final byte[] NULL_QUALS
```
    This should rarely be used, since all reads should have quality scores.
  - NULL_QUALS_STRING
```
public static final java.lang.String NULL_QUALS_STRING
```
    See Also:
    Constant Field Values
  - MAX_INSERT_SIZE
```
public static final int MAX_INSERT_SIZE
```
    abs(insertSize) must be <= this
    
    See Also:
    Constant Field Values
  - mReferenceIndex
```
protected java.lang.Integer mReferenceIndex
```
  - mMateReferenceIndex
```
protected java.lang.Integer mMateReferenceIndex
```
- Constructor Detail
  - SAMRecord
```
public SAMRecord(SAMFileHeader header)
```
- Method Detail
  - getReadName
```
public java.lang.String getReadName()
```
  - getReadNameLength
```
public int getReadNameLength()
```
    This method is preferred over getReadName().length(), because for BAMRecord it may be faster.
    
    Returns:
    length not including a null terminator.
  - setReadName
```
public void setReadName(java.lang.String value)
```
  - getReadString
```
public java.lang.String getReadString()
```
    Returns:
    read sequence as a string of ACGTN=.
  - setReadString
```
public void setReadString(java.lang.String value)
```
  - getReadBases
```
public byte[] getReadBases()
```
    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().
    
    Returns:
    read sequence as ASCII bytes ACGTN=.
  - setReadBases
```
public void setReadBases(byte[] value)
```
  - getReadLength
```
public int getReadLength()
```
    This method is preferred over getReadBases().length, because for BAMRecord it may be faster.
    
    Returns:
    number of bases in the read.
  - getBaseQualityString
```
public java.lang.String getBaseQualityString()
```
    Returns:
    Base qualities, encoded as a FASTQ string.
  - setBaseQualityString
```
public void setBaseQualityString(java.lang.String value)
```
  - getBaseQualities
```
public byte[] getBaseQualities()
```
    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().
    
    Returns:
    Base qualities, as binary phred scores (not ASCII).
  - setBaseQualities
```
public void setBaseQualities(byte[] value)
```
  - getOriginalBaseQualities
```
public byte[] getOriginalBaseQualities()
```
    If the original base quality scores have been store in the "OQ" tag will return the numeric score as a byte[]
  - setOriginalBaseQualities
```
public void setOriginalBaseQualities(byte[] oq)
```
    Sets the original base quality scores into the "OQ" tag as a String. Supplied value should be as phred-scaled numeric qualities.
  - getReferenceName
```
public java.lang.String getReferenceName()
```
    Returns:
    Reference name, or null if record has no reference.
  - setReferenceName
```
public void setReferenceName(java.lang.String value)
```
  - getReferenceIndex
```
public java.lang.Integer getReferenceIndex()
```
    Returns:
    index of the reference sequence for this read in the sequence dictionary, or -1 if read has no reference sequence set, or if a String reference name is not found in the sequence index..
  - setReferenceIndex
```
public void setReferenceIndex(int referenceIndex)
```
    Parameters:
    referenceIndex - Must either equal -1 (indicating no reference), or exist in the sequence dictionary in the header associated with this record.
  - getMateReferenceName
```
public java.lang.String getMateReferenceName()
```
    Returns:
    Mate reference name, or null if one is not assigned.
  - setMateReferenceName
```
public void setMateReferenceName(java.lang.String mateReferenceName)
```
  - getMateReferenceIndex
```
public java.lang.Integer getMateReferenceIndex()
```
    Returns:
    index of the reference sequence for this read's mate in the sequence dictionary, or -1 if mate has no reference sequence set.
  - setMateReferenceIndex
```
public void setMateReferenceIndex(int referenceIndex)
```
    Parameters:
    referenceIndex - Must either equal -1 (indicating no reference), or exist in the sequence dictionary in the header associated with this record.
  - getAlignmentStart
```
public int getAlignmentStart()
```
    Returns:
    1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
  - setAlignmentStart
```
public void setAlignmentStart(int value)
```
    Parameters:
    value - 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
  - getAlignmentEnd
```
public int getAlignmentEnd()
```
    Returns:
    1-based inclusive rightmost position of the clipped sequence, or 0 read if unmapped.
  - getUnclippedStart
```
public int getUnclippedStart()
```
    Returns:
    the alignment start (1-based, inclusive) adjusted for clipped bases. For example if the read has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped) then this method will return 96. Invalid to call on an unmapped read.
  - getUnclippedEnd
```
public int getUnclippedEnd()
```
    Returns:
    the alignment end (1-based, inclusive) adjusted for clipped bases. For example if the read has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped) then this method will return 107. Invalid to call on an unmapped read.
  - getReferencePositionAtReadPosition
```
public int getReferencePositionAtReadPosition(int offset)
```
    Returns:
    1-based inclusive reference position of the unclipped sequence at a given offset, or 0 if there is no position. For example, given the sequence NNNAAACCCGGG, cigar 3S9M, and an alignment start of 1, and a (1-based)offset 10 (start of GGG) it returns 7 (1-based offset starting after the soft clip. For example: given the sequence AAACCCGGGTTT, cigar 4M1D6M, an alignment start of 1, an offset of 4 returns reference position 4, an offset of 5 returns reference position 6. Another example: given the sequence AAACCCGGGTTT, cigar 4M1I6M, an alignment start of 1, an offset of 4 returns reference position 4, an offset of 5 returns 0.
  - getMateAlignmentStart
```
public int getMateAlignmentStart()
```
    Returns:
    1-based inclusive leftmost position of the clipped mate sequence, or 0 if there is no position.
  - setMateAlignmentStart
```
public void setMateAlignmentStart(int mateAlignmentStart)
```
  - getInferredInsertSize
```
public int getInferredInsertSize()
```
    Returns:
    insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0. Negative if mate maps to lower position than read.
  - setInferredInsertSize
```
public void setInferredInsertSize(int inferredInsertSize)
```
  - getMappingQuality
```
public int getMappingQuality()
```
    Returns:
    phred scaled mapping quality. 255 implies valid mapping but quality is hard to compute.
  - setMappingQuality
```
public void setMappingQuality(int value)
```
  - getCigarString
```
public java.lang.String getCigarString()
```
  - setCigarString
```
public void setCigarString(java.lang.String value)
```
  - getCigar
```
public Cigar getCigar()
```
    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()
    
    Returns:
    Cigar object for the read, or null if there is none.
  - getCigarLength
```
public int getCigarLength()
```
    This method is preferred over getCigar().getNumElements(), because for BAMRecord it may be faster.
    
    Returns:
    number of cigar elements (number + operator) in the cigar string.
  - setCigar
```
public void setCigar(Cigar cigar)
```
  - initializeCigar
```
protected void initializeCigar(Cigar cigar)
```
    For setting the Cigar string when BAMRecord has decoded it. Use this rather than setCigar() so that indexing bin doesn't get clobbered.
  - getReadGroup
```
public SAMReadGroupRecord getReadGroup()
```
    Get the SAMReadGroupRecord for this SAMRecord.
    
    Returns:
    The SAMReadGroupRecord from the SAMFileHeader for this SAMRecord, or null if 1) this record has no RG tag, or 2) the header doesn't contain the read group with the given ID.
    
    Throws:
    
    java.lang.NullPointerException - if this.getHeader() returns null.
    
    java.lang.ClassCastException - if RG tag does not have a String value.
  - getFlags
```
public int getFlags()
```
    It is preferable to use the get*Flag() methods that handle the flag word symbolically.
  - setFlags
```
public void setFlags(int value)
```
  - getReadPairedFlag
```
public boolean getReadPairedFlag()
```
    the read is paired in sequencing, no matter whether it is mapped in a pair.
  - getProperPairFlag
```
public boolean getProperPairFlag()
```
    the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
  - getReadUnmappedFlag
```
public boolean getReadUnmappedFlag()
```
    the query sequence itself is unmapped.
  - getMateUnmappedFlag
```
public boolean getMateUnmappedFlag()
```
    the mate is unmapped.
  - getReadNegativeStrandFlag
```
public boolean getReadNegativeStrandFlag()
```
    strand of the query (false for forward; true for reverse strand).
  - getMateNegativeStrandFlag
```
public boolean getMateNegativeStrandFlag()
```
    strand of the mate (false for forward; true for reverse strand).
  - getFirstOfPairFlag
```
public boolean getFirstOfPairFlag()
```
    the read is the first read in a pair.
  - getSecondOfPairFlag
```
public boolean getSecondOfPairFlag()
```
    the read is the second read in a pair.
  - getNotPrimaryAlignmentFlag
```
public boolean getNotPrimaryAlignmentFlag()
```
    the alignment is not primary (a read having split hits may have multiple primary alignment records).
  - getSupplementaryAlignmentFlag
```
public boolean getSupplementaryAlignmentFlag()
```
    the alignment is supplementary (TODO: further explanation?).
  - getReadFailsVendorQualityCheckFlag
```
public boolean getReadFailsVendorQualityCheckFlag()
```
    the read fails platform/vendor quality checks.
  - getDuplicateReadFlag
```
public boolean getDuplicateReadFlag()
```
    the read is either a PCR duplicate or an optical duplicate.
  - setReadPairedFlag
```
public void setReadPairedFlag(boolean flag)
```
    the read is paired in sequencing, no matter whether it is mapped in a pair.
  - setProperPairFlag
```
public void setProperPairFlag(boolean flag)
```
    the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
  - setReadUmappedFlag
```
public void setReadUmappedFlag(boolean flag)
```
    Deprecated.
    
    the query sequence itself is unmapped. This method name is misspelled. Use setReadUnmappedFlag instead.
  - setReadUnmappedFlag
```
public void setReadUnmappedFlag(boolean flag)
```
    the query sequence itself is unmapped.
  - setMateUnmappedFlag
```
public void setMateUnmappedFlag(boolean flag)
```
    the mate is unmapped.
  - setReadNegativeStrandFlag
```
public void setReadNegativeStrandFlag(boolean flag)
```
    strand of the query (false for forward; true for reverse strand).
  - setMateNegativeStrandFlag
```
public void setMateNegativeStrandFlag(boolean flag)
```
    strand of the mate (false for forward; true for reverse strand).
  - setFirstOfPairFlag
```
public void setFirstOfPairFlag(boolean flag)
```
    the read is the first read in a pair.
  - setSecondOfPairFlag
```
public void setSecondOfPairFlag(boolean flag)
```
    the read is the second read in a pair.
  - setNotPrimaryAlignmentFlag
```
public void setNotPrimaryAlignmentFlag(boolean flag)
```
    the alignment is not primary (a read having split hits may have multiple primary alignment records).
  - setSupplementaryAlignmentFlag
```
public void setSupplementaryAlignmentFlag(boolean flag)
```
    the alignment is supplementary (TODO: further explanation?).
  - setReadFailsVendorQualityCheckFlag
```
public void setReadFailsVendorQualityCheckFlag(boolean flag)
```
    the read fails platform/vendor quality checks.
  - setDuplicateReadFlag
```
public void setDuplicateReadFlag(boolean flag)
```
    the read is either a PCR duplicate or an optical duplicate.
  - isSecondaryOrSupplementary
```
public boolean isSecondaryOrSupplementary()
```
    Tests if this record is either a secondary and/or supplementary alignment; equivalent to (getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag()).
  - getValidationStringency
```
public ValidationStringency getValidationStringency()
```
  - setValidationStringency
```
public void setValidationStringency(ValidationStringency validationStringency)
```
    Control validation of lazily-decoded elements.
  - getAttribute
```
public java.lang.Object getAttribute(java.lang.String tag)
```
    Get the value for a SAM tag. WARNING: Some value types (e.g. byte[]) are mutable. It is dangerous to change one of these values in place, because some SAMRecord implementations keep track of when attributes have been changed. If you want to change an attribute value, call setAttribute() to replace the value.
    
    Parameters:
    tag - Two-character tag name.
    
    Returns:
    Appropriately typed tag value, or null if the requested tag is not present.
  - getIntegerAttribute
```
public java.lang.Integer getIntegerAttribute(java.lang.String tag)
```
    Get the tag value and attempt to coerce it into the requested type.
    
    Parameters:
    tag - The requested tag.
    
    Returns:
    The value of a tag, converted into an Integer if possible.
    
    Throws:
    
    java.lang.RuntimeException - If the value is not an integer type, or will not fit in an Integer.
  - getShortAttribute
```
public java.lang.Short getShortAttribute(java.lang.String tag)
```
    Get the tag value and attempt to coerce it into the requested type.
    
    Parameters:
    tag - The requested tag.
    
    Returns:
    The value of a tag, converted into a Short if possible.
    
    Throws:
    
    java.lang.RuntimeException - If the value is not an integer type, or will not fit in a Short.
  - getByteAttribute
```
public java.lang.Byte getByteAttribute(java.lang.String tag)
```
    Get the tag value and attempt to coerce it into the requested type.
    
    Parameters:
    tag - The requested tag.
    
    Returns:
    The value of a tag, converted into a Byte if possible.
    
    Throws:
    
    java.lang.RuntimeException - If the value is not an integer type, or will not fit in a Byte.
  - getStringAttribute
```
public java.lang.String getStringAttribute(java.lang.String tag)
```
  - getCharacterAttribute
```
public java.lang.Character getCharacterAttribute(java.lang.String tag)
```
  - getFloatAttribute
```
public java.lang.Float getFloatAttribute(java.lang.String tag)
```
  - getByteArrayAttribute
```
public byte[] getByteArrayAttribute(java.lang.String tag)
```
    Will work for signed byte array, unsigned byte array, or old-style hex array
  - getUnsignedByteArrayAttribute
```
public byte[] getUnsignedByteArrayAttribute(java.lang.String tag)
```
  - getSignedByteArrayAttribute
```
public byte[] getSignedByteArrayAttribute(java.lang.String tag)
```
    Will work for signed byte array or old-style hex array
  - getUnsignedShortArrayAttribute
```
public short[] getUnsignedShortArrayAttribute(java.lang.String tag)
```
  - getSignedShortArrayAttribute
```
public short[] getSignedShortArrayAttribute(java.lang.String tag)
```
  - getUnsignedIntArrayAttribute
```
public int[] getUnsignedIntArrayAttribute(java.lang.String tag)
```
  - getSignedIntArrayAttribute
```
public int[] getSignedIntArrayAttribute(java.lang.String tag)
```
  - getFloatArrayAttribute
```
public float[] getFloatArrayAttribute(java.lang.String tag)
```
  - isUnsignedArrayAttribute
```
public boolean isUnsignedArrayAttribute(java.lang.String tag)
```
    Returns:
    True if this tag is an unsigned array, else false.
    
    Throws:
    
    SAMException - if the tag is not present.
  - getAttribute
```
public java.lang.Object getAttribute(short tag)
```
    Parameters:
    tag - Binary representation of a 2-char String tag as created by SAMTagUtil.
    See Also:
    getAttribute(java.lang.String)
  - setAttribute
```
public void setAttribute(java.lang.String tag,
                java.lang.Object value)
```
    Set a named attribute onto the SAMRecord. Passing a null value causes the attribute to be cleared.
    
    Parameters:
    tag - two-character tag name. See http://samtools.sourceforge.net/SAM1.pdf for standard and user-defined tags.
    value - Supported types are String, Char, Integer, Float, byte[], short[]. int[], float[]. If value == null, tag is cleared. Byte and Short are allowed but discouraged. If written to a SAM file, these will be converted to Integer, whereas if written to BAM, getAttribute() will return as Byte or Short, respectively. Long with value between 0 and MAX_UINT is allowed for BAM but discouraged. Attempting to write such a value to SAM will cause an exception to be thrown. To set unsigned byte[], unsigned short[] or unsigned int[] (which is discouraged because of poor Java language support), setUnsignedArrayAttribute() must be used instead of this method. String values are not validated to ensure that they conform to SAM spec.
  - setUnsignedArrayAttribute
```
public void setUnsignedArrayAttribute(java.lang.String tag,
                             java.lang.Object value)
```
    Because Java does not support unsigned integer types, we think it is a bad idea to encode them in SAM files. If you must do so, however, you must call this method rather than setAttribute, because calling this method is the way to indicate that, e.g. a short array should be interpreted as unsigned shorts.
    
    Parameters:
    value - must be one of byte[], short[], int[]
  - setAttribute
```
protected void setAttribute(short tag,
                java.lang.Object value)
```
    Parameters:
    tag - Binary representation of a 2-char String tag as created by SAMTagUtil.
    See Also:
    setAttribute(java.lang.String, java.lang.Object)
  - setAttribute
```
protected void setAttribute(short tag,
                java.lang.Object value,
                boolean isUnsignedArray)
```
  - clearAttributes
```
public void clearAttributes()
```
    Removes all attributes.
  - setAttributes
```
protected void setAttributes(SAMBinaryTagAndValue attributes)
```
    Replace any existing attributes with the given linked item.
  - getBinaryAttributes
```
protected SAMBinaryTagAndValue getBinaryAttributes()
```
    Returns:
    Pointer to the first of the tags. Returns null if there are no tags.
  - getContig
```
public java.lang.String getContig()
```
    Description copied from interface: Locatable
    
    Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
    
    Specified by:
    
    getContig in interface Locatable
    
    Returns:
    reference name, null if this is unmapped
  - getStart
```
public int getStart()
```
    an alias of {@link #getAlignmentStart()
    
    Specified by:
    
    getStart in interface Locatable
    
    Returns:
    1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
  - getEnd
```
public int getEnd()
```
    an alias of getAlignmentEnd()
    
    Specified by:
    
    getEnd in interface Locatable
    
    Returns:
    1-based inclusive rightmost position of the clipped sequence, or 0 read if unmapped.
  - getAttributes
```
public java.util.List<SAMRecord.SAMTagAndValue> getAttributes()
```
    Returns:
    list of {tag, value} tuples
  - getHeader
```
public SAMFileHeader getHeader()
```
  - setHeader
```
public void setHeader(SAMFileHeader header)
```
    Setting header into SAMRecord facilitates conversion btw reference sequence names and indices
    
    Parameters:
    header - contains sequence dictionary for this 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.
  - getAttributesBinarySize
```
public int getAttributesBinarySize()
```
    Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.
    
    Returns:
    binary file size of attribute, if known, else -1
  - format
```
public java.lang.String format()
```
    Deprecated. This method is not guaranteed to return a valid SAM text representation of the SAMRecord. To get standard SAM text representation, use htsjdk.samtools.SAMRecord#getSAMString().
    
    Returns:
    String representation of this.
  - eagerDecode
```
protected void eagerDecode()
```
    Force all lazily-initialized data members to be initialized. If a subclass overrides this method, typically it should also call super method.
  - getAlignmentBlocks
```
public java.util.List<AlignmentBlock> getAlignmentBlocks()
```
    Returns blocks of the read sequence that have been aligned directly to the reference sequence. Note that clipped portions of the read and inserted and deleted bases (vs. the reference) are not represented in the alignment blocks.
  - validateCigar
```
public java.util.List<SAMValidationError> validateCigar(long recordNumber)
```
    Run all validations of CIGAR. These include validation that the CIGAR makes sense independent of placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
    
    Parameters:
    recordNumber - For error reporting. -1 if not known.
    
    Returns:
    List of errors, or null if no errors.
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - isValid
```
public java.util.List<SAMValidationError> isValid()
```
    Perform various validations of SAMRecord. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable.
    
    Returns:
    null if valid. If invalid, returns a list of error messages.
  - isValid
```
public java.util.List<SAMValidationError> isValid(boolean firstOnly)
```
    Perform various validations of SAMRecord. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable.
    
    Parameters:
    firstOnly - return only the first error if true, false otherwise
    
    Returns:
    null if valid. If invalid, returns a list of error messages.
  - getFileSource
```
public SAMFileSource getFileSource()
```
    Gets the source of this SAM record -- both the reader that retrieved the record and the position on disk from whence it came.
    
    Returns:
    The file source. Note that the reader will be null if not activated using SAMFileReader.enableFileSource().
  - setFileSource
```
protected void setFileSource(SAMFileSource fileSource)
```
    Sets a marker providing the source reader for this file and the position in the file from which the read originated.
    
    Parameters:
    fileSource - source of the given file.
  - clone
```
public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException
```
    Note that this does a shallow copy of everything, except for the attribute list, for which a copy of the list is made, but the attributes themselves are copied by reference. This should be safe because callers should never modify a mutable value returned by any of the get() methods anyway.
    
    Overrides:
    
    clone in class java.lang.Object
    
    Throws:
    
    java.lang.CloneNotSupportedException
  - toString
```
public java.lang.String toString()
```
    Simple toString() that gives a little bit of useful info about the read.
    
    Overrides:
    
    toString in class java.lang.Object
  - getSAMString
```
public java.lang.String getSAMString()
```
    Returns the record in the SAM line-based text format. Fields are separated by '\t' characters, and the String is terminated by '\n'.
  - getPairedReadName
```
public java.lang.String getPairedReadName()
```

Class SAMRecord

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

UNKNOWN_MAPPING_QUALITY

NO_MAPPING_QUALITY

NO_ALIGNMENT_REFERENCE_NAME

NO_ALIGNMENT_REFERENCE_INDEX

NO_ALIGNMENT_CIGAR

NO_ALIGNMENT_START

NULL_SEQUENCE

NULL_SEQUENCE_STRING

NULL_QUALS

NULL_QUALS_STRING

MAX_INSERT_SIZE

mReferenceIndex

mMateReferenceIndex

Constructor Detail

SAMRecord

Method Detail

getReadName

getReadNameLength

setReadName

getReadString

setReadString

getReadBases

setReadBases

getReadLength

getBaseQualityString

setBaseQualityString

getBaseQualities

setBaseQualities

getOriginalBaseQualities

setOriginalBaseQualities

getReferenceName

setReferenceName

getReferenceIndex

setReferenceIndex

getMateReferenceName

setMateReferenceName

getMateReferenceIndex

setMateReferenceIndex

getAlignmentStart

setAlignmentStart

getAlignmentEnd

getUnclippedStart

getUnclippedEnd

getReferencePositionAtReadPosition

getMateAlignmentStart

setMateAlignmentStart

getInferredInsertSize

setInferredInsertSize

getMappingQuality

setMappingQuality

getCigarString

setCigarString

getCigar

getCigarLength

setCigar

initializeCigar

getReadGroup

getFlags

setFlags

getReadPairedFlag

getProperPairFlag

getReadUnmappedFlag

getMateUnmappedFlag

getReadNegativeStrandFlag

getMateNegativeStrandFlag

getFirstOfPairFlag

getSecondOfPairFlag

getNotPrimaryAlignmentFlag

getSupplementaryAlignmentFlag

getReadFailsVendorQualityCheckFlag

getDuplicateReadFlag

setReadPairedFlag