GATKRead (gatk 4.2.0.0 API)

All Superinterfaces:

htsjdk.samtools.util.Locatable

All Known Implementing Classes:

BDGAlignmentRecordToGATKReadAdapter, SAMRecordToGATKReadAdapter
```
public interface GATKRead
extends htsjdk.samtools.util.Locatable
```
Unified read interface for use throughout the GATK. Adapter classes implementing this interface exist for htsjdk's SAMRecord (SAMRecordToGATKReadAdapter) Since the adapter classes wrap the raw reads without making a copy, care must be taken to avoid exposing the encapsulated reads, particularly if modifying reads in-place. As a result, this interface should probably only be implemented by core engine-level classes. All GATKRead methods that return mutable reference types make defensive copies, with the exception of the conversion method convertToSAMRecord(htsjdk.samtools.SAMFileHeader). Note that Locatable.getContig() and Locatable.getStart() will not expose nominal positions assigned to unmapped reads for sorting purposes -- for unmapped reads, these methods will always return null or 0, respectively. To access positions assigned to unmapped reads for sorting purposes, use getAssignedContig() and getAssignedStart().

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`void`	`clearAttribute(java.lang.String attributeName)` Clear an individual attribute on the read.
`void`	`clearAttributes()` Clear all attributes on the read.
`void`	`clearTransientAttribute(java.lang.String attributeName)` Clear an individual transient attribute on the read.
`default java.lang.String`	`commonToString()` A human-digestable representation of the read.
`htsjdk.samtools.SAMRecord`	`convertToSAMRecord(htsjdk.samtools.SAMFileHeader header)` Convert this read into a SAMRecord.
`GATKRead`	`copy()` Return a copy of this read.
`default int`	`copyBaseQualities(int offset, byte[] destination, int destinationOffset, int maxLength)` Copy base qualities into an existent byte array.
`default int`	`copyBases(int offset, byte[] destination, int destinationOffset, int maxLength)` Copy the base into an existent byte array.
`GATKRead`	`deepCopy()` Return a deep copy of this read.
`boolean`	`failsVendorQualityCheck()`
`default int`	`getAdaptorBoundary()` Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to the read boundary.
`java.lang.String`	`getAssignedContig()`
`int`	`getAssignedStart()`
`byte[]`	`getAttributeAsByteArray(java.lang.String attributeName)` Retrieve the value of a particular attribute typed as a byte array.
`java.lang.Integer`	`getAttributeAsInteger(java.lang.String attributeName)` Retrieve the value of a particular attribute typed as an integer.
`java.lang.String`	`getAttributeAsString(java.lang.String attributeName)` Retrieve the value of a particular attribute typed as a String.
`default byte`	`getBase(int i)`
`byte[]`	`getBaseQualities()`
`default byte[]`	`getBaseQualitiesNoCopy()`
`default byte`	`getBaseQuality(int i)`
`default int`	`getBaseQualityCount()`
`byte[]`	`getBases()`
`default byte[]`	`getBasesNoCopy()`
`default java.lang.String`	`getBasesString()`
`htsjdk.samtools.Cigar`	`getCigar()`
`default htsjdk.samtools.CigarElement`	`getCigarElement(int i)` Return the cigar element at a given index.
`default java.util.List<htsjdk.samtools.CigarElement>`	`getCigarElements()`
`int`	`getFlags()`
`int`	`getFragmentLength()` Returns the observed length of the read's fragment (equivalent to TLEN in SAM).
`int`	`getLength()`
`int`	`getMappingQuality()`
`java.lang.String`	`getMateContig()`
`int`	`getMateStart()`
`java.lang.String`	`getName()`
`default <T> java.util.Optional<T>`	`getOptionalTransientAttribute(java.lang.Object key, java.lang.Class<T> clazz)` Returns a transient attribute value as an `Optional`.
`default java.util.Optional<htsjdk.samtools.SamPairUtil.PairOrientation>`	`getPairOrientation()` Computes the pair orientation
`java.lang.String`	`getReadGroup()`
`java.lang.String`	`getSAMString()` Get a string representation of this read in SAM string format, terminated with '\n'.
`default int`	`getSoftEnd()` Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips.
`default int`	`getSoftStart()` Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips.
`java.lang.Object`	`getTransientAttribute(java.lang.Object key)` This is used to access a transient attribute store provided by the underlying implementation.
`int`	`getUnclippedEnd()` Returns the alignment end (1-based, inclusive) adjusted for clipped bases.
`int`	`getUnclippedStart()` Returns the alignment start (1-based, inclusive) adjusted for clipped bases.
`boolean`	`hasAttribute(java.lang.String attributeName)` Check whether this read has a particular attribute
`default boolean`	`hasBaseQualities()` Indicates whether there is any base-qualities.
`default boolean`	`hasBases()` Indicates whether there are any bases.
`boolean`	`isDuplicate()`
`default boolean`	`isEmpty()`
`boolean`	`isFirstOfPair()`
`boolean`	`isPaired()`
`boolean`	`isProperlyPaired()`
`boolean`	`isReverseStrand()`
`boolean`	`isSecondaryAlignment()`
`boolean`	`isSecondOfPair()`
`boolean`	`isSupplementaryAlignment()`
`boolean`	`isUnmapped()`
`boolean`	`isUnplaced()` Does the read have a position assigned to it for sorting purposes.
`boolean`	`mateIsReverseStrand()`
`boolean`	`mateIsUnmapped()`
`boolean`	`mateIsUnplaced()` Does the reads mate have a position assigned to it for sorting purposes..
`default int`	`numCigarElements()` The number of cigar elements in this read.
`void`	`reverseComplement()` Modify this read by reverse complementing its bases and reversing its quality scores.
`void`	`setAttribute(java.lang.String attributeName, byte[] attributeValue)` Set a byte array attribute on the read.
`void`	`setAttribute(java.lang.String attributeName, java.lang.Integer attributeValue)` Set an integer-valued attribute on the read.
`void`	`setAttribute(java.lang.String attributeName, java.lang.String attributeValue)` Set a String-valued attribute on the read.
`void`	`setBaseQualities(byte[] baseQualities)` Set the read's base qualities.
`void`	`setBases(byte[] bases)` Set the read's sequence.
`void`	`setCigar(htsjdk.samtools.Cigar cigar)` Set the read's Cigar using an existing `Cigar` object describing how the read aligns to the reference.
`void`	`setCigar(java.lang.String cigarString)` Set the read's Cigar using a textual cigar String describing how the read aligns to the reference.
`void`	`setFailsVendorQualityCheck(boolean failsVendorQualityCheck)` Mark the read as failing platform/vendor quality checks
`void`	`setFragmentLength(int fragmentLength)` Set the observed length of the read's fragment (equivalent to TLEN in SAM).
`void`	`setIsDuplicate(boolean isDuplicate)` Mark the read as a PCR or optical duplicate.
`void`	`setIsFirstOfPair()` Mark the read as the first read of a pair.
`void`	`setIsPaired(boolean isPaired)` Mark the read as paired (having a mate) or not paired.
`void`	`setIsProperlyPaired(boolean isProperlyPaired)` Mark the read as properly paired (or not properly paired).
`void`	`setIsReverseStrand(boolean isReverseStrand)` Mark the read as being on the reverse (or forward) strand.
`void`	`setIsSecondaryAlignment(boolean isSecondaryAlignment)` Mark the read as a secondary alignment (an alternative to the primary alignment)
`void`	`setIsSecondOfPair()` Mark the read as the second read of a pair.
`void`	`setIsSupplementaryAlignment(boolean isSupplementaryAlignment)` Mark the read as a supplementary alignment (used in the representation of a chimeric alignment)
`void`	`setIsUnmapped()` Mark the read as unmapped (lacking a defined position on the genome).
`void`	`setIsUnplaced()` Mark the read as unmapped, and also removes mapping information from the read (i.e.
`void`	`setMappingQuality(int mappingQuality)` Set the mapping quality of this alignment, representing how likely the read maps to this position as opposed to other locations.
`void`	`setMateIsReverseStrand(boolean mateIsReverseStrand)` Mark the read's mate as being on the reverse (or forward) strand.
`void`	`setMateIsUnmapped()` Mark the read's mate as unmapped (lacking a defined position on the genome).
`void`	`setMateIsUnplaced()` Mark the read's mate as unmapped (lacking a defined position on the genome).
`void`	`setMatePosition(htsjdk.samtools.util.Locatable locatable)` Set the position of the read's mate using the position of an existing `Locatable`.
`void`	`setMatePosition(java.lang.String contig, int start)` Set the position of the read's mate (the contig and the start position).
`void`	`setName(java.lang.String name)` Set the name of the read (equivalent to QNAME in SAM), or set to `null` if the read has no name.
`void`	`setPosition(htsjdk.samtools.util.Locatable locatable)` Set the position of the read using the position of an existing `Locatable`.
`void`	`setPosition(java.lang.String contig, int start)` Set the position of the read (the contig and the start position).
`void`	`setReadGroup(java.lang.String readGroupID)` Set the ID of the read group this read belongs to, or `null` for none.
`void`	`setTransientAttribute(java.lang.Object key, java.lang.Object value)` This is used to access the transient attribute store in the underlying data type.

Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getContig, getEnd, getLengthOnReference, getStart, overlaps, withinDistanceOf

- Method Detail
  - getName
```
java.lang.String getName()
```
    Returns:
    
    The name of the read (equivalent to QNAME in SAM), or null if the read has no name.
  - getFlags
```
int getFlags()
```
  - setName
```
void setName(java.lang.String name)
```
    Set the name of the read (equivalent to QNAME in SAM), or set to null if the read has no name.
    
    Parameters:
    
    name - new name for the read
  - getLength
```
int getLength()
```
    Returns:
    
    The number of bases in the read Note: This is not necessarily the same as the number of reference bases the read is aligned to.
  - isEmpty
```
default boolean isEmpty()
```
    Returns:
    
    True if the read has no bases, otherwise false
  - setPosition
```
void setPosition(java.lang.String contig,
                 int start)
```
    Set the position of the read (the contig and the start position). Cannot be used to set the read to an unmapped position; use setIsUnmapped() for that purpose.
    
    Parameters:
    
    contig - Contig the read is mapped to
    
    start - Start position of the read (1-based, inclusive)
    
    Throws:
    
    java.lang.IllegalArgumentException - if contig is null or "*", or start is less than 1
  - setPosition
```
void setPosition(htsjdk.samtools.util.Locatable locatable)
```
    Set the position of the read using the position of an existing Locatable. Cannot be used to set the read to an unmapped position; use setIsUnmapped() for that purpose.
    
    Parameters:
    
    locatable - Locatable representing the 1-based, inclusive position to assign to the read
    
    Throws:
    
    java.lang.IllegalArgumentException - if locatable is null, or its contig is null or "*", or its start position is less than 1
  - getAssignedContig
```
java.lang.String getAssignedContig()
```
    Returns:
    
    The actual contig assigned to the read, regardless of unmapped status. Unlike Locatable.getContig(), which does not expose positions assigned to unmapped reads, this method will gladly return a contig assigned to an unmapped read (typically, this will be the contig of its mapped mate). Will return either ReadConstants.UNSET_CONTIG or null for reads with no contig, depending on the underlying read implementation. Useful for sorting reads in standard BAM/SAM file order, with unmapped reads interleaved with their mapped mates -- for other uses, clients should use Locatable.getContig()
  - getAssignedStart
```
int getAssignedStart()
```
    Returns:
    
    The actual start position assigned to the read, regardless of unmapped status. Unlike Locatable.getStart(), which does not expose positions assigned to unmapped reads, this method will gladly return a start position assigned to an unmapped read (typically, this will be the start position of its mapped mate). Will return ReadConstants.UNSET_POSITION for reads with no start position. Useful for sorting reads in standard BAM/SAM file order, with unmapped reads interleaved with their mapped mates -- for other uses, clients should use Locatable.getStart()
  - getUnclippedStart
```
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. For unmapped reads, always returns ReadConstants.UNSET_POSITION
    
    Returns:
    
    The alignment start (1-based, inclusive) adjusted for clipped bases, or ReadConstants.UNSET_POSITION if the read is unmapped.
  - getUnclippedEnd
```
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. For unmapped reads, always returns ReadConstants.UNSET_POSITION
    
    Returns:
    
    The alignment end (1-based, inclusive) adjusted for clipped bases, or ReadConstants.UNSET_POSITION if the read is unmapped.
  - getSoftStart
```
default int getSoftStart()
```
    Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips. Note: getUnclippedStart() adds soft and hard clips, this method only adds soft clips.
    
    Returns:
    
    the unclipped start of the read taking soft clips (but not hard clips) into account
  - getSoftEnd
```
default int getSoftEnd()
```
    Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips. Note: getUnclippedEnd() adds soft and hard clips, this method only adds soft clips.
    
    Returns:
    
    the unclipped end of the read taking soft clips (but not hard clips) into account
  - getAdaptorBoundary
```
default int getAdaptorBoundary()
```
    Finds the adaptor boundary around the read and returns the first base inside the adaptor that is closest to the read boundary. If the read is in the positive strand, this is the first base after the end of the fragment (Picard calls it 'insert'), if the read is in the negative strand, this is the first base before the beginning of the fragment. There are two cases we need to treat here: 1) Our read is in the reverse strand : <----------------------| * |---------------------> in these cases, the adaptor boundary is at the mate start (minus one) 2) Our read is in the forward strand : |----------------------> * <----------------------| in these cases the adaptor boundary is at the start of the read plus the inferred insert size (plus one)
    
    Returns:
    
    the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read). CANNOT_COMPUTE_ADAPTOR_BOUNDARY if the read is unmapped or the mate is mapped to another contig.
  - getMateContig
```
java.lang.String getMateContig()
```
    Returns:
    
    The contig that this read's mate is mapped to, or null if the mate is unmapped
    
    Throws:
    
    java.lang.IllegalStateException - if the read is not paired (has no mate)
  - getMateStart
```
int getMateStart()
```
    Returns:
    
    The alignment start (1-based, inclusive) of this read's mate, or ReadConstants.UNSET_POSITION if the mate is unmapped.
    
    Throws:
    
    java.lang.IllegalStateException - if the read is not paired (has no mate)
  - setMatePosition
```
void setMatePosition(java.lang.String contig,
                     int start)
```
    Set the position of the read's mate (the contig and the start position). Cannot be used to set the read's mate to an unmapped position; use setMateIsUnmapped() for that purpose. Calling this method has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
    
    Parameters:
    
    contig - Contig the read's mate is mapped to
    
    start - Start position of the read's mate (1-based, inclusive)
    
    Throws:
    
    java.lang.IllegalArgumentException - if contig is null or "*", or start is less than 1
  - setMatePosition
```
void setMatePosition(htsjdk.samtools.util.Locatable locatable)
```
    Set the position of the read's mate using the position of an existing Locatable. Cannot be used to set the read's mate to an unmapped position; use setMateIsUnmapped() for that purpose. Calling this method has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
    
    Parameters:
    
    locatable - Locatable representing the 1-based, inclusive position to assign to the read's mate
    
    Throws:
    
    java.lang.IllegalArgumentException - if locatable is null, or its contig is null or "*", or its start position is less than 1
  - getFragmentLength
```
int getFragmentLength()
```
    Returns the observed length of the read's fragment (equivalent to TLEN in SAM). Warning: the precise meaning of this field is implementation/technology dependent.
    
    Returns:
    
    The observed length of the fragment (equivalent to TLEN in SAM), or 0 if unknown. Negative if the mate maps to a lower position than the read.
  - setFragmentLength
```
void setFragmentLength(int fragmentLength)
```
    Set the observed length of the read's fragment (equivalent to TLEN in SAM). Warning: the precise meaning of this field is implementation/technology dependent.
    
    Parameters:
    
    fragmentLength - Observed length of the read's fragment; may be negative if the mate maps to a lower position than the read, or 0 if unknown.
  - getMappingQuality
```
int getMappingQuality()
```
    Returns:
    
    The mapping quality of this alignment, representing the phred-scaled likelihood that the read maps to this position as opposed to other locations. Returns ReadConstants.NO_MAPPING_QUALITY if there is none.
  - setMappingQuality
```
void setMappingQuality(int mappingQuality)
```
    Set the mapping quality of this alignment, representing how likely the read maps to this position as opposed to other locations. Set to ReadConstants.NO_MAPPING_QUALITY if there is none.
    
    Parameters:
    
    mappingQuality - mapping quality of this alignment; must be between 0 and 255, inclusive
    
    Throws:
    
    java.lang.IllegalArgumentException - if the mapping quality is less than 0 or greater than 255
  - getBases
```
byte[] getBases()
```
    Returns:
    
    The read sequence as ASCII bytes ACGTN=, or an empty byte[] if no sequence is present. This method makes a defensive copy of the bases array before returning it, so modifying the returned array will not alter the bases in the read.
  - getBasesNoCopy
```
default byte[] getBasesNoCopy()
```
    Returns:
    
    The read sequence as ASCII bytes ACGTN=, or an empty byte[] if no sequence is present. This method differs from getBases() in that implementations are free to avoid making a defensive copy, if it's possible to avoid a copy. WARNING: This method MAY NOT make a defensive copy of the bases array before returning it, so modifying the returned array MAY alter the bases in the actual read. CALLER BEWARE!
  - copyBases
```
default int copyBases(int offset,
                      byte[] destination,
                      int destinationOffset,
                      int maxLength)
```
    Copy the base into an existent byte array.
    Parameters:
    
    offset - the first base in the read to copy
    
    destination - the destination array.
    
    destinationOffset - the first base in the array to copy to.
    
    maxLength - the maximum number of bases to copy.
    
    Returns:
    
    the number of bases copied, always 0 or greater.
    
    Throws:
    java.lang.IllegalArgumentException - if any of:
    
    destination is null,
    
    any of the offsets is negative or goes beyond the maximum respective valid index (offset for the read bases and destinationOffset for destination).
    
    if there is not enough space in destination to hold to all the bases copied (NOTE: a large maxLength value won't result in an exception if the read does not have enough bases to overflow destination)
  - copyBaseQualities
```
default int copyBaseQualities(int offset,
                              byte[] destination,
                              int destinationOffset,
                              int maxLength)
```
    Copy base qualities into an existent byte array.
    Parameters:
    
    offset - the first base-quality in the read to copy
    
    destination - the destination array.
    
    destinationOffset - the first base-quality in the array to copy to.
    
    maxLength - the maximum number of base-qualities to copy.
    
    Returns:
    
    the number of base-qualities copied, always 0 or greater.
    
    Throws:
    java.lang.IllegalArgumentException - if any of:
    
    destination is null,
    
    any of the offsets is negative or goes beyond the maximum respective valid index (offset for the read base-qualities and destinationOffset for destination).
    
    if there is not enough space in destination to hold to all the base-qualities copied (NOTE: a large maxLength value won't result in an exception if the read does not have enough base-qualities to overflow destination)
  - hasBases
```
default boolean hasBases()
```
    Indicates whether there are any bases.
  - hasBaseQualities
```
default boolean hasBaseQualities()
```
    Indicates whether there is any base-qualities.
    
    Returns:
    
    true iff there is at least one base-quality.
  - getBase
```
default byte getBase(int i)
```
    Returns:
    
    The base at index i. The default implementation returns getBases()[i]. Subclasses may override to provide a more efficient implementations but must preserve the semantics equal to getBases()[i]
    
    Throws:
    
    java.lang.IllegalArgumentException - if i is negative or of i is not smaller than the number of bases (as reported by getLength(). In particular, if no sequence is present.
  - getBasesString
```
default java.lang.String getBasesString()
```
    Returns:
    
    All bases in the read as a single String, or ReadConstants.NULL_SEQUENCE_STRING if the read is empty.
  - setBases
```
void setBases(byte[] bases)
```
    Set the read's sequence.
    
    Parameters:
    
    bases - The read sequence as ASCII bytes ACGTN=. May be empty or null if no sequence is present.
  - getBaseQualities
```
byte[] getBaseQualities()
```
    Returns:
    
    Base qualities as binary phred scores (not ASCII), or an empty byte[] if base qualities are not present. This method makes a defensive copy of the base qualities array before returning it, so modifying the returned array will not alter the base qualities in the read.
  - getBaseQualitiesNoCopy
```
default byte[] getBaseQualitiesNoCopy()
```
    Returns:
    
    Base qualities as binary phred scores (not ASCII), or an empty byte[] if base qualities are not present. This method differs from getBaseQualities() in that implementations are free to avoid making a defensive copy, if it's possible to avoid a copy. WARNING: This method MAY NOT make a defensive copy of the base qualities array before returning it, so modifying the returned array MAY alter the base qualities in the read. CALLER BEWARE!
  - getBaseQualityCount
```
default int getBaseQualityCount()
```
    Returns:
    
    The number of base qualities in the read sequence. This default implementation calls getBaseQualities().length Subclasses may override to provide a more efficient implementation.
  - getBaseQuality
```
default byte getBaseQuality(int i)
```
    Returns:
    
    The base quality at index i. This default implementation returns getBaseQualities()[i]. Subclasses may override to provide a more efficient implementations but must preserve the semantics equal to getBaseQualities()[i]
    
    Throws:
    
    java.lang.IllegalArgumentException - if i is negative or of i is not smaller than the number of base qualities (as reported by getBaseQualityCount().
  - setBaseQualities
```
void setBaseQualities(byte[] baseQualities)
```
    Set the read's base qualities.
    
    Parameters:
    
    baseQualities - Base qualities as binary phred scores (not ASCII); negative values not allowed. May be empty or null if no base qualities are present.
    
    Throws:
    
    java.lang.IllegalArgumentException - if an invalid (negative) base quality is provided
  - getCigar
```
htsjdk.samtools.Cigar getCigar()
```
    Returns:
    
    Cigar object describing how the read aligns to the reference, or an empty Cigar object if no cigar is present. This method makes a defensive copy of the Cigar within the read if necessary, so modifying the return value of this method will not modify the read's Cigar. Callers of this method that only want to iterate over the elements of the Cigar should call getCigarElements() instead which may give better performance by avoiding object creation.
  - getCigarElements
```
default java.util.List<htsjdk.samtools.CigarElement> getCigarElements()
```
    Returns:
    
    Unmodifiable list of the CigarElements from this read. Note: The default implementation returns a unmodifiable view of the protective copy made by calling getCigar().getCigarElements() Subclasses may override.
  - getCigarElement
```
default htsjdk.samtools.CigarElement getCigarElement(int i)
```
    Return the cigar element at a given index. Note: the default implementation return getCigarElements().get(i). Subclasses may override, for example to reduce the memory allocation or improve speed.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= numCigarElements())
  - numCigarElements
```
default int numCigarElements()
```
    The number of cigar elements in this read. The default implementation returns getCigar().numCigarElements(). Subclasses may override to provide more efficient implementations.
  - setCigar
```
void setCigar(htsjdk.samtools.Cigar cigar)
```
    Set the read's Cigar using an existing Cigar object describing how the read aligns to the reference.
    
    Parameters:
    
    cigar - Cigar object describing how the read aligns to the reference; May be null or empty if the read has none.
  - setCigar
```
void setCigar(java.lang.String cigarString)
```
    Set the read's Cigar using a textual cigar String describing how the read aligns to the reference.
    
    Parameters:
    
    cigarString - Cigar String describing how the read aligns to the reference; May be null or empty if the read has none.
  - getReadGroup
```
java.lang.String getReadGroup()
```
    Returns:
    
    The ID of the read group this read belongs to, or null for none.
  - setReadGroup
```
void setReadGroup(java.lang.String readGroupID)
```
    Set the ID of the read group this read belongs to, or null for none.
    
    Parameters:
    
    readGroupID - ID of the read group this read belongs to, or null for none.
  - isPaired
```
boolean isPaired()
```
    Returns:
    
    True if this read is paired (ie., has a mate), otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsPaired
```
void setIsPaired(boolean isPaired)
```
    Mark the read as paired (having a mate) or not paired. Setting this to false has the additional effect of marking the read as not properly paired, as if setIsProperlyPaired(boolean) were invoked with false.
    
    Parameters:
    
    isPaired - True if this read is paired (ie., has a mate), otherwise false.
  - isProperlyPaired
```
boolean isProperlyPaired()
```
    Returns:
    
    True if this read is paired and the orientation and the distance between reads from the fragment are consistent with the sequencing protocol, otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsProperlyPaired
```
void setIsProperlyPaired(boolean isProperlyPaired)
```
    Mark the read as properly paired (or not properly paired). Setting this to true has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
    
    Parameters:
    
    isProperlyPaired - True if this read is paired and the orientation and the distance between reads from the fragment are consistent with the sequencing protocol, otherwise false.
  - isUnmapped
```
boolean isUnmapped()
```
    Returns:
    
    True if this read is unmapped (this includes reads that have a position but are explicitly marked as unmapped, as well as reads that lack a fully-defined position but are not explicitly marked as unmapped). Otherwise false.
  - setIsUnmapped
```
void setIsUnmapped()
```
    Mark the read as unmapped (lacking a defined position on the genome). To mark a read as mapped, use setPosition(java.lang.String, int)
  - isUnplaced
```
boolean isUnplaced()
```
    Does the read have a position assigned to it for sorting purposes.
    
    Returns:
    
    `true iff this read has no assigned position or contig.
  - setIsUnplaced
```
void setIsUnplaced()
```
    Mark the read as unmapped, and also removes mapping information from the read (i.e. sets contig to ReadConstants.UNSET_CONTIG and position to ReadConstants.UNSET_POSITION). NOTE: this does not remove the cigar string from the read, use setCigar(Cigar) To mark a read as mapped, use setPosition(java.lang.String, int)
  - mateIsUnmapped
```
boolean mateIsUnmapped()
```
    Returns:
    
    True if this read's mate is unmapped (this includes mates that have a position but are explicitly marked as unmapped, as well as mates that lack a fully-defined position but are not explicitly marked as unmapped). Otherwise false.
    
    Throws:
    
    java.lang.IllegalStateException - if the read is not paired (has no mate)
  - setMateIsUnmapped
```
void setMateIsUnmapped()
```
    Mark the read's mate as unmapped (lacking a defined position on the genome). (i.e. sets mate contig to ReadConstants.UNSET_CONTIG and position to ReadConstants.UNSET_POSITION). To mark the read's mate as mapped, use setMatePosition(java.lang.String, int) Calling this method has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
  - mateIsUnplaced
```
boolean mateIsUnplaced()
```
    Does the reads mate have a position assigned to it for sorting purposes..
    
    Returns:
    
    `true iff this reads mate has no assigned position or contig.
  - setMateIsUnplaced
```
void setMateIsUnplaced()
```
    Mark the read's mate as unmapped (lacking a defined position on the genome). In contrast with setMateIsUnmapped(), this method will revert the mapping information for the mate (i.e. sets the mate's contig to "*" and position to 0). To mark the read's mate as mapped, use setMatePosition(java.lang.String, int) Calling this method has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
  - isReverseStrand
```
boolean isReverseStrand()
```
    Returns:
    
    True if this read is on the reverse strand as opposed to the forward strand, otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsReverseStrand
```
void setIsReverseStrand(boolean isReverseStrand)
```
    Mark the read as being on the reverse (or forward) strand.
    
    Parameters:
    
    isReverseStrand - True if this read is on the reverse strand as opposed to the forward strand, otherwise false.
  - mateIsReverseStrand
```
boolean mateIsReverseStrand()
```
    Returns:
    
    True if this read's mate is on the reverse strand as opposed to the forward strand, otherwise false.
    
    Throws:
    
    java.lang.IllegalStateException - if the read is not paired (has no mate)
    
    GATKException.MissingReadField - if this information is not available
  - setMateIsReverseStrand
```
void setMateIsReverseStrand(boolean mateIsReverseStrand)
```
    Mark the read's mate as being on the reverse (or forward) strand. Calling this method has the additional effect of marking the read as paired, as if setIsPaired(boolean) were invoked with true.
    
    Parameters:
    
    mateIsReverseStrand - True if this read's mate is on the reverse strand as opposed to the forward strand, otherwise false.
  - isFirstOfPair
```
boolean isFirstOfPair()
```
    Returns:
    
    True if this read is paired and is the first read in the pair, otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsFirstOfPair
```
void setIsFirstOfPair()
```
    Mark the read as the first read of a pair. Calling this method has the additional effects of marking the read as paired, as if setIsPaired(boolean) were invoked with true, and also marks the read as NOT being the second of a pair.
  - isSecondOfPair
```
boolean isSecondOfPair()
```
    Returns:
    
    True if this read is paired and is the second read in the pair, otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsSecondOfPair
```
void setIsSecondOfPair()
```
    Mark the read as the second read of a pair. Calling this method has the additional effects of marking the read as paired, as if setIsPaired(boolean) were invoked with true, and also marks the read as NOT being the first of a pair.
  - isSecondaryAlignment
```
boolean isSecondaryAlignment()
```
    Returns:
    
    True if this is a secondary alignment (an alternative to the primary alignment), otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsSecondaryAlignment
```
void setIsSecondaryAlignment(boolean isSecondaryAlignment)
```
    Mark the read as a secondary alignment (an alternative to the primary alignment)
    
    Parameters:
    
    isSecondaryAlignment - True if this is a secondary alignment, otherwise false.
  - isSupplementaryAlignment
```
boolean isSupplementaryAlignment()
```
    Returns:
    
    True if this is a supplementary alignment (used in the representation of a chimeric alignment), otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsSupplementaryAlignment
```
void setIsSupplementaryAlignment(boolean isSupplementaryAlignment)
```
    Mark the read as a supplementary alignment (used in the representation of a chimeric alignment)
    
    Parameters:
    
    isSupplementaryAlignment - True if this is a supplementary alignment, otherwise false.
  - getPairOrientation
```
default java.util.Optional<htsjdk.samtools.SamPairUtil.PairOrientation> getPairOrientation()
```
    Computes the pair orientation
    
    Throws:
    
    java.lang.IllegalArgumentException - If the read is not paired, or if either read or mate is unmapped
  - failsVendorQualityCheck
```
boolean failsVendorQualityCheck()
```
    Returns:
    
    True if this read fails platform/vendor quality checks, otherwise false
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setFailsVendorQualityCheck
```
void setFailsVendorQualityCheck(boolean failsVendorQualityCheck)
```
    Mark the read as failing platform/vendor quality checks
    
    Parameters:
    
    failsVendorQualityCheck - True if this read fails platform/vendor quality checks, otherwise false
  - isDuplicate
```
boolean isDuplicate()
```
    Returns:
    
    True if this read is a PCR or optical duplicate, otherwise false.
    
    Throws:
    
    GATKException.MissingReadField - if this information is not available
  - setIsDuplicate
```
void setIsDuplicate(boolean isDuplicate)
```
    Mark the read as a PCR or optical duplicate.
    
    Parameters:
    
    isDuplicate - True if this read is a PCR or optical duplicate, otherwise false.
  - hasAttribute
```
boolean hasAttribute(java.lang.String attributeName)
```
    Check whether this read has a particular attribute
    
    Parameters:
    
    attributeName - name of the attribute to search for
    
    Returns:
    
    true if the read has an attribute with the given name, otherwise false
  - getAttributeAsInteger
```
java.lang.Integer getAttributeAsInteger(java.lang.String attributeName)
```
    Retrieve the value of a particular attribute typed as an integer.
    
    Parameters:
    
    attributeName - name of the attribute to retrieve
    
    Returns:
    
    integer value of the requested attribute, or null if the attribute is not present
    
    Throws:
    
    GATKException.ReadAttributeTypeMismatch - if the attribute value cannot be typed as an integer
  - getAttributeAsString
```
java.lang.String getAttributeAsString(java.lang.String attributeName)
```
    Retrieve the value of a particular attribute typed as a String.
    
    Parameters:
    
    attributeName - name of the attribute to retrieve
    
    Returns:
    
    String value of the requested attribute, or null if the attribute is not present
    
    Throws:
    
    GATKException.ReadAttributeTypeMismatch - if the attribute value cannot be typed as a single String value.
  - getAttributeAsByteArray
```
byte[] getAttributeAsByteArray(java.lang.String attributeName)
```
    Retrieve the value of a particular attribute typed as a byte array. Makes a defensive copy of an existing byte array within the read if necessary, so modifying the return value will not modify the attribute value within the read.
    
    Parameters:
    
    attributeName - name of the attribute to retrieve
    
    Returns:
    
    byte array value of the requested attribute, or null if the attribute is not present
    
    Throws:
    
    GATKException.ReadAttributeTypeMismatch - if the attribute value cannot be typed as a byte array.
  - getTransientAttribute
```
java.lang.Object getTransientAttribute(java.lang.Object key)
```
    This is used to access a transient attribute store provided by the underlying implementation. Transient attributes will not be serialized or written out with a record. NOTE: This is an advanced use case for GATKRead and you should probably use getAttribute() instead
    
    Parameters:
    
    key - key whose value is to be stored
  - getOptionalTransientAttribute
```
default <T> java.util.Optional<T> getOptionalTransientAttribute(java.lang.Object key,
                                                                java.lang.Class<T> clazz)
```
    Returns a transient attribute value as an Optional.
    
    Type Parameters:
    
    T - the parametric type of the attribute value.
    
    Parameters:
    
    key - the key to the attribute.
    
    clazz - the expected clazz of the attribute value.
    
    Returns:
    
    never null but a not-present optional instead.
  - setAttribute
```
void setAttribute(java.lang.String attributeName,
                  java.lang.Integer attributeValue)
```
    Set an integer-valued attribute on the read.
    
    Parameters:
    
    attributeName - Name of the attribute to set. Must be legal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
    
    attributeValue - Integer value of the attribute (may be null)
    
    Throws:
    
    java.lang.IllegalArgumentException - if the attribute name is illegal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
  - setAttribute
```
void setAttribute(java.lang.String attributeName,
                  java.lang.String attributeValue)
```
    Set a String-valued attribute on the read.
    
    Parameters:
    
    attributeName - Name of the attribute to set. Must be legal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
    
    attributeValue - String value of the attribute (may be null)
    
    Throws:
    
    java.lang.IllegalArgumentException - if the attribute name is illegal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
  - setAttribute
```
void setAttribute(java.lang.String attributeName,
                  byte[] attributeValue)
```
    Set a byte array attribute on the read.
    
    Parameters:
    
    attributeName - Name of the attribute to set. Must be legal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
    
    attributeValue - byte array value of the attribute (may be null or empty)
    
    Throws:
    
    java.lang.IllegalArgumentException - if the attribute name is illegal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
  - setTransientAttribute
```
void setTransientAttribute(java.lang.Object key,
                           java.lang.Object value)
```
    This is used to access the transient attribute store in the underlying data type. This is used to store temporary attributes and cached data that will not be serialized or written out as a record. NOTE: This is an advanced use case for GATKRead and you should probably use setAttribute() instead
    
    Parameters:
    
    key - key under which the value will be stored
    
    value - value to store
  - clearAttribute
```
void clearAttribute(java.lang.String attributeName)
```
    Clear an individual attribute on the read.
    
    Parameters:
    
    attributeName - Name of the attribute to clear. Must be legal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
    
    Throws:
    
    java.lang.IllegalArgumentException - if the attribute name is illegal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
  - clearAttributes
```
void clearAttributes()
```
    Clear all attributes on the read.
  - clearTransientAttribute
```
void clearTransientAttribute(java.lang.String attributeName)
```
    Clear an individual transient attribute on the read.
    
    Parameters:
    
    attributeName - Name of the attribute to clear. Must be legal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
    
    Throws:
    
    java.lang.IllegalArgumentException - if the attribute name is illegal according to ReadUtils.assertAttributeNameIsLegal(java.lang.String)
  - copy
```
GATKRead copy()
```
    Return a copy of this read.
    
    Returns:
    
    A copy of this read. The copy will not necessarily be a true deep copy (the fields encapsulated by the read itself may be shallow copied), but should be safe to use freely in general given that all GATKRead methods that return mutable reference types make defensive copies (with the exception of the conversion method {@link #convertToSAMRecord, but these are safe to call on copies since the encapsulated reads do get shallow copied at a minimum by this method, so modifications to the fields within a copied read will not alter the original).
  - deepCopy
```
GATKRead deepCopy()
```
    Return a deep copy of this read.
    
    Returns:
    
    A true deep copy of this read.
  - convertToSAMRecord
```
htsjdk.samtools.SAMRecord convertToSAMRecord(htsjdk.samtools.SAMFileHeader header)
```
    Convert this read into a SAMRecord. Warning: the return value is not guaranteed to be independent from this read (eg., if the read is already in SAMRecord format, no copy will be made).
    
    Parameters:
    
    header - required header for the SAMRecord
    
    Returns:
    
    This read as a SAMRecord
  - getSAMString
```
java.lang.String getSAMString()
```
    Get a string representation of this read in SAM string format, terminated with '\n'. Fields are separated by '\t',
    
    Returns:
    
    SAM string representation of this read.
  - reverseComplement
```
void reverseComplement()
```
    Modify this read by reverse complementing its bases and reversing its quality scores. Implementations may also update tags that are known to need updating after the reverse complement operation.
  - commonToString
```
default java.lang.String commonToString()
```
    A human-digestable representation of the read. NOTE: java will not let us have a default method override toString so we need this dance. Subclasses should override toString and call commonToString to get the same toString representation regardless of the underlying adaptee object.

Interface GATKRead

Method Summary

Methods inherited from interface htsjdk.samtools.util.Locatable

Method Detail

getName

getFlags

setName

getLength

isEmpty

setPosition

setPosition

getAssignedContig

getAssignedStart

getUnclippedStart

getUnclippedEnd

getSoftStart

getSoftEnd

getAdaptorBoundary

getMateContig

getMateStart

setMatePosition

setMatePosition

getFragmentLength

setFragmentLength

getMappingQuality

setMappingQuality

getBases

getBasesNoCopy

copyBases

copyBaseQualities

hasBases

hasBaseQualities

getBase

getBasesString

setBases

getBaseQualities

getBaseQualitiesNoCopy

getBaseQualityCount

getBaseQuality

setBaseQualities

getCigar

getCigarElements

getCigarElement

numCigarElements

setCigar

setCigar

getReadGroup

setReadGroup

isPaired

setIsPaired

isProperlyPaired

setIsProperlyPaired

isUnmapped

setIsUnmapped

isUnplaced

setIsUnplaced

mateIsUnmapped

setMateIsUnmapped

mateIsUnplaced

setMateIsUnplaced

isReverseStrand

setIsReverseStrand

mateIsReverseStrand

setMateIsReverseStrand

isFirstOfPair

setIsFirstOfPair

isSecondOfPair

setIsSecondOfPair

isSecondaryAlignment

setIsSecondaryAlignment

isSupplementaryAlignment

setIsSupplementaryAlignment

getPairOrientation

failsVendorQualityCheck

setFailsVendorQualityCheck

isDuplicate

setIsDuplicate

hasAttribute

getAttributeAsInteger

getAttributeAsString