Package htsjdk.samtools.fastq

Class FastqRecord

java.lang.Object

htsjdk.samtools.fastq.FastqRecord

All Implemented Interfaces:

Serializable

public class FastqRecord
extends Object
implements Serializable

Simple representation of a FASTQ record, without any conversion

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
FastqRecord(FastqRecord other)	Copy constructor
FastqRecord(String readName, byte[] readBases, String qualityHeader, byte[] baseQualities)	Constructor for byte[] arrays
FastqRecord(String readName, String readBases, String qualityHeader, String baseQualities)	Default constructor

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
byte[]	getBaseQualities()	Get the base qualities as binary PHRED scores (not ASCII)
String	getBaseQualityHeader()	Get the base quality header
String	getBaseQualityString()	Get the base qualities encoded as a FASTQ string
byte[]	getReadBases()	Get the DNA sequence.
String	getReadHeader()	Deprecated. since 02/2017.
int	getReadLength()	Get the read length
String	getReadName()	Get the read name
String	getReadString()	Get the DNA sequence
int	hashCode()
int	length()	Deprecated. since 02/2017.
String	toFastQString()	Returns the record as the String FASTQ format.
String	toString()	Returns toFastQString().

Methods inherited from class java.lang.Object

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

Constructor Details

FastqRecord

public FastqRecord(String readName,
 String readBases,
 String qualityHeader,
 String baseQualities)

Default constructor

Parameters:

readName - the read name (without FastqConstants.SEQUENCE_HEADER)

readBases - the read sequence bases

qualityHeader - the quality header (without FastqConstants.SEQUENCE_HEADER)

baseQualities - the base quality scores

FastqRecord

public FastqRecord(String readName,
 byte[] readBases,
 String qualityHeader,
 byte[] baseQualities)

Constructor for byte[] arrays

Parameters:

readName - the read name (without FastqConstants.SEQUENCE_HEADER)

readBases - the read sequence bases as ASCII bytes ACGTN=.

qualityHeader - the quality header (without FastqConstants.SEQUENCE_HEADER)

baseQualities - the base qualities as binary PHRED scores (not ASCII)

FastqRecord

public FastqRecord(FastqRecord other)

Copy constructor

Parameters:

other - record to copy

Method Details

getReadHeader

@Deprecated
public String getReadHeader()

Deprecated.

since 02/2017. Use getReadName() instead

Returns:

the read name

getReadName

public String getReadName()

Get the read name

Returns:

the read name (may be null).

getReadString

public String getReadString()

Get the DNA sequence

Returns:

read sequence as a string of ACGTN= (may be null).

getReadBases

public byte[] getReadBases()

Get the DNA sequence.

Returns:

read sequence as ASCII bytes ACGTN=; SAMRecord.NULL_SEQUENCE if no bases are present.

getBaseQualityString

public String getBaseQualityString()

Get the base qualities encoded as a FASTQ string

Returns:

the quality string (may be null).

getBaseQualities

public byte[] getBaseQualities()

Get the base qualities as binary PHRED scores (not ASCII)

Returns:

the base quality; SAMRecord.NULL_QUALS if no bases are present.

getReadLength

public int getReadLength()

Get the read length

Returns:

number of bases in the read

getBaseQualityHeader

public String getBaseQualityHeader()

Get the base quality header

Returns:

the base quality header (may be null).

length

@Deprecated
public int length()

Deprecated.

since 02/2017. Use getReadLength() instead

shortcut to getReadString().length()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toFastQString

public String toFastQString()

Returns the record as the String FASTQ format.

See Also:

• FastqEncoder.encode(FastqRecord)

toString

public String toString()

Returns toFastQString(). WARNING: This method will be changed in the future for a simpler representation of the object. For code relying on the formatting as a FASTQ String, please refactor your code to use toFastQString().

Overrides:

toString in class Object