htsjdk.samtools.fastq

Class FastqRecord

java.lang.Object

htsjdk.samtools.fastq.FastqRecord

All Implemented Interfaces:

java.io.Serializable

public class FastqRecord
extends java.lang.Object
implements java.io.Serializable

Simple representation of a FASTQ record, without any conversion

See Also:

Serialized Form

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqRecord

public FastqRecord(java.lang.String readName,
                   java.lang.String readBases,
                   java.lang.String qualityHeader,
                   java.lang.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(java.lang.String readName,
                   byte[] readBases,
                   java.lang.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 Detail

getReadHeader

@Deprecated
public java.lang.String getReadHeader()

Deprecated. since 02/2017. Use getReadName() instead

Returns:

the read name

getReadName

public java.lang.String getReadName()

Get the read name

Returns:

the read name

getReadString

public java.lang.String getReadString()

Get the DNA sequence

Returns:

read sequence as a string of ACGTN=.

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 java.lang.String getBaseQualityString()

Get the base qualities encoded as a FASTQ string

Returns:

the quality string

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 java.lang.String getBaseQualityHeader()

Get the base quality header

Returns:

the base quality header

length

@Deprecated
public int length()

Deprecated. since 02/2017. Use getReadLength() instead

shortcut to getReadString().length()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

toFastQString

public java.lang.String toFastQString()

Returns the record as the String FASTQ format.

See Also:

FastqEncoder.encode(FastqRecord)

toString

public java.lang.String toString()

Returns toFastQString()

Overrides:

toString in class java.lang.Object