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

Represents a fastq record, fairly literally, i.e. without any conversion.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
FastqRecord(FastqRecord other) copy constructor
FastqRecord(java.lang.String seqHeaderPrefix, java.lang.String seqLine, java.lang.String qualHeaderPrefix, java.lang.String qualLine)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
java.lang.String	getBaseQualityHeader()
java.lang.String	getBaseQualityString()
java.lang.String	getReadHeader()
java.lang.String	getReadString()
int	hashCode()
int	length() shortcut to getReadString().length()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqRecord

public FastqRecord(java.lang.String seqHeaderPrefix,
                   java.lang.String seqLine,
                   java.lang.String qualHeaderPrefix,
                   java.lang.String qualLine)

FastqRecord

public FastqRecord(FastqRecord other)

copy constructor

Method Detail

getReadHeader

public java.lang.String getReadHeader()

Returns:

the read name

getReadString

public java.lang.String getReadString()

Returns:

the read DNA sequence

getBaseQualityHeader

public java.lang.String getBaseQualityHeader()

Returns:

the quality header

getBaseQualityString

public java.lang.String getBaseQualityString()

Returns:

the quality string

length

public int length()

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object