public class FastqRecord
extends java.lang.Object
implements java.io.Serializable
| 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
|
| 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(). |
public FastqRecord(java.lang.String readName,
java.lang.String readBases,
java.lang.String qualityHeader,
java.lang.String baseQualities)
readName - the read name (without FastqConstants.SEQUENCE_HEADER)readBases - the read sequence basesqualityHeader - the quality header (without FastqConstants.SEQUENCE_HEADER)baseQualities - the base quality scorespublic FastqRecord(java.lang.String readName,
byte[] readBases,
java.lang.String qualityHeader,
byte[] baseQualities)
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)public FastqRecord(FastqRecord other)
other - record to copy@Deprecated public java.lang.String getReadHeader()
getReadName() insteadpublic java.lang.String getReadName()
null).public java.lang.String getReadString()
null).public byte[] getReadBases()
SAMRecord.NULL_SEQUENCE if no bases are present.public java.lang.String getBaseQualityString()
null).public byte[] getBaseQualities()
SAMRecord.NULL_QUALS if no bases are present.public int getReadLength()
public java.lang.String getBaseQualityHeader()
null).@Deprecated public int length()
getReadLength() insteadpublic int hashCode()
hashCode in class java.lang.Objectpublic boolean equals(java.lang.Object obj)
equals in class java.lang.Objectpublic java.lang.String toFastQString()
FastqEncoder.encode(FastqRecord)public java.lang.String toString()
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().toString in class java.lang.Object