public class FastqRecord
extends java.lang.Object
implements java.io.Serializable
Constructor and Description |
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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
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Modifier and Type | Method and Description |
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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.Object
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public 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