Serializable
public class FastqRecord extends Object implements Serializable
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
|
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() |
public FastqRecord(String readName, String readBases, String qualityHeader, 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(String readName, byte[] readBases, 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 String getReadHeader()
getReadName()
insteadpublic String getReadName()
public String getReadString()
public byte[] getReadBases()
SAMRecord.NULL_SEQUENCE
if no bases are present.public String getBaseQualityString()
public byte[] getBaseQualities()
SAMRecord.NULL_QUALS
if no bases are present.public int getReadLength()
public String getBaseQualityHeader()
@Deprecated public int length()
getReadLength()
insteadpublic String toFastQString()
FastqEncoder.encode(FastqRecord)
public String toString()
toFastQString()