FastqRecord (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.fastq.FastqRecord

All Implemented Interfaces:

Serializable
```
public class FastqRecord
extends Object
implements Serializable
```
Simple representation of a FASTQ record, without any conversion

See Also:

Serialized Form

Constructor Summary

Constructors
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

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
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()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - FastqRecord
```
public FastqRecord(String readName,
                   String readBases,
                   String qualityHeader,
                   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(String readName,
                   byte[] readBases,
                   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 String getReadHeader()
```
    Deprecated.
    since 02/2017. Use getReadName() instead
    
    Returns:
    
    the read name
  - getReadName
```
public String getReadName()
```
    Get the read name
    
    Returns:
    
    the read name
  - getReadString
```
public 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 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 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 Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - toFastQString
```
public String toFastQString()
```
    Returns the record as the String FASTQ format.
    
    See Also:
    
    FastqEncoder.encode(FastqRecord)
  - toString
```
public String toString()
```
    Returns toFastQString()
    
    Overrides:
    
    toString in class Object

Class FastqRecord

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastqRecord

FastqRecord

FastqRecord

Method Detail

getReadHeader

getReadName

getReadString

getReadBases

getBaseQualityString

getBaseQualities

getReadLength

getBaseQualityHeader

length

hashCode

equals

toFastQString

toString