Package htsjdk.samtools.util

Enum Class FastqQualityFormat

java.lang.Object

java.lang.Enum<FastqQualityFormat>

htsjdk.samtools.util.FastqQualityFormat

All Implemented Interfaces:

Serializable, Comparable<FastqQualityFormat>, Constable

public enum FastqQualityFormat
extends Enum<FastqQualityFormat>

Enumeration for FastQ quality score formats formats.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
Illumina	Recent Solexa/Illumina (pipeline 1.3+) style scores which encode PHRED qualities using an ASCII offset of 64
Solexa	Early Solexa/Illumina (pre pipeline 1.3) style scores which encode Solexa qualities using an ASCII offset of 64
Standard	Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33

Method Summary

Modifier and Type	Method	Description
static FastqQualityFormat	valueOf(String name)	Returns the enum constant of this class with the specified name.
static FastqQualityFormat[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

Solexa

public static final FastqQualityFormat Solexa

Early Solexa/Illumina (pre pipeline 1.3) style scores which encode Solexa qualities using an ASCII offset of 64

Illumina

public static final FastqQualityFormat Illumina

Recent Solexa/Illumina (pipeline 1.3+) style scores which encode PHRED qualities using an ASCII offset of 64

Standard

public static final FastqQualityFormat Standard

Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33

Method Details

values

public static FastqQualityFormat[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static FastqQualityFormat valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null