htsjdk.samtools.util

Enum FastqQualityFormat

java.lang.Object

java.lang.Enum<FastqQualityFormat>

htsjdk.samtools.util.FastqQualityFormat

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<FastqQualityFormat>

public enum FastqQualityFormat
extends java.lang.Enum<FastqQualityFormat>

Enumeration for FastQ quality score formats formats.

Enum Constant Summary

Enum Constants

Enum Constant and 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 and Description
static FastqQualityFormat	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static FastqQualityFormat[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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 Detail

values

public static FastqQualityFormat[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (FastqQualityFormat c : FastqQualityFormat.values())
    System.out.println(c);

Returns:

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

valueOf

public static FastqQualityFormat valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null