Package picard.util
Enum IlluminaUtil.IlluminaAdapterPair
- java.lang.Object
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- java.lang.Enum<IlluminaUtil.IlluminaAdapterPair>
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- picard.util.IlluminaUtil.IlluminaAdapterPair
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- All Implemented Interfaces:
Serializable
,Comparable<IlluminaUtil.IlluminaAdapterPair>
,AdapterPair
- Enclosing class:
- IlluminaUtil
public static enum IlluminaUtil.IlluminaAdapterPair extends Enum<IlluminaUtil.IlluminaAdapterPair> implements AdapterPair
Describes adapters used on each pair of strands
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Enum Constant Summary
Enum Constants Enum Constant Description ALTERNATIVE_SINGLE_END
DUAL_INDEXED
FLUIDIGM
INDEXED
NEXTERA_V1
NEXTERA_V2
PAIRED_END
The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.SINGLE_END
TRUSEQ_SMALLRNA
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description String
get3PrimeAdapter()
byte[]
get3PrimeAdapterBytes()
byte[]
get3PrimeAdapterBytesInReadOrder()
String
get3PrimeAdapterInReadOrder()
String
get5PrimeAdapter()
byte[]
get5PrimeAdapterBytes()
byte[]
get5PrimeAdapterBytesInReadOrder()
String
get5PrimeAdapterInReadOrder()
String
getName()
static IlluminaUtil.IlluminaAdapterPair
valueOf(String name)
Returns the enum constant of this type with the specified name.static IlluminaUtil.IlluminaAdapterPair[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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PAIRED_END
public static final IlluminaUtil.IlluminaAdapterPair PAIRED_END
The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.
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INDEXED
public static final IlluminaUtil.IlluminaAdapterPair INDEXED
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SINGLE_END
public static final IlluminaUtil.IlluminaAdapterPair SINGLE_END
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NEXTERA_V1
public static final IlluminaUtil.IlluminaAdapterPair NEXTERA_V1
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NEXTERA_V2
public static final IlluminaUtil.IlluminaAdapterPair NEXTERA_V2
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DUAL_INDEXED
public static final IlluminaUtil.IlluminaAdapterPair DUAL_INDEXED
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FLUIDIGM
public static final IlluminaUtil.IlluminaAdapterPair FLUIDIGM
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TRUSEQ_SMALLRNA
public static final IlluminaUtil.IlluminaAdapterPair TRUSEQ_SMALLRNA
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ALTERNATIVE_SINGLE_END
public static final IlluminaUtil.IlluminaAdapterPair ALTERNATIVE_SINGLE_END
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Method Detail
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values
public static IlluminaUtil.IlluminaAdapterPair[] 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 (IlluminaUtil.IlluminaAdapterPair c : IlluminaUtil.IlluminaAdapterPair.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static IlluminaUtil.IlluminaAdapterPair valueOf(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:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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get3PrimeAdapter
public String get3PrimeAdapter()
- Specified by:
get3PrimeAdapter
in interfaceAdapterPair
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get5PrimeAdapter
public String get5PrimeAdapter()
- Specified by:
get5PrimeAdapter
in interfaceAdapterPair
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get3PrimeAdapterInReadOrder
public String get3PrimeAdapterInReadOrder()
- Specified by:
get3PrimeAdapterInReadOrder
in interfaceAdapterPair
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get5PrimeAdapterInReadOrder
public String get5PrimeAdapterInReadOrder()
- Specified by:
get5PrimeAdapterInReadOrder
in interfaceAdapterPair
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get3PrimeAdapterBytes
public byte[] get3PrimeAdapterBytes()
- Specified by:
get3PrimeAdapterBytes
in interfaceAdapterPair
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get5PrimeAdapterBytes
public byte[] get5PrimeAdapterBytes()
- Specified by:
get5PrimeAdapterBytes
in interfaceAdapterPair
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get3PrimeAdapterBytesInReadOrder
public byte[] get3PrimeAdapterBytesInReadOrder()
- Specified by:
get3PrimeAdapterBytesInReadOrder
in interfaceAdapterPair
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get5PrimeAdapterBytesInReadOrder
public byte[] get5PrimeAdapterBytesInReadOrder()
- Specified by:
get5PrimeAdapterBytesInReadOrder
in interfaceAdapterPair
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getName
public String getName()
- Specified by:
getName
in interfaceAdapterPair
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