Package picard.illumina.parser
Enum Class IlluminaMetricsCode
- All Implemented Interfaces:
Serializable
,Comparable<IlluminaMetricsCode>
,Constable
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code
(e.g. phasing values are computed from a base of 200).
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum Constants -
Method Summary
Modifier and TypeMethodDescriptionint
static int
getPhasingCode
(int readDescriptorIndex, IlluminaMetricsCode phasingType) Phasing codes are between 200 and 299 (inclusive).static boolean
isPhasing
(IlluminaMetricsCode metricsCode) static IlluminaMetricsCode
Returns the enum constant of this class with the specified name.static IlluminaMetricsCode[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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DENSITY_ID
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CLUSTER_ID
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PHASING_BASE
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PREPHASING_BASE
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Method Details
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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
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valueOf
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 nameNullPointerException
- if the argument is null
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getPhasingCode
Phasing codes are between 200 and 299 (inclusive). Phasing codes are defined as being (200 + ((N - 1) * 2)) for (a 0-based) read descriptor N (i.e., 200, 202, 204, etc.) Prephasing codes are defined as being (201 + ((N - 1) * 2)) for read descriptor N (i.e., 201, 203, 205, etc.). So for a 101T8B101T read structure, there will be phasing codes of 200, 202 and 204 and prephasing codes of 201, 203, 205. -
isPhasing
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getMetricsCode
public int getMetricsCode()
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