Package picard.illumina.parser
Enum IlluminaMetricsCode
- java.lang.Object
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- java.lang.Enum<IlluminaMetricsCode>
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- picard.illumina.parser.IlluminaMetricsCode
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- All Implemented Interfaces:
Serializable
,Comparable<IlluminaMetricsCode>
public enum IlluminaMetricsCode extends Enum<IlluminaMetricsCode>
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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Enum Constant Summary
Enum Constants Enum Constant Description CLUSTER_ID
DENSITY_ID
PHASING_BASE
PREPHASING_BASE
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getMetricsCode()
static int
getPhasingCode(int readDescriptorIndex, IlluminaMetricsCode phasingType)
Phasing codes are between 200 and 299 (inclusive).static boolean
isPhasing(IlluminaMetricsCode metricsCode)
static IlluminaMetricsCode
valueOf(String name)
Returns the enum constant of this type with the specified name.static IlluminaMetricsCode[]
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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DENSITY_ID
public static final IlluminaMetricsCode DENSITY_ID
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CLUSTER_ID
public static final IlluminaMetricsCode CLUSTER_ID
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PHASING_BASE
public static final IlluminaMetricsCode PHASING_BASE
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PREPHASING_BASE
public static final IlluminaMetricsCode PREPHASING_BASE
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Method Detail
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values
public static IlluminaMetricsCode[] 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 (IlluminaMetricsCode c : IlluminaMetricsCode.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 IlluminaMetricsCode 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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getPhasingCode
public static int getPhasingCode(int readDescriptorIndex, IlluminaMetricsCode phasingType)
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.
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isPhasing
public static boolean isPhasing(IlluminaMetricsCode metricsCode)
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getMetricsCode
public int getMetricsCode()
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