Enum Class IlluminaMetricsCode

java.lang.Object
java.lang.Enum<IlluminaMetricsCode>
picard.illumina.parser.IlluminaMetricsCode
All Implemented Interfaces:
Serializable, Comparable<IlluminaMetricsCode>, Constable

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).
  • Enum Constant Details

  • Method Details

    • values

      public static IlluminaMetricsCode[] 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 IlluminaMetricsCode 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
    • 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.
    • isPhasing

      public static boolean isPhasing(IlluminaMetricsCode metricsCode)
    • getMetricsCode

      public int getMetricsCode()