Enum Constant Detail

• INTERVAL_SUBDIVISION

  public static final IntervalListScatterer.Mode INTERVAL_SUBDIVISION

  A simple scatter approach in which all output intervals have size equal to the total base count of the source list divided by the scatter count (except, possibly, in the last interval list).

• BALANCING_WITHOUT_INTERVAL_SUBDIVISION

  public static final IntervalListScatterer.Mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION

  A scatter approach that differs from INTERVAL_SUBDIVISION in a few ways:

  1. No interval will be subdivided, and consequently, the requested IntervalListTools.SCATTER_COUNT is an upper bound of scatter count, not a guarante of the number of IntervalLists that will be produced (e.g., if scatterCount = 10 but there is only one interval in the input, only 1 interval list will be emitted).
  2. When an interval would otherwise be split, it is instead deferred to the next scatter list.
  3. The "target width" of each scatter list may be wider than what is computed for INTERVAL_SUBDIVISION. Specifically, if the widest interval in the source interval list is larger than what would otherwise be the target width, that interval's width is used.
     
     This approach produces more consistently-sized interval lists, which is one of the objectives of scattering.

• BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW

  public static final IntervalListScatterer.Mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW

  A scatter approach that differs from BALANCING_WITHOUT_INTERVAL_SUBDIVISION. This approach tries to balance the number of bases in each interval list by estimating the remaining interval lists sizes. This is computed from the total number of unique bases and the bases we have consumed. This means that the interval list with the most number of unique bases is at most the ideal split length larger than the smallest interval list (unique number of bases).

Method Detail

• values

  public static IntervalListScatterer.Mode[] 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 (IntervalListScatterer.Mode c : IntervalListScatterer.Mode.values())
      System.out.println(c);
  

  Returns:

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

• valueOf

  public static IntervalListScatterer.Mode 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 name

  NullPointerException - if the argument is null