Class IntervalListScattererWithoutSubdivision

java.lang.Object
picard.util.IntervalList.IntervalListScattererByBaseCount
picard.util.IntervalList.IntervalListScattererWithoutSubdivision
All Implemented Interfaces:
IntervalListScatterer
Direct Known Subclasses:
IntervalListScattererWithoutSubdivisionWithOverflow

public class IntervalListScattererWithoutSubdivision extends IntervalListScattererByBaseCount
A BaseCount Scatterer that avoid breaking-up intervals. This is done by by only adding intervals to the current list if the resulting size no larger than the "ideal" size. In addition, the ideal length will not be small than the largest sub-interval in the input list.
  • Constructor Details

    • IntervalListScattererWithoutSubdivision

      public IntervalListScattererWithoutSubdivision()
  • Method Details

    • takeSome

      public List<htsjdk.samtools.util.Interval> takeSome(htsjdk.samtools.util.Interval interval, long idealSplitWeight, long currentSize, double projectedSizeOfRemaining)
      Description copied from interface: IntervalListScatterer
      Figure out how much of the input interval to put into current list and how much to leave for the next interval list.
      Returns:
      a list of two (possibly null) elements. The first element should be added to the current interval list, the second should be offered to the next interval list.
    • shouldIncludeInterval

      protected boolean shouldIncludeInterval(long idealSplitWeight, double projectedSizeOfRemaining, long projectedSize)
    • deduceIdealSplitWeight

      public int deduceIdealSplitWeight(htsjdk.samtools.util.IntervalList intervalList, int nCount)
      Description copied from interface: IntervalListScatterer
      A method that determines the ideal target "weight" of the output IntervalList.
      Specified by:
      deduceIdealSplitWeight in interface IntervalListScatterer
      Overrides:
      deduceIdealSplitWeight in class IntervalListScattererByBaseCount
      Parameters:
      intervalList - the IntervalList that is about to get split
      nCount - the scatter count into which to split intervalList
      Returns:
      The ideal "weight" of the output IntervalList's