Class PhysicalLocationForMateCigarSet

java.lang.Object
picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet

public class PhysicalLocationForMateCigarSet extends Object
This stores records that are comparable for detecting optical duplicates.
  • Constructor Details

    • PhysicalLocationForMateCigarSet

      public PhysicalLocationForMateCigarSet()
  • Method Details

    • add

      public void add(ReadEndsForMateCigar end)
      Adds the end to this set, if not already added based on physical location
    • size

      public int size()
      The number of records in this set
    • remove

      public void remove(ReadEndsForMateCigar end)
      Removes the end from this set, if present
    • getReadEnds

      public Set<ReadEnds> getReadEnds()
      Gets the set of read ends
    • replace

      public void replace(ReadEndsForMateCigar current, ReadEndsForMateCigar other)
      Replaces a given end with the other end. This ensures that that current is in this set