Class SecondaryOrSupplementaryFilter

  • All Implemented Interfaces:
    SamRecordFilter

    public class SecondaryOrSupplementaryFilter
    extends Object
    implements SamRecordFilter
    Filter out SAMRecords with Secondary or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator, in that we did not want to change the functionality of NPSI to no longer match its name $Id$
    • Constructor Detail

      • SecondaryOrSupplementaryFilter

        public SecondaryOrSupplementaryFilter()
    • Method Detail

      • filterOut

        public boolean filterOut​(SAMRecord record)
        Description copied from interface: SamRecordFilter
        Determines whether a SAMRecord matches this filter
        Specified by:
        filterOut in interface SamRecordFilter
        Parameters:
        record - the SAMRecord to evaluate
        Returns:
        true if the SAMRecord matches the filter, otherwise false
      • filterOut

        public boolean filterOut​(SAMRecord first,
                                 SAMRecord second)
        Determines whether a pair of SAMRecord matches this filter
        Specified by:
        filterOut in interface SamRecordFilter
        Parameters:
        first - the first SAMRecord to evaluate
        second - the second SAMRecord to evaluate
        Returns:
        true if the SAMRecords matches the filter, otherwise false