Class SecondaryAlignmentFilter

    • Constructor Detail

      • SecondaryAlignmentFilter

        public SecondaryAlignmentFilter()
    • Method Detail

      • filterOut

        public boolean filterOut​(SAMRecord record)
        Returns true if the read is marked as secondary.
        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)
        Returns true if either read is marked as secondary.
        Specified by:
        filterOut in interface SamRecordFilter
        Parameters:
        first - the first SAMRecord to evaluate
        second - the second SAMRecord to evaluate
        Returns:
        true if the pair of records matches filter, otherwise false