Class SimpleMarkDuplicatesWithMateCigar

  • Direct Known Subclasses:
    UmiAwareMarkDuplicatesWithMateCigar

    @DocumentedFeature
    @ExperimentalFeature
    public class SimpleMarkDuplicatesWithMateCigar
    extends MarkDuplicates
    This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator. Users should continue to use MarkDuplicates in general. The main motivation of this tool was the fact that MarkDuplicates has many, many, many useful test cases, but few unit tests for validating individual duplicate sets. To test the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator, the most expedient method was to write this tool and make sure it behaves similarly to MarkDuplicates. Not the best, I know, but good enough. NH 06/25/2015. See MarkDuplicates for more details.
    • Constructor Detail

      • SimpleMarkDuplicatesWithMateCigar

        public SimpleMarkDuplicatesWithMateCigar()
    • Method Detail

      • main

        public static void main​(String[] args)
        Stock main method.
      • doWork

        protected int doWork()
        Main work method.
        Overrides:
        doWork in class MarkDuplicates
        Returns:
        program exit status.