Package picard.sam

Class CompareSAMs


@DocumentedFeature public class CompareSAMs extends CommandLineProgram
Rudimentary SAM comparer. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info. Summarizes the number of alignments that match, mismatch, are missing, etc.
  • Field Details

    • SAM_FILES

      @PositionalArguments(doc="Exactly two input SAM/BAM/CRAM files to compare to one another.", minElements=2, maxElements=2) public List<File> SAM_FILES
    • OUTPUT

      @Argument(shortName="O", doc="Output file to write comparison results to.", optional=true) public File OUTPUT
    • samComparisonArgumentCollection

      @ArgumentCollection public SAMComparisonArgumentCollection samComparisonArgumentCollection
  • Constructor Details

    • CompareSAMs

      public CompareSAMs()
  • Method Details

    • doWork

      protected int doWork()
      Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.