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 Detail

      • SAM_FILES

        @PositionalArguments(doc="Exactly two input .sam or .bam 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
    • Constructor Detail

      • CompareSAMs

        public CompareSAMs()
    • Method Detail

      • 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.