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

      • samFiles

        @PositionalArguments(minElements=2,
                             maxElements=2)
        public List<File> samFiles
    • Constructor Detail

      • CompareSAMs

        public CompareSAMs()
    • Method Detail

      • main

        public static void main​(String[] argv)
      • 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.
      • getMappingsMatch

        public int getMappingsMatch()
      • getUnmappedBoth

        public int getUnmappedBoth()
      • getUnmappedLeft

        public int getUnmappedLeft()
      • getUnmappedRight

        public int getUnmappedRight()
      • getMappingsDiffer

        public int getMappingsDiffer()
      • getMissingLeft

        public int getMissingLeft()
      • getMissingRight

        public int getMissingRight()
      • areEqual

        public boolean areEqual()