Package picard.analysis

Class CompareMetrics

  • @DocumentedFeature
public class CompareMetrics
extends CommandLineProgram
    Compare two metrics files.

    • Field Detail

      • INPUT

        @Argument(shortName="I",
          doc="Metric files to compare.",
          minElements=2,
          maxElements=2)
public List<File> INPUT

      • OUTPUT

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

      • METRICS_TO_IGNORE

        @Argument(shortName="MI",
          doc="Metrics to ignore. Any metrics specified here will be excluded from comparison by the tool.",
          optional=true)
public List<String> METRICS_TO_IGNORE

      • METRIC_ALLOWABLE_RELATIVE_CHANGE

        @Argument(shortName="MARC",
          doc="Metric Allowable Relative Change. A colon separate pair of metric name and an absolute relative change.  For any metric specified here,  when the values are compared between the two files, the program will allow that much relative change between the  two values.",
          optional=true)
public List<String> METRIC_ALLOWABLE_RELATIVE_CHANGE

      • IGNORE_HISTOGRAM_DIFFERENCES

        @Argument(shortName="IHD",
          doc="Ignore any differences between the two metric file\'s histograms (useful if using the \'METRIC_ALLOWABLE_RELATIVE_CHANGE\')",
          optional=true)
public boolean IGNORE_HISTOGRAM_DIFFERENCES

      • MetricToAllowableRelativeChange

        protected final Map<String,​Double> MetricToAllowableRelativeChange

    • Constructor Detail

      • CompareMetrics

        public CompareMetrics()

    • Method Detail

      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        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.

      • customCommandLineValidation

        protected String[] customCommandLineValidation()
        Description copied from class: CommandLineProgram
        Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
        Overrides:
        customCommandLineValidation in class CommandLineProgram
        Returns:
        null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

      • compareMetricValues

        protected picard.analysis.CompareMetrics.SimpleResult compareMetricValues​(Object value1,
                                                                          Object value2,
                                                                          String metricName)