Package picard.analysis
Class CompareMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CompareMetrics
Compare two metrics files.
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected picard.analysis.CompareMetrics.SimpleResult
compareMetricValues
(Object value1, Object value2, String metricName) protected String[]
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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OUTPUT
@Argument(shortName="O", doc="Output file to write comparison results to.", optional=true) public File OUTPUT -
METRICS_TO_IGNORE
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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
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Constructor Details
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CompareMetrics
public CompareMetrics()
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Method Details
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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 classCommandLineProgram
- Returns:
- program exit status.
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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 classCommandLineProgram
- 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.
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compareMetricValues
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