picard.arrays

Class CreateVerifyIDIntensityContaminationMetricsFile

java.lang.Object

picard.cmdline.CommandLineProgram

picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile

@DocumentedFeature
public class CreateVerifyIDIntensityContaminationMetricsFile
extends CommandLineProgram

A simple program to create a standard picard metrics file from the output of VerifyIDIntensity

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	FILE_EXTENSION
java.io.File	INPUT
java.io.File	OUTPUT

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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CreateVerifyIDIntensityContaminationMetricsFile()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Argument(shortName="I",
          doc="The output of VerifyIDIntensity(typically captured stdout).")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Basename for the metrics file that will be written. Resulting file will be <OUTPUT>.verifyidintensity_metrics")
public java.io.File OUTPUT

FILE_EXTENSION

public static final java.lang.String FILE_EXTENSION

See Also:

Constant Field Values

Constructor Detail

CreateVerifyIDIntensityContaminationMetricsFile

public CreateVerifyIDIntensityContaminationMetricsFile()

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.