Package 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
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Field Summary
FieldsFields 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 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
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Field Details
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INPUT
@Argument(shortName="I", doc="The output of VerifyIDIntensity(typically captured stdout).") public File INPUT -
OUTPUT
@Argument(shortName="O", doc="Basename for the metrics file that will be written. Resulting file will be <OUTPUT>.verifyidintensity_metrics") public File OUTPUT -
FILE_EXTENSION
- See Also:
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Constructor Details
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CreateVerifyIDIntensityContaminationMetricsFile
public CreateVerifyIDIntensityContaminationMetricsFile()
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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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