Package picard.analysis.artifacts
Class ConvertSequencingArtifactToOxoG
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- picard.cmdline.CommandLineProgram
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- picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
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@DocumentedFeature public class ConvertSequencingArtifactToOxoG extends CommandLineProgram
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Field Summary
Fields Modifier and Type Field Description File
INPUT_BASE
File
OUTPUT_BASE
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description ConvertSequencingArtifactToOxoG()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT_BASE
@Argument(shortName="I", doc="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics)") public File INPUT_BASE
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OUTPUT_BASE
@Argument(shortName="O", doc="Basename for output OxoG metrics. Defaults to same basename as input metrics", optional=true) public File OUTPUT_BASE
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Method Detail
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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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