picard.analysis.artifacts

Class ConvertSequencingArtifactToOxoG

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.artifacts.ConvertSequencingArtifactToOxoG

@DocumentedFeature
public class ConvertSequencingArtifactToOxoG
extends CommandLineProgram

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT_BASE
java.io.File	OUTPUT_BASE

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
ConvertSequencingArtifactToOxoG()

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, 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_BASE

@Argument(shortName="I",
          doc="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics)")
public java.io.File INPUT_BASE

OUTPUT_BASE

@Argument(shortName="O",
          doc="Basename for output OxoG metrics. Defaults to same basename as input metrics",
          optional=true)
public java.io.File OUTPUT_BASE

Constructor Detail

ConvertSequencingArtifactToOxoG

public ConvertSequencingArtifactToOxoG()

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.