Package picard.arrays

Class CreateBafRegressMetricsFile

java.lang.Object

picard.cmdline.CommandLineProgram

picard.arrays.CreateBafRegressMetricsFile

@DocumentedFeature
public class CreateBafRegressMetricsFile
extends CommandLineProgram

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

Field Summary

Fields

Modifier and Type	Field	Description
static final String	FILE_EXTENSION
File	INPUT
File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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

Constructor Summary

Constructors

Constructor	Description
CreateBafRegressMetricsFile()

Method Summary

Modifier and Type	Method	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 Details

INPUT

@Argument(shortName="I",
          doc="The output of bafRegress (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>.bafregress_metrics")
public File OUTPUT

FILE_EXTENSION

public static final String FILE_EXTENSION

See Also:

• Constant Field Values

Constructor Details

CreateBafRegressMetricsFile

public CreateBafRegressMetricsFile()

Method Details

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.