picard.vcf

Class RenameSampleInVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.RenameSampleInVcf

public class RenameSampleInVcf
extends CommandLineProgram

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
java.lang.String	NEW_SAMPLE_NAME
java.lang.String	OLD_SAMPLE_NAME
java.io.File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
RenameSampleInVcf()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Option(shortName="I",
        doc="Input single sample VCF.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Output single sample VCF.")
public java.io.File OUTPUT

OLD_SAMPLE_NAME

@Option(doc="Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name",
        optional=true)
public java.lang.String OLD_SAMPLE_NAME

NEW_SAMPLE_NAME

@Option(doc="New name to give sample in output VCF.")
public java.lang.String NEW_SAMPLE_NAME

Constructor Detail

RenameSampleInVcf

public RenameSampleInVcf()

Method Detail

main

public static void main(java.lang.String[] args)

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.