picard.sam

Class CalculateReadGroupChecksum

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.CalculateReadGroupChecksum

public class CalculateReadGroupChecksum
extends CommandLineProgram

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
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
CalculateReadGroupChecksum()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static java.lang.String	getOutputFileName(java.io.File inputFile) Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
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="The input SAM or BAM file. ")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The file to which the hash code should be written.",
        optional=true)
public java.io.File OUTPUT

Constructor Detail

CalculateReadGroupChecksum

public CalculateReadGroupChecksum()

Method Detail

main

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

getOutputFileName

public static java.lang.String getOutputFileName(java.io.File inputFile)

Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.

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.