picard.sam

Class CleanSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.CleanSam

public class CleanSam
extends CommandLineProgram

Author:

alecw@broadinstitute.org

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
CleanSam()

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[] argv)

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 SAM to be cleaned.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Where to write cleaned SAM.")
public java.io.File OUTPUT

Constructor Detail

CleanSam

public CleanSam()

Method Detail

main

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

doWork

protected int doWork()

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.