picard.sam

Class AddOATag

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.AddOATag

@DocumentedFeature
public class AddOATag
extends CommandLineProgram

Field Summary

Fields

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

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
AddOATag()

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

@Argument(shortName="I",
          doc="SAM or BAM input file")
public java.lang.String INPUT

OUTPUT

@Argument(shortName="O",
          doc="SAM or BAM file to write merged result to")
public java.lang.String OUTPUT

INTERVAL_LIST

@Argument(shortName="L",
          doc="If provided, only records that overlap given interval list will have the OA tag added.",
          optional=true)
public java.io.File INTERVAL_LIST

Constructor Detail

AddOATag

public AddOATag()

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.