picard.sam

Class SplitSamByLibrary

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.SplitSamByLibrary

@DocumentedFeature
public class SplitSamByLibrary
extends CommandLineProgram

Command-line program to split a SAM or BAM file into separate files based on library name.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
static int	NO_LIBRARIES_SPECIFIED_IN_HEADER
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, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SplitSamByLibrary()

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, 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="The SAM or BAM file to be split. ")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="The directory where the library SAM or BAM files should be written (defaults to the current directory). ",
          optional=true)
public java.io.File OUTPUT

NO_LIBRARIES_SPECIFIED_IN_HEADER

public static final int NO_LIBRARIES_SPECIFIED_IN_HEADER

See Also:

Constant Field Values

Constructor Detail

SplitSamByLibrary

public SplitSamByLibrary()

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.