picard.sam

Class GatherBamFiles

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.GatherBamFiles

public class GatherBamFiles
extends CommandLineProgram

Program to perform a rapid "gather" operation on BAM files after a scatter operations where the same process has been performed on different regions of a BAM file creating many smaller BAM files that now need to be concatenated back together.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<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
GatherBamFiles()

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="Two or more BAM files or text files containing lists of BAM files (one per line).")
public java.util.List<java.io.File> INPUT

OUTPUT

@Option(shortName="O",
        doc="The output BAM file to write.")
public java.io.File OUTPUT

Constructor Detail

GatherBamFiles

public GatherBamFiles()

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.