picard.sam

Class GatherBamFiles

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.GatherBamFiles

@DocumentedFeature
public class GatherBamFiles
extends CommandLineProgram

Concatenate efficiently BAM files that resulted from a scattered parallel analysis.

This tool performs a rapid "gather" or concatenation on BAM files. This is often needed in operations that have been run in parallel across genomics regions by scattering their execution across computing nodes and cores thus resulting in smaller BAM files.

This tool does not support SAM files.

Inputs

A list of BAM files to combine using the INPUT argument. These files must be provided in the order that they should be concatenated.

Output

A single BAM file. The header is copied from the first input file.

Usage example:

 java -jar picard.jar GatherBamFiles \
      I=input1.bam \
      I=input2.bam \
      O=gathered_files.bam
 

Notes

Operates via copying of the gzip blocks directly for speed but also supports generation of an MD5 on the output and indexing of the output BAM file.

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_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
GatherBamFiles()

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, getCommandLineParserForArgs, 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="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

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

Constructor Detail

GatherBamFiles

public GatherBamFiles()

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.