Package picard.sam
Class GatherBamFiles
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.GatherBamFiles
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@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.
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Field Summary
Fields Modifier and Type Field Description List<File>
INPUT
File
OUTPUT
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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
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Constructor Summary
Constructors Constructor Description GatherBamFiles()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Method Detail
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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 classCommandLineProgram
- Returns:
- program exit status.
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