Package picard.sam
Class SplitSamByLibrary
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.SplitSamByLibrary
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@DocumentedFeature public class SplitSamByLibrary extends CommandLineProgram
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.This tool takes a SAM or BAM file and separates all the reads into one SAM or BAM file per library name. Reads that do not have a read group specified or whose read group does not have a library name are written to a file called 'unknown.' The format (SAM or BAM) of the output files matches that of the input file.
Inputs
- The BAM or SAM file to be split
- The directory where the library SAM or BAM files should be written
Output/h3>
- One SAM or BAM file per library name
Usage example:
java -jar picard.jar SplitSamByLibrary \ I=input_reads.bam \ O=/output/directory/
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Field Summary
Fields Modifier and Type Field Description File
INPUT
static int
NO_LIBRARIES_SPECIFIED_IN_HEADER
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 SplitSamByLibrary()
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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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Field Detail
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INPUT
@Argument(shortName="I", doc="The SAM, BAM of CRAM file to be split. ") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="The directory where the per-library output files should be written (defaults to the current directory). ", optional=true) public File OUTPUT
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NO_LIBRARIES_SPECIFIED_IN_HEADER
public static final int NO_LIBRARIES_SPECIFIED_IN_HEADER
- See Also:
- Constant Field Values
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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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