Package picard.sam
Class AddOrReplaceReadGroups
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.AddOrReplaceReadGroups
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@DocumentedFeature public class AddOrReplaceReadGroups extends CommandLineProgram
Assigns all the reads in a file to a single new read-group.Summary
Many tools (Picard and GATK for example) require or assume the presence of at least oneRG
tag, defining a "read-group" to which each read can be assigned (as specified in theRG
tag in the SAM record). This tool enables the user to assign all the reads in theINPUT
to a single new read-group. For more information about read-groups, see the GATK Dictionary entry.
This tool accepts as INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH).Usage example:
java -jar picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=output.bam \ RGID=4 \ RGLB=lib1 \ RGPL=illumina \ RGPU=unit1 \ RGSM=20
Caveats
The value of the tags must adhere (according to the SAM-spec) with the regex"^[ -~]+$"
(one or more characters from the ASCII range 32 through 126). In particular<Space>
is the only non-printing character allowed.
The program enables only the wholesale assignment of all the reads in theINPUT
to a single read-group. If your file already has reads assigned to multiple read-groups, the originalRG
value will be lost.
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Field Summary
Fields Modifier and Type Field Description String
INPUT
File
OUTPUT
static String
READGROUP_ID_REGEX
String
RGCN
String
RGDS
htsjdk.samtools.util.Iso8601Date
RGDT
String
RGFO
String
RGID
String
RGKS
String
RGLB
String
RGPG
Integer
RGPI
String
RGPL
String
RGPM
String
RGPU
String
RGSM
htsjdk.samtools.SAMFileHeader.SortOrder
SORT_ORDER
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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
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Constructor Summary
Constructors Constructor Description AddOrReplaceReadGroups()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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READGROUP_ID_REGEX
public static final String READGROUP_ID_REGEX
- See Also:
- Constant Field Values
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INPUT
@Argument(shortName="I", doc="Input file (BAM or SAM or a GA4GH url).") public String INPUT
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OUTPUT
@Argument(shortName="O", doc="Output file (BAM or SAM).") public File OUTPUT
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SORT_ORDER
@Argument(shortName="SO", optional=true, doc="Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.") public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
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RGID
@Argument(shortName="ID", doc="Read-Group ID") public String RGID
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RGLB
@Argument(shortName="LB", doc="Read-Group library") public String RGLB
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RGPL
@Argument(shortName="PL", doc="Read-Group platform (e.g. illumina, solid)") public String RGPL
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RGPU
@Argument(shortName="PU", doc="Read-Group platform unit (eg. run barcode)") public String RGPU
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RGSM
@Argument(shortName="SM", doc="Read-Group sample name") public String RGSM
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RGCN
@Argument(shortName="CN", doc="Read-Group sequencing center name", optional=true) public String RGCN
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RGDS
@Argument(shortName="DS", doc="Read-Group description", optional=true) public String RGDS
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RGDT
@Argument(shortName="DT", doc="Read-Group run date", optional=true) public htsjdk.samtools.util.Iso8601Date RGDT
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RGKS
@Argument(shortName="KS", doc="Read-Group key sequence", optional=true) public String RGKS
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RGFO
@Argument(shortName="FO", doc="Read-Group flow order", optional=true) public String RGFO
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RGPI
@Argument(shortName="PI", doc="Read-Group predicted insert size", optional=true) public Integer RGPI
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RGPG
@Argument(shortName="PG", doc="Read-Group program group", optional=true) public String RGPG
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RGPM
@Argument(shortName="PM", doc="Read-Group platform model", optional=true) public String RGPM
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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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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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