AddOrReplaceReadGroups (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.sam.AddOrReplaceReadGroups

```
@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 one RG tag, defining a "read-group" to which each read can be assigned (as specified in the RG tag in the SAM record). This tool enables the user to assign all the reads in the INPUT 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 the INPUT to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost.

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`

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

Constructor Summary

Constructors
Constructor Description

AddOrReplaceReadGroups()

Constructors
Constructor	Description
`AddOrReplaceReadGroups()`

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

READGROUP_ID_REGEX

public static final String READGROUP_ID_REGEX

See Also:: Constant Field Values

INPUT

@Argument(shortName="I",
          doc="Input file (BAM or SAM or a GA4GH url).")
public String INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output file (BAM or SAM).")
public File OUTPUT

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

RGID

@Argument(shortName="ID",
          doc="Read-Group ID")
public String RGID

RGLB

@Argument(shortName="LB",
          doc="Read-Group library")
public String RGLB

RGPL

@Argument(shortName="PL",
          doc="Read-Group platform (e.g. illumina, solid)")
public String RGPL

RGPU

@Argument(shortName="PU",
          doc="Read-Group platform unit (eg. run barcode)")
public String RGPU

RGSM

@Argument(shortName="SM",
          doc="Read-Group sample name")
public String RGSM

RGCN

@Argument(shortName="CN",
          doc="Read-Group sequencing center name",
          optional=true)
public String RGCN

RGDS

@Argument(shortName="DS",
          doc="Read-Group description",
          optional=true)
public String RGDS

RGDT

@Argument(shortName="DT",
          doc="Read-Group run date",
          optional=true)
public htsjdk.samtools.util.Iso8601Date RGDT

RGKS

@Argument(shortName="KS",
          doc="Read-Group key sequence",
          optional=true)
public String RGKS

RGFO

@Argument(shortName="FO",
          doc="Read-Group flow order",
          optional=true)
public String RGFO

RGPI

@Argument(shortName="PI",
          doc="Read-Group predicted insert size",
          optional=true)
public Integer RGPI

RGPG

@Argument(shortName="PG",
          doc="Read-Group program group",
          optional=true)
public String RGPG

RGPM

@Argument(shortName="PM",
          doc="Read-Group platform model",
          optional=true)
public String RGPM

Constructor Detail
- AddOrReplaceReadGroups
```
public AddOrReplaceReadGroups()
```

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.
- 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 class CommandLineProgram
  
  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.

Class AddOrReplaceReadGroups

Summary

Usage example:

Caveats

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

READGROUP_ID_REGEX

INPUT

OUTPUT

SORT_ORDER

RGID

RGLB

RGPL

RGPU

RGSM

RGCN

RGDS

RGDT

RGKS

RGFO

RGPI

RGPG

RGPM

Constructor Detail

AddOrReplaceReadGroups

Method Detail

doWork

customCommandLineValidation