picard.sam

Class AddOrReplaceReadGroups

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.AddOrReplaceReadGroups

public class AddOrReplaceReadGroups
extends CommandLineProgram

Replaces read groups in a BAM file

Author:

mdepristo

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	INPUT
java.io.File	OUTPUT
java.lang.String	RGCN
java.lang.String	RGDS
htsjdk.samtools.util.Iso8601Date	RGDT
java.lang.String	RGID
java.lang.String	RGLB
java.lang.String	RGPG
java.lang.Integer	RGPI
java.lang.String	RGPL
java.lang.String	RGPM
java.lang.String	RGPU
java.lang.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, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
AddOrReplaceReadGroups()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] argv) Required main method implementation.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

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

OUTPUT

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

SORT_ORDER

@Option(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

@Option(shortName="ID",
        doc="Read Group ID")
public java.lang.String RGID

RGLB

@Option(shortName="LB",
        doc="Read Group library")
public java.lang.String RGLB

RGPL

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

RGPU

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

RGSM

@Option(shortName="SM",
        doc="Read Group sample name")
public java.lang.String RGSM

RGCN

@Option(shortName="CN",
        doc="Read Group sequencing center name",
        optional=true)
public java.lang.String RGCN

RGDS

@Option(shortName="DS",
        doc="Read Group description",
        optional=true)
public java.lang.String RGDS

RGDT

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

RGPI

@Option(shortName="PI",
        doc="Read Group predicted insert size",
        optional=true)
public java.lang.Integer RGPI

RGPG

@Option(shortName="PG",
        doc="Read Group program group",
        optional=true)
public java.lang.String RGPG

RGPM

@Option(shortName="PM",
        doc="Read Group platform model",
        optional=true)
public java.lang.String RGPM

Constructor Detail

AddOrReplaceReadGroups

public AddOrReplaceReadGroups()

Method Detail

main

public static void main(java.lang.String[] argv)

Required main method implementation.

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.