uk.ac.sanger.npg.picard
Class SplitBamByReadGroup

java.lang.Object
  net.sf.picard.cmdline.CommandLineProgram
      uk.ac.sanger.npg.picard.PicardCommandLine
          uk.ac.sanger.npg.picard.SplitBamByReadGroup

public class SplitBamByReadGroup
extends PicardCommandLine

Field Summary

java.io.File	INPUT
java.lang.String	OUTPUT_COMMON_RG_HEAD_TO_TRIM
java.lang.String	OUTPUT_PREFIX
java.lang.String	USAGE

Fields inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

version

Fields inherited from class net.sf.picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

SplitBamByReadGroup()

Method Summary

protected int	doWork()
static void	main(java.lang.String[] args)

Methods inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

addProgramRecordToHead, getThisProgramRecord, makeUniqueProgramId

Methods inherited from class net.sf.picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getProgramVersion, getStandardUsagePreamble, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

USAGE

@Usage(programVersion="1.00")
public final java.lang.String USAGE

INPUT

@Option(shortName="I",
        doc="The input SAM or BAM file with multiple read groups.")
public java.io.File INPUT

OUTPUT_PREFIX

@Option(shortName="O",
        doc="The prefix for output bam/sam file.")
public java.lang.String OUTPUT_PREFIX

OUTPUT_COMMON_RG_HEAD_TO_TRIM

@Option(shortName="TRIM",
        doc="The common RG name head to trim from the output file name.",
        optional=true)
public java.lang.String OUTPUT_COMMON_RG_HEAD_TO_TRIM

Constructor Detail

SplitBamByReadGroup

public SplitBamByReadGroup()

Method Detail

doWork

protected int doWork()

Specified by:

doWork in class net.sf.picard.cmdline.CommandLineProgram

main

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