uk.ac.sanger.npg.picard
Class ChangeBamHeader

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

public class ChangeBamHeader
extends PicardCommandLine

Field Summary

java.lang.String	DESCRIPTION
java.io.File	INPUT
java.lang.String	LIBRARY
java.io.File	OUTPUT
java.util.List<java.lang.String>	PG
java.lang.String	SAMPLE
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

ChangeBamHeader()

Method Summary

protected int	doWork()
net.sf.samtools.SAMProgramRecord	getProgramRecordFromString(java.lang.String pg_fields)
static void	main(java.lang.String[] argv)

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. ")
public java.io.File INPUT

OUTPUT

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

PG

@Option(doc="The extra PG line with fields separated by semicolon for bam header including ID, PN, VN and CL etc, PP id will be reset. Each field including tag name and value separated by colon.")
public final java.util.List<java.lang.String> PG

SAMPLE

@Option(shortName="SM",
        doc="The sample name in the only RG group. ",
        optional=true)
public java.lang.String SAMPLE

LIBRARY

@Option(shortName="LB",
        doc="The library name in the only RG group. ",
        optional=true)
public java.lang.String LIBRARY

DESCRIPTION

@Option(shortName="DS",
        doc="The description in the only RG group. ",
        optional=true)
public java.lang.String DESCRIPTION

Constructor Detail

ChangeBamHeader

public ChangeBamHeader()

Method Detail

doWork

protected int doWork()

Specified by:

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

getProgramRecordFromString

public net.sf.samtools.SAMProgramRecord getProgramRecordFromString(java.lang.String pg_fields)

Parameters:

pg_fields -

Returns:

main

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

Parameters:

argv -