uk.ac.sanger.npg.picard
Class BamQualityQuantisation

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

public class BamQualityQuantisation
extends PicardCommandLine

Field Summary

java.io.File	INPUT input sam or bam file
java.io.File	OUTPUT output sam or bam file
java.lang.String	USAGE
java.lang.Boolean	USE_OLD_QUALITY Quantise original quality scores from OQ tag in bam record and set the results as new qualities if true

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

BamQualityQuantisation()

Method Summary

protected int	doWork()
static void	main(java.lang.String[] argv)
byte[]	quantiseQualities(byte[] quals)
byte[]	quantiseQualities(java.lang.String quals)

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

input sam or bam file

OUTPUT

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

output sam or bam file

USE_OLD_QUALITY

@Option(shortName="OQ",
        doc="Use original quality scores from OQ tag. ")
public java.lang.Boolean USE_OLD_QUALITY

Quantise original quality scores from OQ tag in bam record and set the results as new qualities if true

Constructor Detail

BamQualityQuantisation

public BamQualityQuantisation()

Method Detail

doWork

protected int doWork()

Specified by:

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

quantiseQualities

public byte[] quantiseQualities(java.lang.String quals)

Parameters:

quals - quality scores in string

Returns:

quantised scores

quantiseQualities

public byte[] quantiseQualities(byte[] quals)

Parameters:

quals - quality scores to quantise

Returns:

quantised scores

main

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

Parameters:

argv -