uk.ac.sanger.npg.picard
Class PicardCommandLine

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

Direct Known Subclasses:

AlignmentFilter, BamIndexDecoder, BamMerger, BamQualityQuantisation, BamReadTrimmer, BamTagStripper, ChangeBamHeader, Illumina2bam, SplitBamByReadGroup

public abstract class PicardCommandLine
extends net.sf.picard.cmdline.CommandLineProgram

This is the base class for any command line program class

Field Summary

static java.lang.String

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

PicardCommandLine()

Method Summary

void	addProgramRecordToHead(net.sf.samtools.SAMFileHeader header, net.sf.samtools.SAMProgramRecord programRecord)
net.sf.samtools.SAMProgramRecord	getThisProgramRecord(java.lang.String programName, java.lang.String programDS) Generate Program Record for this program itself
net.sf.samtools.SAMProgramRecord	makeUniqueProgramId(java.util.List<net.sf.samtools.SAMProgramRecord> programList, net.sf.samtools.SAMProgramRecord programRecord)

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

customCommandLineValidation, doWork, 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

version

public static final java.lang.String version

See Also:

Constant Field Values

Constructor Detail

PicardCommandLine

public PicardCommandLine()

Method Detail

getThisProgramRecord

public net.sf.samtools.SAMProgramRecord getThisProgramRecord(java.lang.String programName,
                                                             java.lang.String programDS)

Generate Program Record for this program itself

Parameters:

programName -

programDS -

Returns:

this program itself as Program Record

addProgramRecordToHead

public void addProgramRecordToHead(net.sf.samtools.SAMFileHeader header,
                                   net.sf.samtools.SAMProgramRecord programRecord)

Parameters:

header -

programRecord -

makeUniqueProgramId

public net.sf.samtools.SAMProgramRecord makeUniqueProgramId(java.util.List<net.sf.samtools.SAMProgramRecord> programList,
                                                            net.sf.samtools.SAMProgramRecord programRecord)