Package picard.arrays.illumina

Class BpmToNormalizationManifestCsv

java.lang.Object

picard.cmdline.CommandLineProgram

picard.arrays.illumina.BpmToNormalizationManifestCsv

@DocumentedFeature
public class BpmToNormalizationManifestCsv
extends CommandLineProgram

A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .

Field Summary

Fields

Modifier and Type	Field	Description
File	CLUSTER_FILE
File	INPUT
File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
BpmToNormalizationManifestCsv()

Method Summary

Modifier and Type	Method	Description
protected int	doWork()	Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Details

INPUT

@Argument(shortName="I",
          doc="The Illumina Bead Pool Manifest (.bpm) file")
public File INPUT

CLUSTER_FILE

@Argument(shortName="CF",
          doc="An Illumina cluster file (egt)")
public File CLUSTER_FILE

OUTPUT

@Argument(shortName="O",
          doc="The output (bpm.csv) file to write.")
public File OUTPUT

Constructor Details

BpmToNormalizationManifestCsv

public BpmToNormalizationManifestCsv()

Method Details

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.