picard.arrays

Class VcfToAdpc

java.lang.Object

picard.cmdline.CommandLineProgram

picard.arrays.VcfToAdpc

@DocumentedFeature
public class VcfToAdpc
extends CommandLineProgram

A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	OUTPUT
java.io.File	VCF

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
VcfToAdpc()

Method Summary

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

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, 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 Detail

VCF

@Argument(doc="The Input VCF")
public java.io.File VCF

OUTPUT

@Argument(shortName="O",
          doc="The output (adpc.bin) file to write.")
public java.io.File OUTPUT

Constructor Detail

VcfToAdpc

public VcfToAdpc()

Method Detail

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.