picard.arrays

Class GtcToVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.arrays.GtcToVcf

@DocumentedFeature
public class GtcToVcf
extends CommandLineProgram

Class to convert an Illumina GTC file into a VCF file.

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.Integer	ANALYSIS_VERSION_NUMBER
java.io.File	CLUSTER_FILE
boolean	DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
java.lang.String	EXPECTED_GENDER
java.io.File	EXTENDED_ILLUMINA_MANIFEST
java.io.File	FINGERPRINT_GENOTYPES_VCF_FILE
java.io.File	GENDER_GTC
java.io.File	ILLUMINA_BEAD_POOL_MANIFEST_FILE
java.io.File	INPUT
java.io.File	OUTPUT
java.lang.String	PIPELINE_VERSION
java.lang.String	SAMPLE_ALIAS

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
GtcToVcf()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.
static java.lang.String	formatFloatForVcf(float value)
htsjdk.variant.variantcontext.Genotype	getGenotype(java.lang.String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B)
protected boolean	requiresReference()

Methods inherited from class picard.cmdline.CommandLineProgram

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

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(shortName="I",
          doc="GTC file to be converted")
public java.io.File INPUT

OUTPUT

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

EXTENDED_ILLUMINA_MANIFEST

@Argument(shortName="MANIFEST",
          doc="An Extended Illumina Manifest file (csv).  This is an extended version of the Illumina manifest it contains additional reference-specific fields")
public java.io.File EXTENDED_ILLUMINA_MANIFEST

CLUSTER_FILE

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

ILLUMINA_BEAD_POOL_MANIFEST_FILE

@Argument(shortName="BPM_FILE",
          doc="The Illumina Bead Pool Manifest (.bpm) file")
public java.io.File ILLUMINA_BEAD_POOL_MANIFEST_FILE

EXPECTED_GENDER

@Argument(shortName="E_GENDER",
          doc="The expected gender for this sample.",
          optional=true)
public java.lang.String EXPECTED_GENDER

SAMPLE_ALIAS

@Argument(doc="The sample alias")
public java.lang.String SAMPLE_ALIAS

PIPELINE_VERSION

@Argument(doc="The version of the pipeline used to generate this VCF",
          optional=true)
public java.lang.String PIPELINE_VERSION

ANALYSIS_VERSION_NUMBER

@Argument(doc="The analysis version of the data used to generate this VCF",
          optional=true)
public java.lang.Integer ANALYSIS_VERSION_NUMBER

GENDER_GTC

@Argument(shortName="G_GTC",
          doc="An optional GTC file that was generated by calling the chip using a cluster file designed to optimize gender calling.",
          optional=true)
public java.io.File GENDER_GTC

FINGERPRINT_GENOTYPES_VCF_FILE

@Argument(shortName="FP_VCF",
          doc="The fingerprint VCF for this sample",
          optional=true)
public java.io.File FINGERPRINT_GENOTYPES_VCF_FILE

DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS

@Argument(doc="Causes the program to fail if it finds a case where there is a call on an assay that is flagged as \'zeroed-out\' in the Illumina cluster file.",
          optional=true)
public boolean DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS

Constructor Detail

GtcToVcf

public GtcToVcf()

Method Detail

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

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.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

getGenotype

public htsjdk.variant.variantcontext.Genotype getGenotype(java.lang.String sampleName,
                                                          InfiniumGTCRecord infiniumGtcRecord,
                                                          IlluminaManifestRecord record,
                                                          htsjdk.variant.variantcontext.Allele A,
                                                          htsjdk.variant.variantcontext.Allele B)

formatFloatForVcf

public static java.lang.String formatFloatForVcf(float value)