Package picard.arrays
Class GtcToVcf
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.GtcToVcf
Class to convert an Illumina GTC file into a VCF file.
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected String[]
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 String
formatFloatForVcf
(float value) htsjdk.variant.variantcontext.Genotype
getGenotype
(String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B) protected boolean
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
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Field Details
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INPUT
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OUTPUT
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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 File EXTENDED_ILLUMINA_MANIFEST -
CLUSTER_FILE
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ILLUMINA_BEAD_POOL_MANIFEST_FILE
@Argument(shortName="BPM_FILE", doc="The Illumina Bead Pool Manifest (.bpm) file") public File ILLUMINA_BEAD_POOL_MANIFEST_FILE -
EXPECTED_GENDER
@Argument(shortName="E_GENDER", doc="The expected gender for this sample.", optional=true) public String EXPECTED_GENDER -
SAMPLE_ALIAS
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PIPELINE_VERSION
@Argument(doc="The version of the pipeline used to generate this VCF", optional=true) public String PIPELINE_VERSION -
ANALYSIS_VERSION_NUMBER
@Argument(doc="The analysis version of the data used to generate this VCF", optional=true) public 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 File GENDER_GTC -
FINGERPRINT_GENOTYPES_VCF_FILE
@Argument(shortName="FP_VCF", doc="The fingerprint VCF for this sample", optional=true) public 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
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Constructor Details
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GtcToVcf
public GtcToVcf()
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Method Details
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requiresReference
protected boolean requiresReference()- Overrides:
requiresReference
in classCommandLineProgram
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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 classCommandLineProgram
- Returns:
- program exit status.
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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 classCommandLineProgram
- 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.
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getGenotype
public htsjdk.variant.variantcontext.Genotype getGenotype(String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B) -
formatFloatForVcf
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