Package picard.arrays
Class VcfToAdpc
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.VcfToAdpc
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
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Field Summary
FieldsModifier and TypeFieldDescriptionFields 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, 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 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
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Field Details
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VCF
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OUTPUT
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SAMPLES_FILE
@Argument(shortName="SF", doc="A text file into which the names of the samples will be written. These will be in the same order as the data in the adpc.bin file.") public File SAMPLES_FILE -
NUM_MARKERS_FILE
@Argument(shortName="NMF", doc="A text file into which the number of loci in the VCF will be written. This is useful for calling verifyIDIntensity.") public File NUM_MARKERS_FILE
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Constructor Details
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VcfToAdpc
public VcfToAdpc()
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Method Details
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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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