Package picard.arrays
Class VcfToAdpc
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.arrays.VcfToAdpc
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@DocumentedFeature public class VcfToAdpc extends CommandLineProgram
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
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Field Summary
Fields Modifier and Type Field Description File
NUM_MARKERS_FILE
File
OUTPUT
File
SAMPLES_FILE
List<File>
VCF
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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
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Constructor Summary
Constructors Constructor Description VcfToAdpc()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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Field Detail
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OUTPUT
@Argument(shortName="O", doc="The output (adpc.bin) file to write.") public File 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
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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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Method Detail
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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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