Package picard.fingerprint
Class LiftOverHaplotypeMap
java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.LiftOverHaplotypeMap
Liftover SNPs in HaplotypeMaps from one reference to another
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
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, 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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INPUT
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OUTPUT
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SEQUENCE_DICTIONARY
@Argument(doc="Sequence dictionary to write into the output haplotype database. (Any file from which a dictionary is extractable.)", shortName="SD") public File SEQUENCE_DICTIONARY -
CHAIN
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LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
public static final int LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS- See Also:
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Constructor Details
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LiftOverHaplotypeMap
public LiftOverHaplotypeMap()
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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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