Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdClosest
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
- All Implemented Interfaces:
CommandLine
Command line: Find closes marker to each variant
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
FieldsFields inherited from class org.snpeff.SnpEff
args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, usageDb, usageGeneric, usageGenericAndDb
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Field Details
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CLOSEST
- See Also:
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INFO_LINE
- See Also:
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Constructor Details
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SnpEffCmdClosest
public SnpEffCmdClosest() -
SnpEffCmdClosest
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Method Details
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parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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run
public boolean run()Run command- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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setVerbose
public void setVerbose(boolean verbose) - Overrides:
setVerbose
in classSnpEff
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usage
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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