Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdAcat
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
- All Implemented Interfaces:
CommandLine
ACAT: Create ACAT score for T2D project
Note: This is just used to compile 'ACAT' score in T2D-GENES project, not
useful at all for general audience.
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final Stringstatic final doublestatic final Stringstatic final Stringstatic final Stringstatic final Stringstatic final Stringstatic final Stringstatic final StringFields 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 -
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, setVerbose, usageDb, usageGeneric, usageGenericAndDb
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Field Details
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ACAT
- See Also:
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NCCAT
- See Also:
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NCACTIVITY
- See Also:
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NCMARK
- See Also:
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NCFACTOR
- See Also:
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NCELEMENT
- See Also:
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NCCONS
- See Also:
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T2D_GENES
- See Also:
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CONSERVATION_THRESHOLD
public static final double CONSERVATION_THRESHOLD- See Also:
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Constructor Details
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SnpEffCmdAcat
public SnpEffCmdAcat()
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Method Details
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parseArgs
Parse command line arguments- Specified by:
parseArgsin interfaceCommandLine- Overrides:
parseArgsin classSnpEff
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run
public boolean run()Run command- Specified by:
runin interfaceCommandLine- Overrides:
runin classSnpEff
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usage
Show usage and exit- Specified by:
usagein interfaceCommandLine- Overrides:
usagein classSnpEff
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