Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdAcat
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdAcat extends SnpEff
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
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Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
ACAT
static double
CONSERVATION_THRESHOLD
static java.lang.String
NCACTIVITY
static java.lang.String
NCCAT
static java.lang.String
NCCONS
static java.lang.String
NCELEMENT
static java.lang.String
NCFACTOR
static java.lang.String
NCMARK
static java.lang.String
T2D_GENES
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Fields 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 Constructor Description SnpEffCmdAcat()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run commandvoid
usage(java.lang.String message)
Show usage and exit-
Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, error, fatalError, 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, warning
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Field Detail
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ACAT
public static final java.lang.String ACAT
- See Also:
- Constant Field Values
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NCCAT
public static final java.lang.String NCCAT
- See Also:
- Constant Field Values
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NCACTIVITY
public static final java.lang.String NCACTIVITY
- See Also:
- Constant Field Values
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NCMARK
public static final java.lang.String NCMARK
- See Also:
- Constant Field Values
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NCFACTOR
public static final java.lang.String NCFACTOR
- See Also:
- Constant Field Values
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NCELEMENT
public static final java.lang.String NCELEMENT
- See Also:
- Constant Field Values
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NCCONS
public static final java.lang.String NCCONS
- See Also:
- Constant Field Values
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T2D_GENES
public static final java.lang.String T2D_GENES
- See Also:
- Constant Field Values
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CONSERVATION_THRESHOLD
public static final double CONSERVATION_THRESHOLD
- See Also:
- Constant Field Values
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Method Detail
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parseArgs
public void parseArgs(java.lang.String[] args)
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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usage
public void usage(java.lang.String message)
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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