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
-
Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final double
static final String
static final String
static final String
static final String
static final String
static final String
static final String
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, tags, tagsNo, testing, 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, filterTags, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setTesting, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
-
Field Details
-
ACAT
- See Also:
-
NCCAT
- See Also:
-
NCACTIVITY
- See Also:
-
NCMARK
- See Also:
-
NCFACTOR
- See Also:
-
NCELEMENT
- See Also:
-
NCCONS
- See Also:
-
T2D_GENES
- See Also:
-
CONSERVATION_THRESHOLD
public static final double CONSERVATION_THRESHOLD- See Also:
-
-
Constructor Details
-
SnpEffCmdAcat
public SnpEffCmdAcat()
-
-
Method Details
-
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
-
run
public boolean run()Run command- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
-
usage
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
-