Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdGsa
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdGsa extends SnpEff
Command line: Gene-Sets Analysis Perform gene set analysys- 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 int
MAX_WARNS
static int
READ_INPUT_SHOW_EVERY
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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, 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, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors Constructor Description SnpEffCmdGsa()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
config()
Read config file, load & build databasevoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run commandprotected boolean
runAnalisis()
Run commandprotected boolean
runAnalisisRand()
Run enrichment analysis using random scoresprotected boolean
runCommands()
Read "command" lines from file.void
usage(java.lang.String message)
Show usage and exit-
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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Method Detail
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config
protected void config()
Read config file, load & build database
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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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runAnalisis
protected boolean runAnalisis()
Run command
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runAnalisisRand
protected boolean runAnalisisRand()
Run enrichment analysis using random scores
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runCommands
protected boolean runCommands()
Read "command" lines from file. Loads database only once to save time- Returns:
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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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