Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdGsa
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
- All Implemented Interfaces:
CommandLine
Command line: Gene-Sets Analysis
Perform gene set analysys
- 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, 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, treatAllAsProteinCoding, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
config()
Read config file, load & build databasevoid
Parse command line argumentsboolean
run()
Run commandprotected boolean
Run commandprotected boolean
Run enrichment analysis using random scoresprotected boolean
Read "command" lines from file.void
Show usage and exitMethods 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, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
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Field Details
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READ_INPUT_SHOW_EVERY
public static int READ_INPUT_SHOW_EVERY -
MAX_WARNS
public static int MAX_WARNS
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Constructor Details
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SnpEffCmdGsa
public SnpEffCmdGsa()
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Method Details
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config
protected void config()Read config file, load & build database -
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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runAnalisis
protected boolean runAnalisis()Run command -
runAnalisisRand
protected boolean runAnalisisRand()Run enrichment analysis using random scores -
runCommands
protected boolean runCommands()Read "command" lines from file. Loads database only once to save time- Returns:
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usage
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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