Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdShow
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdShow
- All Implemented Interfaces:
CommandLine
Command line program: Show a transcript or a gene
- Author:
- pcingola
-
Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
-
Field Summary
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, 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, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
-
Constructor Details
-
SnpEffCmdShow
public SnpEffCmdShow()
-
-
Method Details
-
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
-
run
public boolean run()Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
-
usage
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
-