Package org.snpeff.snpEffect.commandLine
Interface CommandLine
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- All Known Subinterfaces:
VcfAnnotator
- All Known Implementing Classes:
FastqSplit
,SnpEff
,SnpEffCmdAcat
,SnpEffCmdBuild
,SnpEffCmdBuildNextProt
,SnpEffCmdCds
,SnpEffCmdClosest
,SnpEffCmdCount
,SnpEffCmdDatabases
,SnpEffCmdDownload
,SnpEffCmdDump
,SnpEffCmdEff
,SnpEffCmdGenes2Bed
,SnpEffCmdGsa
,SnpEffCmdLen
,SnpEffCmdPdb
,SnpEffCmdProtein
,SnpEffCmdSeq
,SnpEffCmdShow
,SnpEffCmdSpliceAnalysis
,SnpEffCmdTranslocationsReport
,VcfAnnotatorChain
public interface CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }- Author:
- pcingola
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String[]
getArgs()
void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run the commandvoid
usage(java.lang.String message)
Show 'usage' message and exit with an error code '-1'
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