Package org.snpeff.snpEffect.commandLine

Interface CommandLine

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

Method Summary

Modifier and Type	Method	Description
java.lang.String[]	getArgs()
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run the command
void	usage(java.lang.String message)	Show 'usage' message and exit with an error code '-1'

Method Detail

getArgs

java.lang.String[] getArgs()

parseArgs

void parseArgs(java.lang.String[] args)

Parse command line arguments

run

boolean run()

Run the command

usage

void usage(java.lang.String message)

Show 'usage' message and exit with an error code '-1'