org.utgenome.shell
Class FastqToSAM

java.lang.Object
  extended by org.utgenome.core.cui.UTGBCommandBase
      extended by org.utgenome.shell.UTGBShellCommandBase
          extended by org.utgenome.shell.UTGBShellCommand
              extended by org.utgenome.shell.FastqToSAM
All Implemented Interfaces:
Comparable<org.xerial.util.opt.Command>, org.xerial.util.opt.Command

public class FastqToSAM
extends UTGBShellCommand


Field Summary
 
Fields inherited from class org.utgenome.shell.UTGBShellCommand
APP_FOLDER, EXPLODED_WEBAPP_DIR, SRC_FOLDER, WEBAPP_FOLDER
 
Fields inherited from class org.utgenome.shell.UTGBShellCommandBase
globalOption
 
Constructor Summary
FastqToSAM()
           
 
Method Summary
 void execute(String[] args)
           
 String getOneLinerDescription()
           
 String name()
           
 
Methods inherited from class org.utgenome.shell.UTGBShellCommand
compareTo, createContextXML, createFileFromTemplate, createFileFromTemplate, execute, getConfigFile, getHelpMessageResource, getObsolteConfigurationFile, getOneLineDescription, getOptionHolder, getPath, getProjectResourcePath, getProjectRoot, isInProjectRoot, loadUTGBConfig, maven, maven
 
Methods inherited from class org.utgenome.shell.UTGBShellCommandBase
execute
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FastqToSAM

public FastqToSAM()
Method Detail

execute

public void execute(String[] args)
             throws Exception
Specified by:
execute in interface org.xerial.util.opt.Command
Specified by:
execute in class UTGBShellCommand
Throws:
Exception

getOneLinerDescription

public String getOneLinerDescription()
Specified by:
getOneLinerDescription in class UTGBShellCommand

name

public String name()
Specified by:
name in interface org.xerial.util.opt.Command
Specified by:
name in class UTGBShellCommand


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