Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdSeq

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
All Implemented Interfaces:
CommandLine
public class SnpEffCmdSeq extends SnpEff
Command line program: Show a transcript or a gene
Author:
pcingola

  • Constructor Details

    • SnpEffCmdSeq

      public SnpEffCmdSeq()

  • Method Details

    • parseArgs

      public void parseArgs(String[] args)
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine
      Overrides:
      parseArgs in class SnpEff

    • run

      public boolean run()
      Run according to command line options
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • usage

      public void usage(String message)
      Show 'usage' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine
      Overrides:
      usage in class SnpEff