Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdBuild

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
All Implemented Interfaces:
CommandLine
public class SnpEffCmdBuild extends SnpEff
Command line program: Build database
Author:
pcingola

  • Constructor Details

    • SnpEffCmdBuild

      public SnpEffCmdBuild()

  • Method Details

    • fileExists

      protected boolean fileExists(String path)
      Does either 'path' or 'path'+'.gz' exist?

    • getSnpEffCmdCds

      public SnpEffCmdCds getSnpEffCmdCds()

    • getSnpEffCmdProtein

      public SnpEffCmdProtein getSnpEffCmdProtein()

    • guessGenesFormat

      protected SnpEff.GeneDatabaseFormat guessGenesFormat()
      Try to guess database format by checking which file type is present

    • 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()
      Build database
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • setCheckNumOk

      public void setCheckNumOk(boolean checkNumOk)

    • setStoreAlignments

      public void setStoreAlignments(boolean storeAlignments)

    • 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