Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdGsa

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
All Implemented Interfaces:
CommandLine
public class SnpEffCmdGsa extends SnpEff
Command line: Gene-Sets Analysis Perform gene set analysys
Author:
pcingola

  • Field Details

    • READ_INPUT_SHOW_EVERY

      public static int READ_INPUT_SHOW_EVERY

    • MAX_WARNS

      public static int MAX_WARNS

  • Constructor Details

    • SnpEffCmdGsa

      public SnpEffCmdGsa()

  • Method Details

    • config

      protected void config()
      Read config file, load & build database

    • 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 command
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • runAnalisis

      protected boolean runAnalisis()
      Run command

    • runAnalisisRand

      protected boolean runAnalisisRand()
      Run enrichment analysis using random scores

    • runCommands

      protected boolean runCommands()
      Read "command" lines from file. Loads database only once to save time
      Returns:

    • usage

      public void usage(String message)
      Show usage and exit
      Specified by:
      usage in interface CommandLine
      Overrides:
      usage in class SnpEff