Class SnpEffCmdSpliceAnalysis

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdSpliceAnalysis
    extends SnpEff
    Analyze sequences from splice sites
    Author:
    pcingola
    • Field Detail

      • P_VALUE_THRESHOLD

        public static double P_VALUE_THRESHOLD
      • SIZE_CONSENSUS_DONOR

        public static int SIZE_CONSENSUS_DONOR
      • SIZE_CONSENSUS_ACCEPTOR

        public static int SIZE_CONSENSUS_ACCEPTOR
      • THRESHOLD_BRANCH_U12_PERCENTILE

        public static final double THRESHOLD_BRANCH_U12_PERCENTILE
        See Also:
        Constant Field Values
      • THRESHOLD_U12_OBSERVED_EXPECTED

        public static final double THRESHOLD_U12_OBSERVED_EXPECTED
        See Also:
        Constant Field Values
      • HTML_WIDTH

        public static int HTML_WIDTH
      • HTML_HEIGHT

        public static int HTML_HEIGHT
    • Constructor Detail

      • SnpEffCmdSpliceAnalysis

        public SnpEffCmdSpliceAnalysis()
    • Method Detail

      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Description copied from class: SnpEff
        Parse command line arguments
        Specified by:
        parseArgs in interface CommandLine
        Overrides:
        parseArgs in class SnpEff
      • run

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

        public void usage​(java.lang.String message)
        Description copied from class: SnpEff
        Show 'usage' message and exit with an error code '-1'
        Specified by:
        usage in interface CommandLine
        Overrides:
        usage in class SnpEff