Class SnpEffCmdCds

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdCds
    extends SnpEff
    Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures

    Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.

    Author:
    pcingola
    • Field Detail

      • onlyOneError

        public static boolean onlyOneError
      • MAX_ERROR_RATE

        public static double MAX_ERROR_RATE
      • MAX_ALIGN_LENGTH

        public static int MAX_ALIGN_LENGTH
    • Constructor Detail

      • SnpEffCmdCds

        public SnpEffCmdCds()
      • SnpEffCmdCds

        public SnpEffCmdCds​(Config config)
      • SnpEffCmdCds

        public SnpEffCmdCds​(java.lang.String genomeVer,
                            java.lang.String configFile,
                            java.lang.String cdsFile)
    • Method Detail

      • parseArgs

        public void parseArgs​(java.lang.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
      • setCheckNumOk

        public void setCheckNumOk​(boolean checkNumOk)
      • setMaxErrorRate

        public void setMaxErrorRate​(double maxErrorRate)
      • setStoreAlignments

        public void setStoreAlignments​(boolean storeAlignments)
      • usage

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