Class SnpEffCmdProtein

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdProtein
    extends SnpEff
    Command line: Read protein 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
    • Constructor Detail

      • SnpEffCmdProtein

        public SnpEffCmdProtein()
      • SnpEffCmdProtein

        public SnpEffCmdProtein​(Config config)
      • SnpEffCmdProtein

        public SnpEffCmdProtein​(Config config,
                                java.lang.String proteinFile)
      • SnpEffCmdProtein

        public SnpEffCmdProtein​(java.lang.String genomeVer,
                                java.lang.String configFile,
                                java.lang.String proteinFile)
    • Method Detail

      • diffCount

        public static int diffCount​(java.lang.String s1,
                                    java.lang.String s2)
        Count number of differences between strings
      • diffStr

        public static java.lang.String diffStr​(java.lang.String s1,
                                               java.lang.String s2)
        Show difference between two strings
      • getAlignmentByTrId

        public java.util.HashMap<java.lang.String,​SmithWaterman> getAlignmentByTrId()
      • getTotalErrors

        public int getTotalErrors()
      • getTotalNotFound

        public int getTotalNotFound()
      • getTotalOk

        public int getTotalOk()
      • getTotalWarnings

        public int getTotalWarnings()
      • 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)
      • setProteinByTrId

        public void setProteinByTrId​(java.util.Map<java.lang.String,​java.lang.String> proteinByTrId)
      • 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