Class SnpEffCmdProtein

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.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 Details

    • onlyOneError

      public static boolean onlyOneError
    • MAX_ERROR_RATE

      public static double MAX_ERROR_RATE
  • Constructor Details

    • SnpEffCmdProtein

      public SnpEffCmdProtein()
    • SnpEffCmdProtein

      public SnpEffCmdProtein(Config config, String proteinFile)
  • Method Details

    • getAlignmentByTrId

      public HashMap<String,SmithWaterman> getAlignmentByTrId()
    • getTotalErrors

      public int getTotalErrors()
    • getTotalNotFound

      public int getTotalNotFound()
    • getTotalOk

      public int getTotalOk()
    • getTotalWarnings

      public int getTotalWarnings()
    • 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
    • setCheckNumOk

      public void setCheckNumOk(boolean checkNumOk)
    • setProteinByTrId

      public void setProteinByTrId(Map<String,String> proteinById)
    • setMaxErrorRate

      public void setMaxErrorRate(double maxErrorRate)
    • setStoreAlignments

      public void setStoreAlignments(boolean storeAlignments)
    • usage

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