Class SnpEffCmdEff

    • Field Detail

      • SUMMARY_TEMPLATE

        public static final java.lang.String SUMMARY_TEMPLATE
        See Also:
        Constant Field Values
      • SUMMARY_CSV_TEMPLATE

        public static final java.lang.String SUMMARY_CSV_TEMPLATE
        See Also:
        Constant Field Values
      • SUMMARY_GENES_TEMPLATE

        public static final java.lang.String SUMMARY_GENES_TEMPLATE
        See Also:
        Constant Field Values
      • DEFAULT_SUMMARY_HTML_FILE

        public static final java.lang.String DEFAULT_SUMMARY_HTML_FILE
        See Also:
        Constant Field Values
      • DEFAULT_SUMMARY_CSV_FILE

        public static final java.lang.String DEFAULT_SUMMARY_CSV_FILE
        See Also:
        Constant Field Values
      • DEFAULT_SUMMARY_GENES_FILE

        public static final java.lang.String DEFAULT_SUMMARY_GENES_FILE
        See Also:
        Constant Field Values
    • Constructor Detail

      • SnpEffCmdEff

        public SnpEffCmdEff()
    • Method Detail

      • annotate

        public boolean annotate​(java.lang.String inputFile,
                                java.lang.String outputFile)
        Annotate: Calculate the effect of variants and show results
      • annotate

        public boolean annotate​(VcfEntry vcfEntry)
        Annotate a VCF entry
        Specified by:
        annotate in interface VcfAnnotator
        Returns:
        true if the entry was annotated
      • annotateFinish

        public boolean annotateFinish​(VcfFileIterator vcfFile)
        Finish annotations and create reports
        Specified by:
        annotateFinish in interface VcfAnnotator
        Returns:
        true if OK, false on error
      • annotateInit

        protected void annotateInit​(java.lang.String outputFile)
        Calculate the effect of variants and show results
      • annotateInit

        public boolean annotateInit​(VcfFileIterator vcfFile)
        Description copied from interface: VcfAnnotator
        Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.
        Specified by:
        annotateInit in interface VcfAnnotator
        Returns:
        true if OK, false on error
      • getTotalErrs

        public int getTotalErrs()
      • parseArgs

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

        public java.util.HashMap<java.lang.String,​java.lang.String> reportValues()
        Description copied from class: SnpEff
        Additional values to be reported
        Overrides:
        reportValues in class SnpEff
      • run

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

        public java.util.List<VcfEntry> run​(boolean createList)
        Run according to command line options
      • setFormatVersion

        public void setFormatVersion​(EffFormatVersion formatVersion)
      • usage

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