Interface VcfAnnotator

    • Method Detail

      • addHeaders

        boolean addHeaders​(VcfFileIterator vcfFile)
        Add annotation headers to VCF file
        Returns:
        true if OK, false on error
      • annotate

        boolean annotate​(VcfEntry vcfEntry)
        Annotate a VCF file entry
        Returns:
        true if the entry was annotated
      • annotateFinish

        boolean annotateFinish​(VcfFileIterator vcfFile)
        This method is called after all annotations have been performed. The vcfFile might have already been closed by this time (i.e. the VcfFileIterator reached the end).
        Returns:
        true if OK, false on error
      • annotateInit

        boolean annotateInit​(VcfFileIterator vcfFile)
        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.
        Returns:
        true if OK, false on error
      • setConfig

        void setConfig​(Config config)
        Set configuration
      • setDebug

        void setDebug​(boolean debug)
        Set debug mode
      • setVerbose

        void setVerbose​(boolean verbose)
        Set verbose mode