Package org.snpeff.snpEffect

Interface VcfAnnotator

All Superinterfaces:
CommandLine
All Known Implementing Classes:
SnpEffCmdEff, VcfAnnotatorChain
public interface VcfAnnotator extends CommandLine
Annotate a VCF file: E.g. add information to INFO column

  • Method Details

    • 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