Package org.snpeff.snpEffect

Class VcfAnnotatorChain

java.lang.Object
org.snpeff.snpEffect.VcfAnnotatorChain
All Implemented Interfaces:
CommandLine, VcfAnnotator
public class VcfAnnotatorChain extends Object implements VcfAnnotator
Maintains a list of VcfAnnotators and applies them one by one in the specified order

  • Constructor Details

    • VcfAnnotatorChain

      public VcfAnnotatorChain()

  • Method Details

    • add

      public void add(VcfAnnotator vcfAnnotator)
      Add a new annotator

    • addHeaders

      public boolean addHeaders(VcfFileIterator vcfFile)
      Description copied from interface: VcfAnnotator
      Add annotation headers to VCF file
      Specified by:
      addHeaders in interface VcfAnnotator
      Returns:
      true if OK, false on error

    • annotate

      public boolean annotate(VcfEntry vcfEntry)
      Description copied from interface: VcfAnnotator
      Annotate a VCF file entry
      Specified by:
      annotate in interface VcfAnnotator
      Returns:
      true if the entry was annotated

    • annotateFinish

      public boolean annotateFinish(VcfFileIterator vcf)
      Description copied from interface: VcfAnnotator
      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).
      Specified by:
      annotateFinish in interface VcfAnnotator
      Returns:
      true if OK, false on error

    • 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

    • getArgs

      public String[] getArgs()
      Specified by:
      getArgs in interface CommandLine

    • parseArgs

      public void parseArgs(String[] args)
      Description copied from interface: CommandLine
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine

    • run

      public boolean run()
      Description copied from interface: CommandLine
      Run the command
      Specified by:
      run in interface CommandLine

    • setConfig

      public void setConfig(Config config)
      Description copied from interface: VcfAnnotator
      Set configuration
      Specified by:
      setConfig in interface VcfAnnotator

    • setDebug

      public void setDebug(boolean debug)
      Description copied from interface: VcfAnnotator
      Set debug mode
      Specified by:
      setDebug in interface VcfAnnotator

    • setVerbose

      public void setVerbose(boolean verbose)
      Description copied from interface: VcfAnnotator
      Set verbose mode
      Specified by:
      setVerbose in interface VcfAnnotator

    • usage

      public void usage(String message)
      Description copied from interface: CommandLine
      Show 'usage' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine