Package org.snpeff.snpEffect

Class VcfAnnotatorChain

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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(VcfAnnotator vcfAnnotator)
      Add a new annotator
      boolean addHeaders​(VcfFileIterator vcfFile)
      Add annotation headers to VCF file
      boolean annotate​(VcfEntry vcfEntry)
      Annotate a VCF file entry
      boolean annotateFinish​(VcfFileIterator vcf)
      This method is called after all annotations have been performed.
      boolean annotateInit​(VcfFileIterator vcfFile)
      Initialize annotator: This method is called after vcfFile is opened, but before the header is output.
      java.lang.String[] getArgs()  
      void parseArgs​(java.lang.String[] args)
      Parse command line arguments
      boolean run()
      Run the command
      void setConfig​(Config config)
      Set configuration
      void setDebug​(boolean debug)
      Set debug mode
      void setVerbose​(boolean verbose)
      Set verbose mode
      void usage​(java.lang.String message)
      Show 'usage' message and exit with an error code '-1'

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • VcfAnnotatorChain

        public VcfAnnotatorChain()

    • Method Detail

      • add

        public void add​(VcfAnnotator vcfAnnotator)
        Add a new annotator

      • 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 java.lang.String[] getArgs()
        Specified by:
        getArgs in interface CommandLine

      • parseArgs

        public void parseArgs​(java.lang.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

      • 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​(java.lang.String message)
        Description copied from interface: CommandLine
        Show 'usage' message and exit with an error code '-1'
        Specified by:
        usage in interface CommandLine