Interface DbMarker<Q extends org.snpeff.interval.Marker,​R extends org.snpeff.interval.Marker>

  • All Known Implementing Classes:
    DbNsfp, DbVcf, DbVcfMem, DbVcfSorted, DbVcfTabix

    public interface DbMarker<Q extends org.snpeff.interval.Marker,​R extends org.snpeff.interval.Marker>
    Use a file as a 'marker' database. E.g. A VCF file, dbNSFP file/s, GTF, etc. Basically any genomic data file format that could be queried by genomic interval (e.g. by using Tabix, CSI or some other index).
    Author:
    pcingola
    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void close()
      Close database, free resources
      void open()
      Open database (load index in memory if required)
      java.util.Collection<R> query​(Q queryMarker)
      Find matching entries in the database
      void setDebug​(boolean debug)  
      void setVerbose​(boolean verbose)  
    • Method Detail

      • close

        void close()
        Close database, free resources
      • open

        void open()
        Open database (load index in memory if required)
      • query

        java.util.Collection<R> query​(Q queryMarker)
        Find matching entries in the database
      • setDebug

        void setDebug​(boolean debug)
      • setVerbose

        void setVerbose​(boolean verbose)