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

    Modifier and Type
    Method
    Description
    void
    Close database, free resources
    void
    Open database (load index in memory if required)
    query(Q queryMarker)
    Find matching entries in the database
    void
    setDebug(boolean debug)
     
    void
    setVerbose(boolean verbose)
     
  • Method Details

    • close

      void close()
      Close database, free resources
    • open

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

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

      void setDebug(boolean debug)
    • setVerbose

      void setVerbose(boolean verbose)