Package org.snpsift.annotate

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()
    Close database, free resources
    void
    open()
    Open database (load index in memory if required)
    Collection<R>
    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)