Class DbVcfMem

  • All Implemented Interfaces:
    DbMarker<org.snpeff.interval.Variant,​org.snpeff.vcf.VariantVcfEntry>

    public class DbVcfMem
    extends DbVcf
    Loads a VCF file into memory. WARNING: This is used only for testing and debugging purposes and should never be used in production!
    Author:
    pcingola
    • Constructor Summary

      Constructors 
      Constructor Description
      DbVcfMem​(java.lang.String dbFileName)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Close database, free resources
      void open()
      Open database annotation file
      java.util.List<org.snpeff.vcf.VariantVcfEntry> query​(org.snpeff.interval.Variant variant)
      Find matching entries in the database
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • DbVcfMem

        public DbVcfMem​(java.lang.String dbFileName)
    • Method Detail

      • close

        public void close()
        Description copied from interface: DbMarker
        Close database, free resources
        Specified by:
        close in interface DbMarker<org.snpeff.interval.Variant,​org.snpeff.vcf.VariantVcfEntry>
        Specified by:
        close in class DbVcf
      • open

        public void open()
        Open database annotation file
        Specified by:
        open in interface DbMarker<org.snpeff.interval.Variant,​org.snpeff.vcf.VariantVcfEntry>
        Specified by:
        open in class DbVcf
      • query

        public java.util.List<org.snpeff.vcf.VariantVcfEntry> query​(org.snpeff.interval.Variant variant)
        Description copied from class: DbVcf
        Find matching entries in the database
        Specified by:
        query in interface DbMarker<org.snpeff.interval.Variant,​org.snpeff.vcf.VariantVcfEntry>
        Specified by:
        query in class DbVcf