Package org.snpsift.annotate

Class DbVcfTabix

  • All Implemented Interfaces:
    DbMarker<org.snpeff.interval.Variant,​org.snpeff.vcf.VariantVcfEntry>
    public class DbVcfTabix
extends DbVcf
    Use a bgzip-compressed, tabix indexed VCF file as a database for annotations
    Author:
    pcingola

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected java.lang.String chrPrepend  
      protected htsjdk.tribble.readers.TabixReader tabixReader  
      protected org.snpeff.fileIterator.VcfFileIterator vcf  

    • Constructor Summary

      Constructors 
      Constructor Description
      DbVcfTabix​(java.lang.String dbFileName)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Close database, free resources
      protected boolean initTabix​(java.lang.String fileName)
      Initialize tabix reader
      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

    • Field Detail

      • tabixReader

        protected htsjdk.tribble.readers.TabixReader tabixReader

      • vcf

        protected org.snpeff.fileIterator.VcfFileIterator vcf

      • chrPrepend

        protected java.lang.String chrPrepend

    • Constructor Detail

      • DbVcfTabix

        public DbVcfTabix​(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

      • initTabix

        protected boolean initTabix​(java.lang.String fileName)
        Initialize tabix reader

      • 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