Class DbVcfTabix

java.lang.Object
org.snpsift.annotate.DbVcf
org.snpsift.annotate.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 Details

    • tabixReader

      protected htsjdk.tribble.readers.TabixReader tabixReader
    • vcf

      protected org.snpeff.fileIterator.VcfFileIterator vcf
    • chrPrepend

      protected String chrPrepend
  • Constructor Details

    • DbVcfTabix

      public DbVcfTabix(String dbFileName)
  • Method Details

    • 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(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 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