Class DbVcfMem

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

  • Field Details

  • Constructor Details

    • DbVcfMem

      public DbVcfMem(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

    • 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