Class DbVcfSorted

java.lang.Object
org.snpsift.annotate.DbVcf
org.snpsift.annotate.DbVcfSorted
All Implemented Interfaces:
DbMarker<org.snpeff.interval.Variant,org.snpeff.vcf.VariantVcfEntry>

public class DbVcfSorted extends DbVcf
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed. Each VCF entry should be sorted according to position (as the VCF norm specifies). Chromosome order does not matter (e.g. all entries for chr10 can be before entries for chr2). But entries for the same chromosome should be together. Note: Old VCF specifications did not require VCF files to be sorted.
Author:
pcingola
  • Constructor Details

    • DbVcfSorted

      public DbVcfSorted(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 VCF 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
    • setMaxBlockSize

      public void setMaxBlockSize(int maxBlockSize)