Class 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 Summary

      Constructors 
      Constructor Description
      DbVcfSorted​(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 VCF database annotation file
      java.util.List<org.snpeff.vcf.VariantVcfEntry> query​(org.snpeff.interval.Variant variant)
      Find matching entries in the database
      void setMaxBlockSize​(int maxBlockSize)  
      • Methods inherited from class java.lang.Object

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

      • DbVcfSorted

        public DbVcfSorted​(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 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 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
      • setMaxBlockSize

        public void setMaxBlockSize​(int maxBlockSize)