Package htsjdk.variant.vcf

Interface VCFReader

All Superinterfaces:
AutoCloseable, Closeable, Iterable<VariantContext>
All Known Implementing Classes:
VCFFileReader
public interface VCFReader extends Closeable, Iterable<VariantContext>
Interface for reading VCF/BCF files.

  • Method Details

    • getHeader

      VCFHeader getHeader()
      Returns the VCFHeader associated with this VCFReader.

    • query

      CloseableIterator<VariantContext> query(String chrom, int start, int end)
      Queries for records overlapping the region specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.
      Parameters:
      chrom - the chomosome to query
      start - query interval start
      end - query interval end
      Returns:
      non-null iterator over VariantContexts

    • query

      default CloseableIterator<VariantContext> query(Locatable locatable)
      Queries for records overlapping the Locatable specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.
      Returns:
      non-null iterator over VariantContexts

    • isQueryable

      boolean isQueryable()
      A method to check if the reader is query-able, i.e. if a call to VCFFileReader.query(String, int, int) can be successful
      Returns:
      true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.

    • iterator

      CloseableIterator<VariantContext> iterator()
      Specified by:
      iterator in interface Iterable<VariantContext>