Interface VCFReader

    • Method Detail

      • 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.