Package htsjdk.variant.vcf

Class VCF3Codec

java.lang.Object
htsjdk.tribble.AbstractFeatureCodec<VariantContext,LineIterator>
htsjdk.tribble.AsciiFeatureCodec<VariantContext>
htsjdk.variant.vcf.AbstractVCFCodec
htsjdk.variant.vcf.VCF3Codec
All Implemented Interfaces:
FeatureCodec<VariantContext,LineIterator>, NameAwareCodec
public class VCF3Codec extends AbstractVCFCodec
A feature codec for the VCF3 specification, to read older VCF files. VCF3 has been depreciated in favor of VCF4 (See VCF codec for the latest information)

Reads historical VCF3 encoded files (1000 Genomes Pilot results, for example)

See also: @see VCF specification
See also: @see VCF spec. publication

Since:
2010

  • Field Details

  • Constructor Details

    • VCF3Codec

      public VCF3Codec()

  • Method Details

    • readActualHeader

      public Object readActualHeader(LineIterator reader)
      Description copied from class: AsciiFeatureCodec
      Read and return the header, or null if there is no header.
      Specified by:
      readActualHeader in class AsciiFeatureCodec<VariantContext>
      Parameters:
      reader - the line reader to take header lines from
      Returns:
      the number of header lines

    • parseFilters

      protected List<String> parseFilters(String filterString)
      parse the filter string, first checking to see if we already have parsed it in a previous attempt
      Specified by:
      parseFilters in class AbstractVCFCodec
      Parameters:
      filterString - the string to parse
      Returns:
      a set of the filters applied

    • canDecode

      public boolean canDecode(String potentialInput)
      Description copied from interface: FeatureCodec

      This function returns true iff the File potentialInput can be parsed by this codec. Note that checking the file's extension is a perfectly acceptable implementation of this method and file contents only rarely need to be checked.

      There is an assumption that there's never a situation where two different Codecs return true for the same file. If this occurs, the recommendation would be to error out.

      Note this function must never throw an error. All errors should be trapped and false returned.
      Parameters:
      potentialInput - the file to test for parsability with this codec
      Returns:
      true if potentialInput can be parsed, false otherwise