Package htsjdk.variant.bcf2

Class BCF2Codec

    • Field Detail

      • ALLOWED_MAJOR_VERSION

        protected static final int ALLOWED_MAJOR_VERSION
        See Also:
        Constant Field Values

      • ALLOWED_MINOR_VERSION

        protected static final int ALLOWED_MINOR_VERSION
        See Also:
        Constant Field Values

      • ALLOWED_BCF_VERSION

        public static final BCFVersion ALLOWED_BCF_VERSION

      • SIZEOF_BCF_HEADER

        public static final int SIZEOF_BCF_HEADER
        sizeof a BCF header (+ min/max version). Used when trying to detect when a streams starts with a bcf header

    • Constructor Detail

      • BCF2Codec

        public BCF2Codec()

    • Method Detail

      • decodeLoc

        public Feature decodeLoc​(PositionalBufferedStream inputStream)
        Description copied from interface: FeatureCodec
        Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
        Parameters:
        inputStream - the input stream from which to decode the next record
        Returns:
        Return the FeatureLoc encoded by the line, or null if the line does not represent a feature (e.g. is a comment)

      • decode

        public VariantContext decode​(PositionalBufferedStream inputStream)
        Description copied from interface: FeatureCodec
        Decode a single Feature from the FeatureCodec, reading no further in the underlying source than beyond that feature.
        Parameters:
        inputStream - the input stream from which to decode the next record
        Returns:
        Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is a comment)

      • getFeatureType

        public Class<VariantContext> getFeatureType()
        Description copied from interface: FeatureCodec

        This function returns the object the codec generates. This is allowed to be Feature in the case where conditionally different types are generated. Be as specific as you can though.

        This function is used by reflections based tools, so we can know the underlying type

        Returns:
        the feature type this codec generates.

      • validateVersionCompatibility

        protected void validateVersionCompatibility​(BCFVersion supportedVersion,
                                            BCFVersion actualVersion)
        Validate the actual version against the supported version to determine compatibility. Throws a TribbleException if the actualVersion is not compatible with the supportedVersion. Subclasses can override this to provide a custom version compatibility policy, but allowing something other than the supported version is dangerous and should be done with great care. The default policy is to require an exact version match.
        Parameters:
        supportedVersion - the current BCF implementation version
        actualVersion - the actual version

      • readHeader

        public FeatureCodecHeader readHeader​(PositionalBufferedStream inputStream)
        Description copied from interface: FeatureCodec
        Read and return the header, or null if there is no header. Note: Implementers of this method must be careful to read exactly as much from FeatureCodec as needed to parse the header, and no more. Otherwise, data that might otherwise be fed into parsing a Feature may be lost.
        Parameters:
        inputStream - the source from which to decode the header
        Returns:
        header object

      • canDecode

        public boolean canDecode​(String path)
        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:
        path - the file to test for parsability with this codec
        Returns:
        true if potentialInput can be parsed, false otherwise

      • getDictionaryString

        protected final String getDictionaryString​(int offset)

      • getHeader

        protected VCFHeader getHeader()
        Returns:
        the VCFHeader we found in this BCF2 file

      • tryReadBCFVersion

        public static BCFVersion tryReadBCFVersion​(BufferedInputStream uncompressedBufferedInput)
                                    throws IOException
        try to read a BCFVersion from an uncompressed BufferedInputStream. The buffer must be large enough to contain SIZEOF_BCF_HEADER
        Parameters:
        uncompressedBufferedInput - the uncompressed input stream
        Returns:
        the BCFVersion if it can be decoded, or null if not found.
        Throws:
        IOException