htsjdk.variant.bcf2

Class BCF2Codec

java.lang.Object

htsjdk.tribble.BinaryFeatureCodec<VariantContext>

htsjdk.variant.bcf2.BCF2Codec

All Implemented Interfaces:

FeatureCodec<VariantContext,PositionalBufferedStream>

public class BCF2Codec
extends BinaryFeatureCodec<VariantContext>

Decode BCF2 files

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BCF2Codec.LazyData
protected static class	BCF2Codec.SitesInfoForDecoding

Field Summary

Fields

Modifier and Type	Field and Description
static BCFVersion	ALLOWED_BCF_VERSION
protected static int	ALLOWED_MAJOR_VERSION
protected static int	ALLOWED_MINOR_VERSION
static int	SIZEOF_BCF_HEADER sizeof a BCF header (+ min/max version).

Constructor Summary

Constructors

Constructor and Description
BCF2Codec()

Method Summary

Modifier and Type	Method and Description
boolean	canDecode(java.lang.String path) This function returns true iff the File potentialInput can be parsed by this codec.
VariantContext	decode(PositionalBufferedStream inputStream) Decode a single Feature from the SOURCE, reading no further in the underlying source than beyond that feature.
Feature	decodeLoc(PositionalBufferedStream inputStream) Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
protected void	error(java.lang.String message)
protected java.lang.String	getDictionaryString(int offset)
java.lang.Class<VariantContext>	getFeatureType() This function returns the object the codec generates.
protected BCF2GenotypeFieldDecoders.Decoder	getGenotypeFieldDecoder(java.lang.String field)
protected VCFHeader	getHeader()
FeatureCodecHeader	readHeader(PositionalBufferedStream inputStream) Read and return the header, or null if there is no header.
static BCFVersion	tryReadBCFVersion(java.io.BufferedInputStream uncompressedBufferedInput) try to read a BCFVersion from an uncompressed BufferedInputStream.
protected void	validateVersionCompatibility(BCFVersion supportedVersion, BCFVersion actualVersion) Validate the actual version against the supported version to determine compatibility.

Methods inherited from class htsjdk.tribble.BinaryFeatureCodec

close, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.tribble.FeatureCodec

getPathToDataFile

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 SOURCE, 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 java.lang.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 SOURCE 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(java.lang.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 java.lang.String getDictionaryString(int offset)

getHeader

protected VCFHeader getHeader()

Returns:

the VCFHeader we found in this BCF2 file

getGenotypeFieldDecoder

protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(java.lang.String field)

error

protected void error(java.lang.String message)
              throws java.lang.RuntimeException

Throws:

java.lang.RuntimeException

tryReadBCFVersion

public static BCFVersion tryReadBCFVersion(java.io.BufferedInputStream uncompressedBufferedInput)
                                    throws java.io.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:

java.io.IOException