Package htsjdk.variant.bcf2
Class BCF2Codec
- java.lang.Object
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- htsjdk.tribble.BinaryFeatureCodec<VariantContext>
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- htsjdk.variant.bcf2.BCF2Codec
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- All Implemented Interfaces:
FeatureCodec<VariantContext,PositionalBufferedStream>
public final class BCF2Codec extends BinaryFeatureCodec<VariantContext>
Decode BCF2 files
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BCF2Codec.LazyData
protected static class
BCF2Codec.SitesInfoForDecoding
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Constructor Summary
Constructors Constructor Description BCF2Codec()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
canDecode(String path)
This function returns true iff the File potentialInput can be parsed by this codec.VariantContext
decode(PositionalBufferedStream inputStream)
Decode a singleFeature
from theFeatureCodec
, 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 String
getDictionaryString(int offset)
Class<VariantContext>
getFeatureType()
This function returns the object the codec generates.protected BCF2GenotypeFieldDecoders.Decoder
getGenotypeFieldDecoder(String field)
protected VCFHeader
getHeader()
FeatureCodecHeader
readHeader(PositionalBufferedStream inputStream)
Read and return the header, or null if there is no header.-
Methods inherited from class htsjdk.tribble.BinaryFeatureCodec
close, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream
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Method Detail
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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)
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decode
public VariantContext decode(PositionalBufferedStream inputStream)
Description copied from interface:FeatureCodec
Decode a singleFeature
from theFeatureCodec
, 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)
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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.
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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 fromFeatureCodec
as needed to parse the header, and no more. Otherwise, data that might otherwise be fed into parsing aFeature
may be lost.- Parameters:
inputStream
- the source from which to decode the header- Returns:
- header object
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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
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getDictionaryString
protected final String getDictionaryString(int offset)
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getHeader
protected VCFHeader getHeader()
- Returns:
- the VCFHeader we found in this BCF2 file
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getGenotypeFieldDecoder
protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(String field)
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