Package htsjdk.variant.vcf
Class VCF3Codec
- java.lang.Object
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- htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>
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- htsjdk.tribble.AsciiFeatureCodec<VariantContext>
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- htsjdk.variant.vcf.AbstractVCFCodec
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- htsjdk.variant.vcf.VCF3Codec
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- 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
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Field Summary
Fields Modifier and Type Field Description static String
VCF3_MAGIC_HEADER
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Fields inherited from class htsjdk.variant.vcf.AbstractVCFCodec
alleleMap, doOnTheFlyModifications, filterHash, genotypeParts, header, lineNo, locParts, MAX_ALLELE_SIZE_BEFORE_WARNING, name, NUM_STANDARD_FIELDS, parts, remappedSampleName, stringCache, validate, version, warnedAboutNoEqualsForNonFlag
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Constructor Summary
Constructors Constructor Description VCF3Codec()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
canDecode(String potentialInput)
This function returns true iff the File potentialInput can be parsed by this codec.protected List<String>
parseFilters(String filterString)
parse the filter string, first checking to see if we already have parsed it in a previous attemptObject
readActualHeader(LineIterator reader)
Read and return the header, or null if there is no header.-
Methods inherited from class htsjdk.variant.vcf.AbstractVCFCodec
canDecodeFile, createGenotypeMap, decode, decodeLoc, disableOnTheFlyModifications, generateException, generateException, getCachedString, getHeader, getName, getTabixFormat, getVersion, oneAllele, parseAlleles, parseGenotypeAlleles, parseHeaderFromLines, parseQual, setName, setRemappedSampleName, setVCFHeader
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Methods inherited from class htsjdk.tribble.AsciiFeatureCodec
close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader
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Methods inherited from class htsjdk.tribble.AbstractFeatureCodec
decodeLoc, getFeatureType
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Field Detail
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VCF3_MAGIC_HEADER
public static final String VCF3_MAGIC_HEADER
- See Also:
- Constant Field Values
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Method Detail
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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 classAsciiFeatureCodec<VariantContext>
- Parameters:
reader
- the line reader to take header lines from- Returns:
- the number of header lines
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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 classAbstractVCFCodec
- Parameters:
filterString
- the string to parse- Returns:
- a set of the filters applied
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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
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