public class VCF3Codec extends AbstractVCFCodec
Reads historical VCF3 encoded files (1000 Genomes Pilot results, for example)
See also: @see VCF specification
See also: @see VCF spec. publication
Modifier and Type | Field and Description |
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static java.lang.String |
VCF3_MAGIC_HEADER |
alleleMap, doOnTheFlyModifications, filterHash, genotypeParts, header, lineNo, locParts, MAX_ALLELE_SIZE_BEFORE_WARNING, name, NUM_STANDARD_FIELDS, parts, remappedSampleName, stringCache, validate, version, warnedAboutNoEqualsForNonFlag
Constructor and Description |
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VCF3Codec() |
Modifier and Type | Method and Description |
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boolean |
canDecode(java.lang.String potentialInput)
This function returns true iff the File potentialInput can be parsed by this
codec.
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protected java.util.List<java.lang.String> |
parseFilters(java.lang.String filterString)
parse the filter string, first checking to see if we already have parsed it in a previous attempt
|
java.lang.Object |
readActualHeader(LineIterator reader)
Read and return the header, or null if there is no header.
|
canDecodeFile, createGenotypeMap, decode, decodeLoc, disableOnTheFlyModifications, generateException, generateException, getCachedString, getName, oneAllele, parseAlleles, parseGenotypeAlleles, parseHeaderFromLines, parseQual, setName, setRemappedSampleName, setVCFHeader
close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader
decodeLoc, getFeatureType
public static final java.lang.String VCF3_MAGIC_HEADER
public java.lang.Object readActualHeader(LineIterator reader)
AsciiFeatureCodec
readActualHeader
in class AsciiFeatureCodec<VariantContext>
reader
- the line reader to take header lines fromprotected java.util.List<java.lang.String> parseFilters(java.lang.String filterString)
parseFilters
in class AbstractVCFCodec
filterString
- the string to parsepublic boolean canDecode(java.lang.String potentialInput)
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.potentialInput
- the file to test for parsability with this codec