Information for one VCF record.
We store most information as strings and without structure since the VCF format's definition is quite loose. We plan to provide classes for structured access to these strings later.
class VcfRecord
Include Headers
Although all positions in the VCF text format are 1-based, they are stored 0-based in the VcfRecord. Positions in string members are stored verbatim in the VcfRecord's members, e.g. 1-based.
Invalid qualities are stored as a float NaN (not a number). To test a float quality q for being NaN, test for q != q. Only NaN has the property that NaN != NaN.
Data Members
altAlternative bases in the variants, comma-separated if multiple (CharString).
beginPosPosition of the VCF record (__int32).
filterValue of FILTER field, empty if "." in VCF file (CharString).
formatValue of the VCF FORMAT field, empty if "." in VCF file (CharString).
genotypeInfosGenotype information, as in VCF file (StringSet<CharString>).
idTextual identifier of the variant (CharString).
infoValue of the INFO field, empty if "." in VCF file (CharString).
INVALID_POSStatic member as marker for invalid position (__int32)
INVALID_REFIDStatic member as marker for invalid reference (__int32)
qualQuality, NaN if invalid (float).
refBases in the reference (CharString).
rIDStatic member as marker for invalid reference (__int32)
Member Functions
MISSING_QUALReturn IEEE NaN float value.
VcfRecordDefault constructor.
clearClear a VcfRecord.
readRecordRead a record from a VcfStream
writeRecordWrite a record to a VcfStream
SeqAn - Sequence Analysis Library -

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