Class
VcfRecordInformation for one VCF record.
Information for one VCF record.
Implements | FormattedFileRecordConcept |
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All Impl'd | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept |
Defined in | <seqan/vcf_io.h> |
Signature |
class VcfRecord;
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Member Function Overview
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float VcfRecord::MISSING_QUAL();
Return IEEE NaN float value. -
VcfRecord::VcfRecord();
Default constructor.
Member Functions Inherited From AssignableConcept
Interface Function Overview
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void clear(record);
Clear a VcfRecord.
Interface Functions Inherited From AssignableConcept
Member Variable Overview
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VariableType VcfRecord::alt
Alternative bases in the variants, comma-separated if multiple (CharString). -
VariableType VcfRecord::beginPos
Position of the VCF record (int32_t). -
VariableType VcfRecord::filter
Value of FILTER field, empty if "." in VCF file (CharString). -
VariableType VcfRecord::format
Value of the VCF FORMAT field, empty if "." in VCF file (CharString). -
VariableType VcfRecord::genotypeInfos
Genotype information, as in VCF file (StringSet<CharString>). -
VariableType VcfRecord::id
Textual identifier of the variant (CharString). -
VariableType VcfRecord::info
Value of the INFO field, empty if "." in VCF file (CharString). -
VariableType VcfRecord::INVALID_POS
Static member as marker for invalid position (int32_t) -
VariableType VcfRecord::INVALID_REFID
Static member as marker for invalid reference (int32_t) -
VariableType VcfRecord::qual
Quality, NaN if invalid (float). -
VariableType VcfRecord::ref
Bases in the reference (CharString). -
VariableType VcfRecord::rID
Static member as marker for invalid reference (int32_t)
Detailed Description
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.
Remarks
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.
Member Functions Detail
float VcfRecord::MISSING_QUAL();
Return IEEE NaN float value.
Remarks
This cannot be implemented portably as a constant in a header-only library. In C++11, there is a function std::nanf() that could be used instead. For C++98, this is the best we can do.
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
VcfRecord::VcfRecord();
Default constructor.
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
Interface Functions Detail
void clear(record);
Clear a VcfRecord.
Parameters
record
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The VcfRecord to clear. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
Member Variables Detail
VariableType VcfRecord::alt
Alternative bases in the variants, comma-separated if multiple (CharString).
VariableType VcfRecord::beginPos
Position of the VCF record (int32_t).
VariableType VcfRecord::filter
Value of FILTER field, empty if "." in VCF file (CharString).
VariableType VcfRecord::format
Value of the VCF FORMAT field, empty if "." in VCF file (CharString).
VariableType VcfRecord::genotypeInfos
Genotype information, as in VCF file (StringSet<CharString>).
VariableType VcfRecord::id
Textual identifier of the variant (CharString).
VariableType VcfRecord::info
Value of the INFO field, empty if "." in VCF file (CharString).
VariableType VcfRecord::INVALID_POS
Static member as marker for invalid position (int32_t)
VariableType VcfRecord::INVALID_REFID
Static member as marker for invalid reference (int32_t)
VariableType VcfRecord::qual
Quality, NaN if invalid (float).
VariableType VcfRecord::ref
Bases in the reference (CharString).
VariableType VcfRecord::rID
Static member as marker for invalid reference (int32_t)