Class VcfRecord

Information for one VCF record.

/*!
 * @class VcfRecord
 * 
 * @headerfile <seqan/vcf_io.h>
 * 
 * @brief Information for one VCF record.
 * 
 * @signature class VcfRecord;
 * 
 * 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.
 * 
 * @section Remarks
 * 
 * Although all positions in the VCF text format are 1-based, they are stored
 * 0-based in the @link VcfRecord @endlink. Positions in string members are
 * stored verbatim in the @link VcfRecord @endlink's members, e.g. 1-based.
 * 
 * Invalid qualities are stored as a float <tt>NaN</tt> (not a number). To test
 * a float quality <tt>q</tt> for being <tt>NaN</tt>, test for <tt>q != q</tt>.
 * Only <tt>NaN</tt> has the property that <tt>NaN != NaN</tt>.
 * 
 * @fn VcfRecord::MISSING_QUAL
 * 
 * @brief Return IEEE <tt>NaN</tt> float value.
 * 
 * @signature float VcfRecord::MISSING_QUAL();
 * 
 * @section Remarks
 * 
 * This cannot be implemented portably as a constant in a header-only library.
 * In C++11, there is a function <tt>std::nanf()</tt> that could be used
 * instead. For C++98, this is the best we can do.
 * 
 * @fn VcfRecord::VcfRecord
 * 
 * @brief Default constructor.
 * 
 * @signature VcfRecord::VcfRecord();
 * 
 * @var VariableType VcfRecord::ref;
 * 
 * @brief Bases in the reference (@link CharString @endlink).
 * 
 * @var VariableType VcfRecord::genotypeInfos;
 * 
 * @brief Genotype information, as in VCF file (@link StringSet @endlink<@link
 *        CharString @endlink>).
 * 
 * @var VariableType VcfRecord::info;
 * 
 * @brief Value of the INFO field, empty if "." in VCF file (@link CharString
 *        @endlink).
 * 
 * @var VariableType VcfRecord::INVALID_REFID;
 * 
 * @brief Static member as marker for invalid reference (<tt>__int32</tt>)
 * 
 * @var VariableType VcfRecord::format;
 * 
 * @brief Value of the VCF FORMAT field, empty if "." in VCF file (@link
 *        CharString @endlink).
 * 
 * @var VariableType VcfRecord::alt;
 * 
 * @brief Alternative bases in the variants, comma-separated if multiple (@link
 *        CharString @endlink).
 * 
 * @var VariableType VcfRecord::qual;
 * 
 * @brief Quality, <tt>NaN</tt> if invalid (<tt>float</tt>).
 * 
 * @var VariableType VcfRecord::filter;
 * 
 * @brief Value of FILTER field, empty if "." in VCF file (@link CharString
 *        @endlink).
 * 
 * @var VariableType VcfRecord::rID;
 * 
 * @brief Static member as marker for invalid reference (<tt>__int32</tt>)
 * 
 * @var VariableType VcfRecord::beginPos;
 * 
 * @brief Position of the VCF record (<tt>__int32</tt>).
 * 
 * @var VariableType VcfRecord::INVALID_POS;
 * 
 * @brief Static member as marker for invalid position (<tt>__int32</tt>)
 * 
 * @var VariableType VcfRecord::id;
 * 
 * @brief Textual identifier of the variant (@link CharString @endlink).
 * 
 * @fn VcfRecord#clear
 * 
 * @brief Clear a VcfRecord.
 * 
 * @signature void clear(record);
 * 
 * @param[in,out] record The VcfRecord to clear.
 */