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#ifndef _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
#define _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
#include <string>
#include <pbdata/sam/SAMKeywordValuePair.hpp>
class SAMReferenceSequence
{
public:
std::string sequenceName;
uint64_t length;
std::string GetSequenceName() { return sequenceName; }
//
// By definining accessor functions here but no data, we can
// economize on the amount of space used for each element. This is
// no big deal for references, but for pairwise alignments, it is
// big.
//
std::string GetMD5() { return ""; }
uint64_t GetLength() { return length; }
std::string GetGenomeAssembly() { return ""; }
std::string GetSpecies() { return ""; }
std::string GetURI() { return ""; }
enum SAMReferenceSequenceRequiredFields
{
SQ_SN,
SQ_LN
};
static const char* SAMReferenceSequenceFieldNames[];
void StoreValues(std::vector<SAMKeywordValuePair>& kvPairs, uint64_t lineNumber = 0);
};
class SAMFullReferenceSequence : public SAMReferenceSequence
{
public:
std::string md5;
std::string species;
std::string uri;
std::string genomeAssembly;
std::string GetMD5() { return md5; }
std::string GetSpecies() { return species; }
std::string GetURI() { return uri; }
std::string GetGenomeAssembly() { return genomeAssembly; }
enum FullReferenceSequenceRequiredFields
{
SQ_AS,
SQ_M5,
SQ_SP,
SQ_UR
};
static const char* SAMFullReferenceSequenceFieldNames[];
void StoreValues(std::vector<SAMKeywordValuePair>& kvPairs, uint64_t lineNumber = 0);
};
#endif
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