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#ifndef _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
#define _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
#include <alignment/datastructures/alignmentset/SAMQVConversion.hpp>
#include <pbdata/SMRTSequence.hpp>
class SupplementalQVList
{
public:
//enum QVList {InsertionQV=0x1, DeletionQV=0x2, SubstitutionQV=0x4, MergeQV=0x8, SubstitutionTag=0x10, DeletionTag=0x20};
//enum QVIndex {I_InsertionQV=1,I_DeletionQV=2,I_SubstitutionQV=3,I_MergeQV=4,I_SubstitutionTag=5,I_DeletionTag=6};
//defined in FASTQSequence.
unsigned int useqv;
void SetDefaultQV()
{
useqv = InsertionQV | DeletionQV | SubstitutionQV | MergeQV | DeletionTag;
}
static const char *qvTags[];
static const char *qvNames[];
static int nqvTags;
static int nTags;
int UseQV(std::vector<std::string> &qvList);
void FormatQVOptionalFields(SMRTSequence &alignedSubsequence);
void PrintQVOptionalFields(SMRTSequence &alignedSubsequence, std::ostream &out);
void clear();
};
#endif
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