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#ifndef _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
#define _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
#include <pbdata/DNASequence.hpp>
#include <pbdata/FASTQSequence.hpp>
#include <pbdata/qvs/QualityValue.hpp>
template <typename T_MatchList, typename T_Sequence>
class LISQValueWeightor
{
public:
T_Sequence *seq;
float operator()(const T_MatchList &matchList);
};
template <typename T_MatchList, typename T_Sequence>
float LISQValueWeightor<T_MatchList, T_Sequence>::operator()(const T_MatchList &matchList)
{
float totalQ;
DNALength nBases;
VectorIndex i;
totalQ = 0.0;
nBases = 0;
for (i = 0; i < matchList.size(); i++) {
DNALength mp;
for (mp = matchList[i].q; mp < matchList[i].q + matchList[i].w; mp++) {
totalQ += (*seq).qual[mp];
}
nBases += matchList[i].w;
}
if (nBases > 0) {
return totalQ / nBases;
}
}
#endif
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