/usr/include/pbseq/alignment/algorithms/anchoring/LISQValueWeightor.hpp is in libblasr-dev 0~20161219-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | #ifndef _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
#define _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
// pbdata
#include "../../../pbdata/qvs/QualityValue.hpp"
#include "../../../pbdata/DNASequence.hpp"
#include "../../../pbdata/FASTQSequence.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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