/usr/include/pbseq/alignment/tuples/TupleMatching.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 | #ifndef _BLASR_TUPLE_MATCHING_HPP_
#define _BLASR_TUPLE_MATCHING_HPP_
#include "TupleMetrics.hpp"
#include "TupleList.hpp"
#include "BaseTuple.hpp"
#include "DNATuple.hpp"
#include "TupleMatching.hpp"
template<typename Sequence, typename T_TupleList>
int SequenceToTupleList(
Sequence &seq, TupleMetrics &tm, T_TupleList &tupleList);
template<typename TSequence, typename TMatch, typename T_TupleList>
int StoreMatchingPositions(
TSequence &querySeq, TupleMetrics &tm, T_TupleList &targetTupleList,
std::vector<TMatch> &matchSet);
template<typename Sequence, typename Tuple>
int StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm,
std::vector<int> &uniqueTuplePosList);
#include "TupleMatchingImpl.hpp"
#endif // _BLASR_TUPLE_MATCHING_HPP_
|