/usr/include/blasr/datastructures/alignment/AlignmentMap.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-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 | #ifndef _BLASR_ALIGNMENT_MAP_HPP_
#define _BLASR_ALIGNMENT_MAP_HPP_
#include <vector>
class AlignmentMap {
public:
int qPos, tPos;
std::vector<int> alignPos;
};
// Build a map of positions from (unaligned) bases to an aligned sequence
void
CreateSequenceToAlignmentMap(const std::string & alignedSequence,
std::vector<int> & baseToAlignmentMap);
#endif // _BLASR_ALIGNMENT_MAP_HPP_
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