#ifndef _BLASR_ALIGNMENT_MAP_HPP_
#define _BLASR_ALIGNMENT_MAP_HPP_

#include <string>
#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_
