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/usr/include/blasr/datastructures/alignment/AlignedPair.h is in libblasr-dev 0~20151014+gitbe5d1bf-2.

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#ifndef ALIGNED_PAIR_H_
#define ALIGNED_PAIR_H_

#include <string>

template<typename T_AlignChar=char>
class AlignedPair {
 public:
	int length;
	T_AlignChar *tAlignmentSeq;
	T_AlignChar *qAlignmentSeq;
};


inline
void ReadCompareSequencesAlignment {

}
#endif