/usr/include/blasr/datastructures/alignment/AlignmentContext.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 20 21 22 23 24 25 26 27 28 29 30 31 32 | #ifndef _BLASR_ALIGNMENT_CONTEXT_HPP_
#define _BLASR_ALIGNMENT_CONTEXT_HPP_
#include <string>
#include "Enumerations.h"
class AlignmentContext {
public:
bool isPrimary;
int subreadIndex;
int numProperlyAlignedSubreads;
bool allSubreadsProperlyAligned;
bool isFinal;
int nextSubreadPos;
int nextSubreadDir;
bool hasNextSubreadPos;
int nSubreads;
std::string rNext;
std::string readGroupId;
std::string chipId;
AlignMode alignMode;
int editDist;
AlignmentContext();
bool IsFirst();
bool IsLast();
bool AllSubreadsAligned();
};
#endif // _BLASR_ALIGNMENT_CONTEXT_HPP_
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