/usr/include/smithwaterman/LeftAlign.h is in libsmithwaterman-dev 0.0+20160702-3.
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 __LEFTALIGN_H
#define __LEFTALIGN_H
#include <algorithm>
#include <map>
#include <vector>
#include <list>
#include <utility>
#include <sstream>
#include "IndelAllele.h"
#include "convert.h"
#ifdef VERBOSE_DEBUG
#define LEFTALIGN_DEBUG(msg) \
if (debug) { cerr << msg; }
#else
#define LEFTALIGN_DEBUG(msg)
#endif
using namespace std;
bool leftAlign(string& alternateQuery, string& cigar, string& referenceSequence, int& offset, bool debug = false);
bool stablyLeftAlign(string alternateQuery, string& cigar, string referenceSequence, int& offset, int maxiterations = 20, bool debug = false);
int countMismatches(string& alternateQuery, string& cigar, string& referenceSequence);
string mergeCIGAR(const string& c1, const string& c2);
vector<pair<int, string> > splitCIGAR(const string& cigarStr);
string joinCIGAR(const vector<pair<int, string> >& cigar);
#endif
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