/usr/include/smithwaterman/IndelAllele.h is in libsmithwaterman-dev 0.0+20160702-1+b1.
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 33 34 35 36 37 | #ifndef __INDEL_ALLELE_H
#define __INDEL_ALLELE_H
#include <string>
#include <iostream>
#include <sstream>
using namespace std;
class IndelAllele {
friend ostream& operator<<(ostream&, const IndelAllele&);
friend bool operator==(const IndelAllele&, const IndelAllele&);
friend bool operator!=(const IndelAllele&, const IndelAllele&);
friend bool operator<(const IndelAllele&, const IndelAllele&);
public:
bool insertion;
int length;
int referenceLength(void);
int readLength(void);
int position;
int readPosition;
string sequence;
bool homopolymer(void);
IndelAllele(bool i, int l, int p, int rp, string s)
: insertion(i), length(l), position(p), readPosition(rp), sequence(s)
{ }
};
bool homopolymer(string sequence);
ostream& operator<<(ostream& out, const IndelAllele& indel);
bool operator==(const IndelAllele& a, const IndelAllele& b);
bool operator!=(const IndelAllele& a, const IndelAllele& b);
bool operator<(const IndelAllele& a, const IndelAllele& b);
#endif
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