/usr/include/bamtools/api/SamReadGroupDictionary.h is in libbamtools-dev 2.4.1+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// SamReadGroupDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamReadGroup entries.
// ***************************************************************************
#ifndef SAM_READGROUP_DICTIONARY_H
#define SAM_READGROUP_DICTIONARY_H
#include "api/api_global.h"
#include "api/SamReadGroup.h"
#include <map>
#include <string>
#include <vector>
namespace BamTools {
typedef std::vector<SamReadGroup> SamReadGroupContainer;
typedef SamReadGroupContainer::iterator SamReadGroupIterator;
typedef SamReadGroupContainer::const_iterator SamReadGroupConstIterator;
class API_EXPORT SamReadGroupDictionary {
// ctor & dtor
public:
SamReadGroupDictionary(void);
SamReadGroupDictionary(const SamReadGroupDictionary& other);
~SamReadGroupDictionary(void);
// query/modify read group data
public:
// adds a read group
void Add(const SamReadGroup& readGroup);
void Add(const std::string& readGroupId);
// adds multiple read groups
void Add(const SamReadGroupDictionary& readGroups);
void Add(const std::vector<SamReadGroup>& readGroups);
void Add(const std::vector<std::string>& readGroupIds);
// clears all read group entries
void Clear(void);
// returns true if dictionary contains this read group
bool Contains(const SamReadGroup& readGroup) const;
bool Contains(const std::string& readGroupId) const;
// returns true if dictionary is empty
bool IsEmpty(void) const;
// removes read group, if found
void Remove(const SamReadGroup& readGroup);
void Remove(const std::string& readGroupId);
// removes multiple read groups
void Remove(const std::vector<SamReadGroup>& readGroups);
void Remove(const std::vector<std::string>& readGroupIds);
// returns number of read groups in dictionary
int Size(void) const;
// retrieves a modifiable reference to the SamReadGroup object associated with this ID
SamReadGroup& operator[](const std::string& readGroupId);
// retrieve STL-compatible iterators
public:
SamReadGroupIterator Begin(void); // returns iterator to begin()
SamReadGroupConstIterator Begin(void) const; // returns const_iterator to begin()
SamReadGroupConstIterator ConstBegin(void) const; // returns const_iterator to begin()
SamReadGroupIterator End(void); // returns iterator to end()
SamReadGroupConstIterator End(void) const; // returns const_iterator to end()
SamReadGroupConstIterator ConstEnd(void) const; // returns const_iterator to end()
// data members
private:
SamReadGroupContainer m_data;
std::map<std::string, size_t> m_lookupData;
};
} // namespace BamTools
#endif // SAM_READGROUP_DICTIONARY_H
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