/usr/include/bamtools/api/SamReadGroup.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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// SamReadGroup.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides direct read/write access to the SAM read group data fields.
// ***************************************************************************
#ifndef SAM_READGROUP_H
#define SAM_READGROUP_H
#include "api/api_global.h"
#include "api/BamAux.h"
#include <string>
#include <vector>
namespace BamTools {
struct API_EXPORT SamReadGroup {
// ctor & dtor
SamReadGroup(void);
SamReadGroup(const std::string& id);
SamReadGroup(const SamReadGroup& other);
~SamReadGroup(void);
// query/modify entire read group
void Clear(void); // clears all data fields
// convenience query methods
bool HasDescription(void) const; // returns true if read group has a description
bool HasFlowOrder(void) const; // returns true if read group has a flow order entry
bool HasID(void) const; // returns true if read group has a group ID
bool HasKeySequence(void) const; // returns true if read group has a key sequence
bool HasLibrary(void) const; // returns true if read group has a library name
bool HasPlatformUnit(void) const; // returns true if read group has a platform unit ID
bool HasPredictedInsertSize(void) const; // returns true if read group has a predicted insert size
bool HasProductionDate(void) const; // returns true if read group has a production date
bool HasProgram(void) const; // returns true if read group has a program entry
bool HasSample(void) const; // returns true if read group has a sample name
bool HasSequencingCenter(void) const; // returns true if read group has a sequencing center ID
bool HasSequencingTechnology(void) const; // returns true if read group has a sequencing technology ID
// data fields
std::string Description; // DS:<Description>
std::string FlowOrder; // FO:<FlowOrder>
std::string ID; // ID:<ID> *Required for valid SAM header*
std::string KeySequence; // KS:<KeySequence>
std::string Library; // LB:<Library>
std::string PlatformUnit; // PU:<PlatformUnit>
std::string PredictedInsertSize; // PI:<PredictedInsertSize>
std::string ProductionDate; // DT:<ProductionDate>
std::string Program; // PG:<Program>
std::string Sample; // SM:<Sample>
std::string SequencingCenter; // CN:<SequencingCenter>
std::string SequencingTechnology; // PL:<SequencingTechnology>
std::vector<CustomHeaderTag> CustomTags; // optional custom tags
};
/*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs)
\brief tests equality by comparing read group IDs
*/
API_EXPORT inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) {
return lhs.ID == rhs.ID;
}
} // namespace BamTools
#endif // SAM_READGROUP_H
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