/usr/include/bamtools/api/SamHeader.h is in libbamtools-dev 2.4.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// SamHeader.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 header data fields.
// ***************************************************************************
#ifndef SAM_HEADER_H
#define SAM_HEADER_H
#include "api/api_global.h"
#include "api/BamAux.h"
#include "api/SamProgramChain.h"
#include "api/SamReadGroupDictionary.h"
#include "api/SamSequenceDictionary.h"
#include <string>
#include <vector>
namespace BamTools {
struct API_EXPORT SamHeader {
// ctor & dtor
SamHeader(const std::string& headerText = "");
SamHeader(const SamHeader& other);
~SamHeader(void);
// query/modify entire SamHeader
void Clear(void); // clears all header contents
std::string GetErrorString(void) const;
bool HasError(void) const;
bool IsValid(bool verbose = false) const; // returns true if SAM header is well-formed
void SetHeaderText(const std::string& headerText); // replaces data fields with contents of SAM-formatted text
std::string ToString(void) const; // returns the printable, SAM-formatted header text
// convenience query methods
bool HasVersion(void) const; // returns true if header contains format version entry
bool HasSortOrder(void) const; // returns true if header contains sort order entry
bool HasGroupOrder(void) const; // returns true if header contains group order entry
bool HasSequences(void) const; // returns true if header contains any sequence entries
bool HasReadGroups(void) const; // returns true if header contains any read group entries
bool HasPrograms(void) const; // returns true if header contains any program record entries
bool HasComments(void) const; // returns true if header contains comments
// --------------
// data members
// --------------
// header metadata (@HD line)
std::string Version; // VN:<Version> *Required, if @HD record is present*
std::string SortOrder; // SO:<SortOrder>
std::string GroupOrder; // GO:<GroupOrder>
std::vector<CustomHeaderTag> CustomTags; // optional custom tags on @HD line
// header sequences (@SQ entries)
SamSequenceDictionary Sequences;
// header read groups (@RG entries)
SamReadGroupDictionary ReadGroups;
// header program data (@PG entries)
SamProgramChain Programs;
// header comments (@CO entries)
std::vector<std::string> Comments;
// internal data
private:
mutable std::string m_errorString;
};
} // namespace BamTools
#endif // SAM_HEADER_H
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