/usr/include/bamtools/api/BamIndex.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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// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************
#ifndef BAM_INDEX_H
#define BAM_INDEX_H
#include "api/api_global.h"
#include "api/BamAux.h"
#include <string>
namespace BamTools {
namespace Internal {
class BamReaderPrivate;
} // namespace Internal
/*! \class BamTools::BamIndex
\brief Provides methods for generating & loading BAM index files.
This class straddles the line between public API and internal
implementation detail. Most client code should never have to use this
class directly.
It is exposed to the public API to allow advanced users to implement
their own custom indexing schemes.
*/
class API_EXPORT BamIndex {
// enums
public:
// list of supported BamIndex types
enum IndexType { BAMTOOLS = 0
, STANDARD
};
// ctor & dtor
public:
BamIndex(Internal::BamReaderPrivate* reader) : m_reader(reader) { }
virtual ~BamIndex(void) { }
// index interface
public:
// builds index from associated BAM file & writes out to index file
virtual bool Create(void) =0;
// returns a human-readable description of the last error encountered
std::string GetErrorString(void) { return m_errorString; }
// returns whether reference has alignments or no
virtual bool HasAlignments(const int& referenceID) const =0;
// attempts to use index data to jump to @region, returns success/fail
// a "successful" jump indicates no error, but not whether this region has data
// * thus, the method sets a flag to indicate whether there are alignments
// available after the jump position
virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
// loads existing data from file into memory
virtual bool Load(const std::string& filename) =0;
// returns the 'type' enum for derived index format
virtual BamIndex::IndexType Type(void) const =0;
//! \cond
// internal methods
protected:
void SetErrorString(const std::string& where, const std::string& what) const {
m_errorString = where + ": " + what;
}
// data members
protected:
Internal::BamReaderPrivate* m_reader; // copy, not owned
mutable std::string m_errorString;
//! \endcond
};
} // namespace BamTools
#endif // BAM_INDEX_H
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