/usr/include/bamtools/api/BamReader.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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// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 18 November 2012 (DB)
// ---------------------------------------------------------------------------
// Provides read access to BAM files.
// ***************************************************************************
#ifndef BAMREADER_H
#define BAMREADER_H
#include "api/api_global.h"
#include "api/BamAlignment.h"
#include "api/BamIndex.h"
#include "api/SamHeader.h"
#include <string>
namespace BamTools {
namespace Internal {
class BamReaderPrivate;
} // namespace Internal
class API_EXPORT BamReader {
// constructor / destructor
public:
BamReader(void);
~BamReader(void);
// public interface
public:
// ----------------------
// BAM file operations
// ----------------------
// closes the current BAM file
bool Close(void);
// returns filename of current BAM file
const std::string GetFilename(void) const;
// returns true if a BAM file is open for reading
bool IsOpen(void) const;
// performs random-access jump within BAM file
bool Jump(int refID, int position = 0);
// opens a BAM file
bool Open(const std::string& filename);
// returns internal file pointer to beginning of alignment data
bool Rewind(void);
// sets the target region of interest
bool SetRegion(const BamRegion& region);
// sets the target region of interest
bool SetRegion(const int& leftRefID,
const int& leftPosition,
const int& rightRefID,
const int& rightPosition);
// ----------------------
// access alignment data
// ----------------------
// retrieves next available alignment
bool GetNextAlignment(BamAlignment& alignment);
// retrieves next available alignmnet (without populating the alignment's string data fields)
bool GetNextAlignmentCore(BamAlignment& alignment);
// ----------------------
// access header data
// ----------------------
// returns a read-only reference to SAM header data
const SamHeader& GetConstSamHeader(void) const;
// returns an editable copy of SAM header data
SamHeader GetHeader(void) const;
// returns SAM header data, as SAM-formatted text
std::string GetHeaderText(void) const;
// ----------------------
// access reference data
// ----------------------
// returns the number of reference sequences
int GetReferenceCount(void) const;
// returns all reference sequence entries
const RefVector& GetReferenceData(void) const;
// returns the ID of the reference with this name
int GetReferenceID(const std::string& refName) const;
// ----------------------
// BAM index operations
// ----------------------
// creates an index file for current BAM file, using the requested index type
bool CreateIndex(const BamIndex::IndexType& type = BamIndex::STANDARD);
// returns true if index data is available
bool HasIndex(void) const;
// looks in BAM file's directory for a matching index file
bool LocateIndex(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
// opens a BAM index file
bool OpenIndex(const std::string& indexFilename);
// sets a custom BamIndex on this reader
void SetIndex(BamIndex* index);
// ----------------------
// error handling
// ----------------------
// returns a human-readable description of the last error that occurred
std::string GetErrorString(void) const;
// private implementation
private:
Internal::BamReaderPrivate* d;
};
} // namespace BamTools
#endif // BAMREADER_H
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