/usr/include/bamtools/api/BamMultiReader.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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// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 14 January 2013 (DB)
// ---------------------------------------------------------------------------
// Convenience class for reading multiple BAM files.
// ***************************************************************************
#ifndef BAMMULTIREADER_H
#define BAMMULTIREADER_H
#include "api/api_global.h"
#include "api/BamReader.h"
#include <map>
#include <sstream>
#include <string>
#include <utility>
namespace BamTools {
namespace Internal {
class BamMultiReaderPrivate;
} // namespace Internal
class API_EXPORT BamMultiReader {
// enums
public:
// possible merge order strategies
enum MergeOrder { RoundRobinMerge = 0
, MergeByCoordinate
, MergeByName
};
// constructor / destructor
public:
BamMultiReader(void);
~BamMultiReader(void);
// public interface
public:
// ----------------------
// BAM file operations
// ----------------------
// closes all open BAM files
bool Close(void);
// close only the requested BAM file
bool CloseFile(const std::string& filename);
// returns list of filenames for all open BAM files
const std::vector<std::string> Filenames(void) const;
// returns curent merge order strategy
BamMultiReader::MergeOrder GetMergeOrder(void) const;
// returns true if multireader has any open BAM files
bool HasOpenReaders(void) const;
// performs random-access jump within current BAM files
bool Jump(int refID, int position = 0);
// opens BAM files
bool Open(const std::vector<std::string>& filenames);
// opens a single BAM file, adding to any other current BAM files
bool OpenFile(const std::string& filename);
// returns file pointers to beginning of alignments
bool Rewind(void);
// sets an explicit merge order, regardless of the BAM files' SO header tag
bool SetExplicitMergeOrder(BamMultiReader::MergeOrder order);
// 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 alignment (without populating the alignment's string data fields)
bool GetNextAlignmentCore(BamAlignment& alignment);
// ----------------------
// access auxiliary data
// ----------------------
// returns unified SAM header for all files
SamHeader GetHeader(void) const;
// returns unified SAM header text for all files
std::string GetHeaderText(void) const;
// returns number of reference sequences
int GetReferenceCount(void) const;
// returns all reference sequence entries.
const BamTools::RefVector GetReferenceData(void) const;
// returns the ID of the reference with this name.
int GetReferenceID(const std::string& refName) const;
// ----------------------
// BAM index operations
// ----------------------
// creates index files for current BAM files
bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD);
// returns true if all BAM files have index data available
bool HasIndexes(void) const;
// looks for index files that match current BAM files
bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
// opens index files for current BAM files.
bool OpenIndexes(const std::vector<std::string>& indexFilenames);
// ----------------------
// error handling
// ----------------------
// returns a human-readable description of the last error that occurred
std::string GetErrorString(void) const;
// private implementation
private:
Internal::BamMultiReaderPrivate* d;
};
} // namespace BamTools
#endif // BAMMULTIREADER_H
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