/usr/include/blasr/format/BAMPrinter.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | #ifndef _BLASR_FORMAT_BAMPRINTER_HPP_
#define _BLASR_FORMAT_BAMPRINTER_HPP_
#ifdef USE_PBBAM
#include <sstream>
#include <stdint.h>
#include "format/SAMPrinter.hpp"
#include "pbbam/BamHeader.h"
#include "pbbam/BamWriter.h"
namespace BAMOutput {
template<typename T_Sequence>
void SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
T_Sequence &alignedSeq);
template<typename T_Sequence>
void CreateCIGARString(T_AlignmentCandidate &alignment,
T_Sequence &read, std::string &cigarString, const bool cigarUseSeqMatch);
template<typename T_Sequence>
void AlignmentToBamRecord(T_AlignmentCandidate & alignment,
T_Sequence & read, PacBio::BAM::BamRecord & bamRecord,
AlignmentContext & context, SupplementalQVList & qvList,
Clipping clipping, bool cigarUseSeqMatch);
template<typename T_Sequence>
void PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read,
PacBio::BAM::BamWriter &bamWriter, AlignmentContext &context,
SupplementalQVList & qvList, Clipping clipping,
bool cigarUseSeqMatch=false);
}
#include "BAMPrinterImpl.hpp"
#endif
#endif
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