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#ifndef _BLASR_FORMAT_BAMPRINTER_HPP_
#define _BLASR_FORMAT_BAMPRINTER_HPP_
#ifdef USE_PBBAM
#include <sstream>
#include <stdint.h>
#include "SAMPrinter.hpp"
#include <pbbam/BamHeader.h>
#include <pbbam/BamWriter.h>
template<typename T_Sequence>
void AlignmentToBamRecord(T_AlignmentCandidate & alignment,
T_Sequence & read, T_Sequence & subread,
PacBio::BAM::BamRecord & bamRecord,
AlignmentContext & context, SupplementalQVList & qvList,
Clipping clipping,
bool cigarUseSeqMatch=false, const bool allowAdjacentIndels=true);
namespace BAMOutput {
template<typename T_Sequence>
void PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read,
T_Sequence & subread,
PacBio::BAM::IRecordWriter &bamWriter, AlignmentContext &context,
SupplementalQVList & qvList, Clipping clipping,
bool cigarUseSeqMatch=false, const bool allowAdjacentIndels=true);
}
#include "BAMPrinterImpl.hpp"
#endif
#endif
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