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#ifndef _BLASR_FORMAT_BAMPRINTER_HPP_
#define _BLASR_FORMAT_BAMPRINTER_HPP_
#ifdef USE_PBBAM
#include <cstdint>
#include <sstream>
#include <pbbam/BamHeader.h>
#include <pbbam/BamWriter.h>
#include <alignment/format/SAMPrinter.hpp>
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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