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// Author: Derek Barnett

#include "pbbam/CigarOperation.h"
#include <htslib/sam.h>
#include <array>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace std;

namespace internal {

typedef array<CigarOperationType, 128> CigarLookup;

static
CigarLookup InitCigarLookup(void)
{
    CigarLookup cl;
    cl.fill(CigarOperationType::UNKNOWN_OP);
    cl['M'] = CigarOperationType::ALIGNMENT_MATCH;
    cl['I'] = CigarOperationType::INSERTION;
    cl['D'] = CigarOperationType::DELETION;
    cl['N'] = CigarOperationType::REFERENCE_SKIP;
    cl['S'] = CigarOperationType::SOFT_CLIP;
    cl['H'] = CigarOperationType::HARD_CLIP;
    cl['P'] = CigarOperationType::PADDING;
    cl['='] = CigarOperationType::SEQUENCE_MATCH;
    cl['X'] = CigarOperationType::SEQUENCE_MISMATCH;
    return cl;
}

const static CigarLookup cigarLookup_ = InitCigarLookup();

} // namespace internal

CigarOperationType CigarOperation::CharToType(const char c)
{   return (static_cast<uint8_t>(c) >= 128 ? CigarOperationType::UNKNOWN_OP
                                           : internal::cigarLookup_[c] );
}

char CigarOperation::TypeToChar(const CigarOperationType type)
{ return bam_cigar_opchr(static_cast<int>(type)); }
