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#ifndef _BLASR_COMPRESSED_DNA_TUPLE_HPP_
#define _BLASR_COMPRESSED_DNA_TUPLE_HPP_
#include <alignment/tuples/DNATuple.hpp>
#include <pbdata/CompressedSequence.hpp>
template <typename T_Sequence>
class CompressedDNATuple : public DNATuple
{
static const unsigned char mask = 0xf;
public:
CompressedDNATuple(const CompressedDNATuple &rhs) : DNATuple(rhs) {}
int FromStringLR(Nucleotide *strPtr, TupleMetrics &tm)
{
//
// Make sure the sequence contains all valid characters.
//
if (!CompressedSequence<T_Sequence>::Only4BitACTG(strPtr, tm.tupleSize)) return 0;
if (tm.tupleSize == 0) return 1;
tuple = 0;
Nucleotide *p;
Nucleotide *endPtr = &strPtr[tm.tupleSize - 1];
for (p = strPtr; p != endPtr; p++) {
tuple += TwoBit[*p & mask];
tuple <<= 2;
}
//
// The tuple size is guaranteed to be at least
// 1, so it's safe to add the last value.
// This cannot be in the previous loop since
// the shift shouldn't happen.
tuple += TwoBit[*p & mask];
return 1;
}
int FromStringRL(Nucleotide *strPtr, TupleMetrics &tm)
{
if (!CompressedSequence<T_Sequence>::Only4BitACTG((CompressedNucleotide *)strPtr,
tm.tupleSize))
return 0;
if (tm.tupleSize == 0) return 1;
tuple = 0;
Nucleotide *p;
for (p = strPtr + tm.tupleSize - 1; p > strPtr; p--) {
tuple += TwoBit[*p & mask];
tuple <<= 2;
}
//
// The tuple size is guaranteed to be at least
// 1, so it's safe to add the last value.
// This cannot be in the previous loop since
// the shift shouldn't happen.
tuple += TwoBit[*p & mask];
return 1;
}
};
#endif // _BLASR_COMPRESSED_DNA_TUPLE_HPP_
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