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#ifndef _BLASR_POS_HPP_
#define _BLASR_POS_HPP_
#include <fstream>
#include <vector>
#include <pbdata/Types.h>
#include <alignment/bwt/PackedHash.hpp>
#include <pbdata/DNASequence.hpp>
#include <pbdata/utils/BitUtils.hpp>
template <typename T_BWT_Sequence>
class Pos
{
public:
static const unsigned int stride = 8;
PackedHash packedHash;
std::vector<int> hashCount;
std::vector<int> fullPos;
int hasDebugInformation;
void Write(std::ostream &out) { packedHash.Write(out); }
void Read(std::istream &in) { packedHash.Read(in); }
void InitializeFromSuffixArray(DNALength suffixArray[], DNALength suffixArrayLength)
{
DNALength p;
packedHash.Allocate(suffixArrayLength);
std::fill(hashCount.begin(), hashCount.end(), 0);
for (p = 0; p < suffixArrayLength; p++) {
if (suffixArray[p] % stride == 0) {
packedHash.AddValue(p, suffixArray[p]);
}
}
}
int Lookup(DNALength bwtPos, DNALength &seqPos)
{
return packedHash.LookupValue(bwtPos - 1, seqPos);
}
};
#endif // _BLASR_POS_HPP_
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