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#include <cstring>
#include <iostream>
#include <string>
#include <alignment/bwt/BWT.hpp>
#include <alignment/suffixarray/SuffixArray.hpp>
#include <alignment/suffixarray/SuffixArrayTypes.hpp>
int main(int argc, char* argv[])
{
std::string bwtFileName, saFileName;
if (argc < 3) {
std::cout << "usage: bwt2sa bwtfile safile " << std::endl;
std::exit(EXIT_FAILURE);
}
bwtFileName = argv[1];
saFileName = argv[2];
Bwt<PackedDNASequence, FASTASequence> bwt;
DNASuffixArray suffixArray;
bwt.Read(bwtFileName);
suffixArray.AllocateSuffixArray(bwt.bwtSequence.length - 1);
SAIndex index;
for (index = 1; index < bwt.bwtSequence.length + 1; index++) {
suffixArray.index[index - 1] = bwt.Locate(index);
}
suffixArray.Write(saFileName);
}
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