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#include <string>
#include <iostream>
#include "utils.hpp"
#include "suffixarray/SuffixArray.hpp"
#include "suffixarray/SuffixArrayTypes.hpp"
using namespace std;
int main(int argc, char* argv[]) {
if (argc <= 1) {
cout << "sals checks if a suffix array has lookup table or not." <<endl;
cout << "usage sals genome.sa" <<endl;
exit(1);
}
string saFileName = argv[1];
DNASuffixArray sa;
if (!sa.LightRead(saFileName)) {
cout << "The file is not in a sa format." << endl;
exit(1);
}
if (sa.componentList[DNASuffixArray::CompArray]) {
cout << " * has a suffix array." << endl;
}
else {
cout << " * does not contain a suffix array." << endl;
}
if (sa.componentList[DNASuffixArray::CompLookupTable]) {
cout << " * has a lookup table for word size. " << sa.lookupPrefixLength
<< endl;
}
else {
cout << " * does not have a lookup table." << endl;
}
}
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