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#include <random>
std::string generateRandomSequence(size_t length, std::uniform_int_distribution<>& dis, std::mt19937& gen) {
char nucs[] = {'A', 'C', 'G', 'T'};
std::string s(length, 'N');
for (size_t i = 0; i < length; ++i) {
s[i] = nucs[dis(gen)];
}
return s;
}
SCENARIO("GC sampling works properly") {
GIVEN("A collection of random transcript sequences") {
std::random_device rd;
std::mt19937 gen(rd());
std::mt19937 gen2(rd());
std::uniform_int_distribution<> dis(0, 3);
std::uniform_int_distribution<> dis2(500, 1500);
char** txpSeqs = new char*[1000];
char** names = new char*[1000];
std::vector<size_t> lengths;
for (size_t tn = 0; tn < 1000; ++tn) {
auto l = dis2(gen2);
lengths.emplace_back(l);
auto s = generateRandomSequence(l, dis, gen);
txpSeqs[tn] = new char[s.length() + 1];
names[tn] = new char[3];
//names[tn] = "HI\0";
std::strcpy(txpSeqs[tn], s.c_str());
}
std::vector<Transcript> txpsSampled;
std::vector<Transcript> txpsUnSampled;
for (size_t tn = 0; tn < 1000; ++tn) {
auto len = lengths[tn];
txpsSampled.emplace_back(tn, names[tn], len);
txpsUnSampled.emplace_back(tn, names[tn], len);
txpsSampled[tn].setSequenceBorrowed(txpSeqs[tn], true, 5);
txpsUnSampled[tn].setSequenceBorrowed(txpSeqs[tn], true, 1);
}
for (size_t tn = 0; tn < 1000; ++tn) {
WHEN("Computing GC content") {
auto l = txpsSampled[tn].RefLength;
for (size_t i = 0; i < l; ++i) {
THEN("Sampled is the same as unsampled") {
REQUIRE(txpsSampled[tn].gcAt(i) == txpsUnSampled[tn].gcAt(i));
}
}
}
}
for (size_t tn = 0; tn < 1000; ++tn) {
delete [] txpSeqs[tn];
delete [] names[tn];
}
delete txpSeqs;
delete names;
} // end GIVEN
}
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