int main() {
const string ref = "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA";
const string query = "CTGAGCCGGTAAATC";
// Declares a default Aligner
StripedSmithWaterman::Aligner aligner;
// Declares a default filter
StripedSmithWaterman::Filter filter;
// Declares an alignment that stores the result
StripedSmithWaterman::Alignment alignment;
// Aligns the query to the ref
aligner.Align(query.c_str(), ref.c_str(), ref.size(), filter, &alignment);
PrintAlignment(alignment);
return 0;
}
TEST(Alignment, SpeedTest) {
const std::string seq = "ATCTACTGACGCTGCTGCTGGTCTGCTGCTCCTCGCTGCCCAGCCGGCGATGGCTAGCTCCTATGAGCTGACTCAGCCGCCCTCCCTCTCTGCATCTCCGGGATCATCTGTCAGACTCGCCTGCA";
const std::string ref = "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA";
StripedSmithWaterman::Aligner aligner;
StripedSmithWaterman::Filter filter;
StripedSmithWaterman::Alignment alignment;
aligner.SetReferenceSequence(ref.c_str(), ref.length());
clock_t start = clock();
for (int i = 0; i < ITERS; ++i) {
aligner.Align(seq.c_str(), filter, &alignment);
}
clock_t ends = clock();
LOG4CXX_INFO(logger, "Processor Time Spent for " << ITERS << " alignments: " << (double) (ends - start) / CLOCKS_PER_SEC << " seconds.");
}