void ExternalAligner::align_seqs_impl(Strings& seqs) const {
std::string input = tmp_file();
ASSERT_FALSE(input.empty());
std::string output = tmp_file();
ASSERT_FALSE(output.empty());
{
boost::shared_ptr<std::ostream> file = name_to_ostream(input);
std::ostream& out = *file;
for (int i = 0; i < seqs.size(); i++) {
write_fasta(out, TO_S(i), "", seqs[i], 60);
}
}
align_file(input, output);
Strings rows;
read_alignment(rows, output);
ASSERT_EQ(rows.size(), seqs.size());
seqs.swap(rows);
if (!go("NPGE_DEBUG").as<bool>()) {
remove_file(input);
remove_file(output);
}
}
