void H5Writer::init(const std::string& fname, int num_bootstrap, uint compression,
size_t index_version, const std::string& shell_call,
const std::string& start_time)
{
primed_ = true;
num_bootstrap_ = num_bootstrap;
compression_ = compression;
file_id_ = H5Fcreate(fname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
root_ = H5Gopen(file_id_, "/", H5P_DEFAULT);
aux_ = H5Gcreate(file_id_, "/aux", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (num_bootstrap_ > 0) {
bs_ = H5Gcreate(file_id_, "/bootstrap", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
std::vector<int> n_bs {num_bootstrap};
vector_to_h5(n_bs, aux_, "num_bootstrap", false, compression_);
// info about run
std::vector<std::string> kal_version{ KALLISTO_VERSION };
vector_to_h5(kal_version, aux_, "kallisto_version", true, compression_);
std::vector<int> idx_version{ static_cast<int>(index_version) };
vector_to_h5(idx_version, aux_, "index_version", false, compression_);
std::vector<std::string> call{ shell_call };
vector_to_h5(call, aux_, "call", true, compression_);
std::vector<std::string> s_time{ start_time };
vector_to_h5(s_time, aux_, "start_time", true, compression_);
}
void H5Writer::write_main(const EMAlgorithm& em,
const std::vector<std::string>& targ_ids,
const std::vector<int>& lengths) {
vector_to_h5(em.alpha_, root_, "est_counts", false, compression_);
vector_to_h5(targ_ids, aux_, "ids", true, compression_);
vector_to_h5(em.eff_lens_, aux_, "eff_lengths", false, compression_);
vector_to_h5(lengths, aux_, "lengths", false, compression_);
}
void H5Writer::write_bootstrap(const EMAlgorithm& em, int bs_id) {
std::string bs_id_str("bs" + std::to_string( bs_id ));
vector_to_h5(em.alpha_, bs_, bs_id_str.c_str(), false, compression_);
}
