void sorted_dumper<storage_t,atomic_t>::_dump() {
std::ofstream _out;
assert(dump_mutex.try_lock());
if(one_file) {
_out.open(file_prefix.c_str());
} else {
open_next_file(file_prefix.c_str(), &file_index, _out);
}
out = &_out;
unique = distinct = total = max_count = 0;
tr.reset();
thread_info[0].writer.write_header(out);
exec_join(threads);
ary->zero_blocks(0, nb_blocks); // zero out last group of blocks
update_stats();
_out.close();
dump_mutex.unlock();
}
void do_it()
{
// Setup output stream for jellyfish initialisation
std::ostream* out_stream = args->verbose ? &cerr : (std::ostream*)0;
// Load the jellyfish hash for sequential access
hash = jfh->loadHash(true, out_stream);
// Create matrix of appropriate size (adds 1 to cvg bins to account for 0)
gcp_mx = new ThreadedSparseMatrix<uint64_t>(hash->get_mer_len(), args->cvg_bins + 1, args->threads_arg);
// Process batch with worker threads
// Process each sequence is processed in a different thread.
// In each thread lookup each K-mer in the hash
exec_join(args->threads_arg);
// Merge the contamination matrix
gcp_mx->mergeThreadedMatricies();
}
void do_it()
{
if (args->verbose)
{
cerr << "Loading hash..." << endl;
}
std::ostream* out_stream = args->verbose ? &cerr : (std::ostream*)0;
// Load the hashes
hash = jfh->loadHash(true, out_stream);
if (args->verbose)
cerr << endl
<< "Hash loaded successfully." << endl
<< "Starting threads...";
exec_join(args->threads);
if (args->verbose)
cerr << "done." << endl;
}
