Function loadFile

Bloom/Bloom.h:78–118

	/** Load a sequence file into a bloom filter */
	template <typename BF>
	inline static void loadFile(BF& bloomFilter, unsigned k, const std::string& path,
			bool verbose = false, size_t taskIOBufferSize = 100000)
	{
		assert(!path.empty());
		if (verbose)
			std::cerr << "Reading `" << path << "'...\n";
		FastaReader in(path.c_str(), FastaReader::FOLD_CASE);
		uint64_t count = 0;
#pragma omp parallel
		for (std::vector<std::string> buffer(taskIOBufferSize);;) {
			buffer.clear();
			size_t bufferSize = 0;
			bool good = true;
#pragma omp critical(in)
			for (; good && bufferSize < taskIOBufferSize;) {
				std::string seq;
				good = in >> seq;
				if (good) {
					buffer.push_back(seq);
					bufferSize += seq.length();
				}
			}
			if (buffer.size() == 0)
				break;
			for (size_t j = 0; j < buffer.size(); j++) {
				loadSeq(bloomFilter, k, buffer.at(j));
				if (verbose)
#pragma omp critical(cerr)
				{
					count++;
					if (count % LOAD_PROGRESS_STEP == 0)
						std::cerr << "Loaded " << count << " reads into bloom filter\n";
				}
			}
		}
		assert(in.eof());
		if (verbose) {
			std::cerr << "Loaded " << count << " reads from `"
				<< path << "` into bloom filter\n";
		}
	}

	/** Load a sequence (string) into a bloom filter */
	template <typename BF>