ReadStreamStat ToBinaryForThread(io::ReadStream<Read>& stream, size_t buf_size,
size_t thread_num, LibraryOrientation orientation) {
ReadBinaryWriter<Read> read_writer(orientation);
size_t buffer_reads = buf_size / (sizeof (Read) * 4);
std::vector<Read> buf(buffer_reads);
ReadStreamStat stat;
file_ds_[thread_num]->seekp(0);
stat.write(*file_ds_[thread_num]);
size_t current = 0;
while (!stream.eof()) {
Read& r = buf[current];
stream >> r;
stat.increase(r);
++current;
if (stat.read_count_ % buffer_reads == 0) {
FlushBuffer(buf, read_writer, *file_ds_[thread_num]);
current = 0;
}
}
buf.resize(current);
FlushBuffer(buf, read_writer, *file_ds_[thread_num]);
file_ds_[thread_num]->seekp(0);
stat.write(*file_ds_[thread_num]);
return stat;
}
ReadStreamStat get_stat() const {
ReadStreamStat stat;
for (size_t i = 0; i < readers_.size(); ++i) {
stat.merge(readers_[i]->get_stat());
}
return stat;
}
ReadStreamStat ToBinary(io::ReadStream<Read>& stream, size_t buf_size,
LibraryOrientation orientation) {
ReadBinaryWriter<Read> read_writer(orientation);
size_t buffer_reads = buf_size / (sizeof (Read) * 4);
size_t reads_to_flush = buffer_reads * file_num_;
std::vector< std::vector<Read> > buf(file_num_, std::vector<Read>(buffer_reads) );
std::vector< ReadStreamStat > read_stats(file_num_);
std::vector< size_t > current_buf_sizes(file_num_, 0);
size_t read_count = 0;
for (size_t i = 0; i < file_num_; ++i) {
file_ds_[i]->seekp(0);
read_stats[i].write(*file_ds_[i]);
}
size_t buf_index;
while (!stream.eof()) {
buf_index = read_count % file_num_;
Read& r = buf[buf_index][current_buf_sizes[buf_index]];
stream >> r;
read_stats[buf_index].increase(r);
++current_buf_sizes[buf_index];
VERBOSE_POWER(++read_count, " reads processed");
if (read_count % reads_to_flush == 0) {
for (size_t i = 0; i < file_num_; ++i) {
FlushBuffer(buf[i], read_writer, *file_ds_[i]);
current_buf_sizes[i] = 0;
}
}
}
ReadStreamStat result;
for (size_t i = 0; i < file_num_; ++i) {
buf[i].resize(current_buf_sizes[i]);
FlushBuffer(buf[i], read_writer, *file_ds_[i]);
file_ds_[i]->seekp(0);
read_stats[i].write(*file_ds_[i]);
result.merge(read_stats[i]);
}
INFO(read_count << " reads written");
return result;
}
