/// Size is the number of buffers to keep around. It should be
/// larger than the number of thread expected to read from this
/// class. nb_sequences is the number of sequences to read into a
/// buffer. 'begin' and 'end' are iterators to a range of istream.
whole_sequence_parser(uint32_t size, uint32_t nb_sequences,
uint32_t max_producers, StreamIterator& streams) :
super(max_producers, size),
streams_(max_producers),
streams_iterator_(streams)
{
for(auto it = super::element_begin(); it != super::element_end(); ++it) {
it->nb_filled = 0;
it->data.resize(nb_sequences);
}
for(uint32_t i = 0; i < max_producers; ++i) {
streams_.init(i);
open_next_file(streams_[i]);
}
}
/// Max_producers is the maximum number of concurrent threads than
/// can produce data simultaneously. Size is the number of buffer to
/// keep around. It should be larger than the number of thread
/// expected to read from this class. buf_size is the size of each
/// buffer. A StreamIterator is expected to have a next() method,
/// which is thread safe, and which returns (move) a
/// std::unique<std::istream> object.
mer_overlap_sequence_parser(uint16_t mer_len, uint32_t max_producers, uint32_t size, size_t buf_size,
StreamIterator& streams) :
super(max_producers, size),
mer_len_(mer_len),
buf_size_(buf_size),
buffer(new char[size * buf_size]),
seam_buffer(new char[max_producers * (mer_len - 1)]),
streams_(max_producers),
streams_iterator_(streams),
files_read_(0), reads_read_(0)
{
for(sequence_ptr* it = super::element_begin(); it != super::element_end(); ++it)
it->start = it->end = buffer + (it - super::element_begin()) * buf_size;
for(uint32_t i = 0; i < max_producers; ++i) {
streams_.init(i);
streams_[i].seam = seam_buffer + i * (mer_len - 1);
open_next_file(streams_[i]);
}
}