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/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent No laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikal Salson mikael.salson@lifl.fr
Hlne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/**
* FILE: readsqueue.hpp
* Created: Nov 06, 2017 Mon
*/
#pragma once
#include <string>
#include <thread>
#include <mutex>
#include <condition_variable>
#include <sstream>
#include <atomic>
#include "common.hpp"
#include "read.hpp"
#if defined(CONCURRENTQUEUE)
# include <concurrentqueue/moodycamel/concurrentqueue.h>
#elif defined(LOCKQUEUE)
# include <queue>
#endif
/**
* Queue for Reads' records. Concurrently accessed by the Reader (producer) and the Processors (consumers)
*/
class ReadsQueue
{
public:
std::string id;
size_t capacity; // max size of the queue
unsigned reads_tot; // total number of reads expected to be pushed/popped
std::atomic_uint num_pushed;
unsigned count_to_print;
unsigned max_print_count;
std::atomic_uint num_popped;
std::atomic_uint num_poppers;
#if defined(CONCURRENTQUEUE)
moodycamel::ConcurrentQueue<std::string> queue; // lockless queue
#elif defined(LOCKQUEUE)
std::queue<Read> recs; // shared: Reader & Processors, Writer & Processors
std::mutex qlock; // lock for push/pop on queue
std::condition_variable cvQueue;
#endif
public:
ReadsQueue(std::string id = "", std::size_t capacity = 100, std::size_t num_reads_tot = 0, std::size_t poppers = 0)
:
id(id),
capacity(capacity),
reads_tot(num_reads_tot),
num_pushed(0),
count_to_print(0),
max_print_count(reads_tot/20),
num_popped(0),
num_poppers(poppers)
#ifdef CONCURRENTQUEUE
,
queue(capacity) // set initial capacity
#endif
{
INFO("created Reads queue with capacity [", capacity, "] Total reads to process: ", num_reads_tot);
}
//~ReadsQueue()
/**
* Synchronized. Blocks until queue has capacity for more reads
* pushing stops automatically upon EOF which sets is_done_push = true
*/
bool push(const std::string& rec)
{
bool ret = false;
#if defined(CONCURRENTQUEUE)
while (!(ret = queue.try_enqueue(rec))) {
std::this_thread::sleep_for(std::chrono::nanoseconds(5));
}
if (ret) {
num_pushed.fetch_add(1, std::memory_order_relaxed);
++count_to_print;
}
if (count_to_print == max_print_count)
{
INFO_MEM("Thread [", std::this_thread::get_id(), "] Pushed another: ", max_print_count, ". Queue size: ", queue.size_approx());
count_to_print = 0;
}
if (reads_tot == num_pushed.load(std::memory_order_relaxed))
{
INFO("Thread [" , std::this_thread::get_id(), "] done Push reads total: ", reads_tot, ". Queue size: ", queue.size_approx());
}
#elif defined(LOCKQUEUE)
std::unique_lock<std::mutex> lmq(qlock);
cvQueue.wait(lmq, [this] { return recs.size() < capacity; });
recs.push(std::move(rec));
cvQueue.notify_one();
#endif
return ret;
}
// synchronized
// return false when is_done_push == true && num_pushed == num_popped
bool pop(std::string& rec)
{
bool ret = false;
//unsigned num_pop_tries = 0;
#if defined(CONCURRENTQUEUE)
for (; !(ret = queue.try_dequeue(rec)); ) {
std::this_thread::sleep_for(std::chrono::nanoseconds(1));
// acquire
// num_pushed.load(std::memory_order_relaxed) == reads_tot && queue.size_approx() == 0
if (num_popped.load(std::memory_order_relaxed) == reads_tot) {
break;
}
//INFO("Thread [", std::this_thread::get_id(), "] Queue size: ", queue.size_approx());
//else if (num_pop_tries > 1000) {
// INFO("Thread [", std::this_thread::get_id(), "] done after max Pop tries: ", num_pop_tries, ". Queue size: ", queue.size_approx());
// break;
//}
}
if (ret)
num_popped.fetch_add(1, std::memory_order_relaxed); // ++num_out store release
#elif defined(LOCKQUEUE)
std::unique_lock<std::mutex> lmq(qlock);
cvQueue.wait(lmq, [this] { return (pushers.load() == 0 && recs.empty()) || !recs.empty(); }); // if False - keep waiting, else - proceed.
if (!recs.empty())
{
rec = recs.front();
recs.pop();
++numPopped;
if (numPopped.load() % 100000 == 0)
{
std::stringstream ss;
ss << STAMP << id << " Popped read number: " << rec.read_num << "\r";
std::cout << ss.str();
}
}
cvQueue.notify_one();
#endif
return ret;
}
void reset() {
num_pushed = 0;
num_popped = 0;
}
}; // ~class ReadsQueue
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