From f18bd36bbc601d8b6911ddee94ac4109d36e088f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vladimir=20Nikoli=C4=87?= <vladimir.nik94@gmail.com>
Date: Fri, 24 Aug 2018 19:07:09 +0200
Subject: [PATCH] Parallelize gap sealing (#249)

---
 Sealer/sealer.cc | 47 +++++++++++++++++++++++++++++------------------
 1 file changed, 29 insertions(+), 18 deletions(-)

diff --git a/Sealer/sealer.cc b/Sealer/sealer.cc
index 288492d95..a4c827f4b 100644
--- a/Sealer/sealer.cc
+++ b/Sealer/sealer.cc
@@ -420,8 +420,8 @@ template <typename Graph>
 string merge(const Graph& g,
 	unsigned k,
 	const Gap& gap,
-	FastaRecord &read1,
-	FastaRecord &read2,
+	const FastaRecord &read1,
+	const FastaRecord &read2,
 	const ConnectPairsParams& params,
 	Counters& g_count,
 	ofstream& traceStream)
@@ -583,7 +583,6 @@ void kRun(const ConnectPairsParams& params,
 	map<FastaRecord, map<FastaRecord, Gap> >::iterator read1_it;
 	map<FastaRecord, Gap>::iterator read2_it;
 	unsigned uniqueGapsClosed = 0;
-	bool success;
 
 	Counters g_count;
 	g_count.noStartOrGoalKmer = 0;
@@ -603,38 +602,50 @@ void kRun(const ConnectPairsParams& params,
 
 	printLog(logStream, "Flanks inserted into k run = " + IntToString(flanks.size()) + "\n");
 
-	for (read1_it = flanks.begin(); read1_it != flanks.end();) {
-		success = false;
+	int counter = 0;
+	vector<map<FastaRecord, map<FastaRecord, Gap> >::iterator> flanks_closed;
+#pragma omp parallel private(read1_it, read2_it) firstprivate(counter)
+	for (read1_it = flanks.begin(); read1_it != flanks.end(); ++read1_it) {
 		FastaRecord read1 = read1_it->first;
-		for (read2_it = flanks[read1].begin(); read2_it != flanks[read1].end(); read2_it++) {
+		bool success = false;
+		for (read2_it = flanks[read1].begin(); read2_it != flanks[read1].end(); ++read2_it, ++counter) {
+#if _OPENMP
+			if (counter % omp_get_num_threads() != omp_get_thread_num())
+				continue;
+#endif
 			FastaRecord read2 = read2_it->first;
 
 			int startposition = read2_it->second.gapStart();
 			string tempSeq = merge(g, k, read2_it->second, read1, read2, params, g_count, traceStream);
 			if (!tempSeq.empty()) {
 				success = true;
+#pragma omp critical (allmerged)
 				allmerged[read1.id.substr(0,read1.id.length()-2)][startposition]
 					= ClosedGap(read2_it->second, tempSeq);
-//#pragma omp atomic
-				gapsclosed++;
-//#pragma omp atomic
-				uniqueGapsClosed++;
-				if (gapsclosed % 100 == 0)
+#pragma omp atomic
+				++uniqueGapsClosed;
+#pragma omp critical (gapsclosed)
+				if (++gapsclosed % 100 == 0)
 					printLog(logStream, IntToString(gapsclosed) + " gaps closed so far\n");
 
-				if (!opt::gapfilePath.empty()) {
+				if (!opt::gapfilePath.empty())
+#pragma omp critical (gapStream)
 					gapStream << ">" << read1.id.substr(0,read1.id.length()-2)
 						  << "_" << read2_it->second.gapStart() << "-" << read2_it->second.gapEnd()
-						  << " LN:i:" << tempSeq.length() << '\n';
-					gapStream << tempSeq << '\n';
-				}
+						  << " LN:i:" << tempSeq.length() << '\n'
+						  << tempSeq << '\n';
 			}
 		}
 		if (success) {
-			flanks.erase(read1_it++);
+#pragma omp critical (flanks_closed)
+			flanks_closed.push_back(read1_it);
 		}
-		else
-			read1_it++;
+	}
+
+	for (vector<map<FastaRecord, map<FastaRecord, Gap> >::iterator>::iterator it = flanks_closed.begin();
+			it != flanks_closed.end(); ++it) {
+		if (flanks.count((*it)->first) > 0)
+		    flanks.erase(*it);
 	}
 
 	printLog(logStream, IntToString(uniqueGapsClosed) + " unique gaps closed for k" + IntToString(k) + "\n");