Add functionality to create full errorless graph (code to be uncommen…

…t before building).
swacisko · Nov 21, 2020 · 96f3f7d · 96f3f7d
1 parent ab3f43b
commit 96f3f7d
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Showing 2 changed files with 3 additions and 30 deletions.
diff --git a/src/GraphCreators/GraphCreatorPrefSuf.cpp b/src/GraphCreators/GraphCreatorPrefSuf.cpp
@@ -383,6 +383,9 @@ void GraphCreatorPrefSuf::nextPrefSufIterationJobAddEdges(int a, int b, int thre
                 if (prefId != suffId && prefixKmers[prefId] == suffHash &&
                     prefixKmersAdditional[prefId] == suffHashAdditional) {
 
+                    // uncomment the following section to create full errorless graph
+//                    {G->lockNode(prefId); G->pushDirectedEdge(prefId, suffId, offset);  G->unlockNode(prefId); continue;}
+
                     if (GATHER_STATISTICS) goodPrefSufChecks++;
 
                     if (Read::calculateReadOverlap((*reads)[suffId], (*reads)[prefId], offset) < currentPrefSufLength)

diff --git a/src/main.cpp b/src/main.cpp
@@ -57,36 +57,6 @@ class MemTestClass {
 int main(int argc, char **argv) {
     initilizeStaticData();
 
-    const bool TESTING = false;
-    if (TESTING) { // just for testing/debugging in IDE
-        Params::inStreamFilePath1 = "/home/sylwester/Documents/PhD/ECBiG/GenomeAlignment/RealSequences/lux2_musket_k21_1.fastq";
-        Params::inStreamFilePath2 = "/home/sylwester/Documents/PhD/ECBiG/GenomeAlignment/RealSequences/lux2_musket_k21_2.fastq";
-        Params::outStreamFileName = "alga_test_test";
-        Params::INPUT_FILE_TYPE = Params::FASTQ;
-
-        Params::SERIALIZE_GRAPH_BEFORE_SIMPLIFIER = 1;
-        Params::SERIALIZE_GRAPH_AFTER_SIMPLIFIER = 1;
-        Params::DESERIALIZE_GRAPH = 1;
-
-        Params::THREADS = 6;
-    } else {
-        DEBUG(sizeof(MemTestClass));
-        DEBUG(sizeof(std::mutex));
-        DEBUG(sizeof(VILPII));
-        DEBUG(sizeof(list<pair<int, int>>));
-        DEBUG(sizeof(PII));
-        DEBUG(sizeof(vector<int>));
-        DEBUG(sizeof(PII[3]));
-        DEBUG(sizeof(pair<unsigned, char>));
-        DEBUG(sizeof(Kmer));
-        DEBUG(sizeof(KmerGCPS));
-        DEBUG(sizeof(pair<short, char>));
-        DEBUG(sizeof(Read));
-        DEBUG(sizeof(Bitset));
-        DEBUG(sizeof(Contig));
-        DEBUG(sizeof(vector<pair<Read *, int> >));
-//        exit(1);
-    }
 
     ios_base::sync_with_stdio(0);
     cin.tie(NULL);