From 15f7d8e7a7ccc982a3d3d03a71e06f708c504cae Mon Sep 17 00:00:00 2001
From: AlphaSquad <afritz@helmholtz-hzi.de>
Date: Wed, 7 Apr 2021 14:25:02 +0200
Subject: [PATCH] Fixed debug and protected the privates

---
 UnitigGraph.cpp | 2 +-
 UnitigGraph.h   | 4 ++--
 main.cpp        | 3 +--
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/UnitigGraph.cpp b/UnitigGraph.cpp
index 9fce7aa..af4daed 100644
--- a/UnitigGraph.cpp
+++ b/UnitigGraph.cpp
@@ -21,7 +21,7 @@ UnitigGraph::UnitigGraph() : cc_(1)
 // constructor of the so-called UnitigGraph
 // unifies all simple paths in the deBruijnGraph to a single source->sink path
 // all remaining nodes have either indegree != outdegree or indegree == outdegree > 1
-UnitigGraph::UnitigGraph(deBruijnGraph& dbg, std::string p, std::string logf, float error_rate, unsigned int strict, unsigned int filter, int thresh, bool l=false) : cc_(1), logfile_(logf), filter_length_(filter), thresh_(thresh), long_(l), true_(false)
+UnitigGraph::UnitigGraph(deBruijnGraph& dbg, std::string p, std::string logf, float error_rate, unsigned int strict, unsigned int filter, int thresh, bool l, bool debug) : cc_(1), logfile_(logf), filter_length_(filter), thresh_(thresh), long_(l), true_(false), debug_(debug)
 {
     std::ofstream log;
     log.open(logfile_, std::ofstream::out | std::ofstream::app);
diff --git a/UnitigGraph.h b/UnitigGraph.h
index a45c0b0..88ee889 100644
--- a/UnitigGraph.h
+++ b/UnitigGraph.h
@@ -100,7 +100,7 @@ typedef std::vector<UVertex> Connected_Component; // to distinguish from regular
 class UnitigGraph {
 public:
 	// create a UnitigGraph from a dBg and its unbalanced vertices
-	UnitigGraph(deBruijnGraph&, std::string, std::string, float, unsigned int, unsigned int, int, bool); 
+	UnitigGraph(deBruijnGraph&, std::string, std::string, float, unsigned int, unsigned int, int, bool, bool); 
 	UnitigGraph(); // debug
     ~UnitigGraph();
     void set_debug();
@@ -109,7 +109,6 @@ class UnitigGraph {
     void printGraph(std::ostream&, unsigned int cc);
     void dijkstra(UEdge seed, bool residual, bool local, unsigned int cc);
     std::vector<UEdge> greedy(UEdge seed, bool residual, bool local, unsigned int cc);
-    bool debug_;
 private:
 	void connectUnbalanced(Vertex*, unsigned int*, std::string, deBruijnGraph&, float, float threshold);
 	std::vector<std::pair<Vertex*,std::string> > addNeighbours(std::string& curr, const std::vector<char>&, const std::vector<char>&, deBruijnGraph&, unsigned int*, UVertex&, float threshold, float error);
@@ -164,6 +163,7 @@ class UnitigGraph {
     int thresh_;
     bool long_;
     bool true_;
+    bool debug_;
 	
 };
 
diff --git a/main.cpp b/main.cpp
index a45bc6e..3675d0e 100644
--- a/main.cpp
+++ b/main.cpp
@@ -87,8 +87,7 @@ int main (int argc, char* argv[])
     logfile << "Building deBruijnGraph took " << (clock() - t)/1000000. << " seconds." << std::endl;
     logfile.close();
     t = clock();
-    UnitigGraph ug = UnitigGraph(*dbg, cov, log, e, strict, filter, thresh, l); //argv[2] is k
-    ug.debug_ = debug;
+    UnitigGraph ug = UnitigGraph(*dbg, cov, log, e, strict, filter, thresh, l, debug); //argv[2] is k
     delete dbg;
     if (true_flow)
     {