<commit_before>#include<vector>
#include<string>

struct overlap
{
	int read1;
	int read2;
	char orientation;
	int ahg;
	int bhg;
};

class Chunk{
	public: 
		int id;
		std::vector< int > members;
};

class OverlapGraph
{
	private:
		std::vector<std::string> reads;
		std::vector<overlap> overlaps;
		std::vector<int> nonContainedReads;
		std::vector< std::vector<overlap> > graph;
		std::vector< std::vector<overlap> > reducedGraph;
		std::vector< Chunk > collapsedReducedGraph;
		void initialize();
		void containedReadRemoval();
		void transitiveEdgeRemoval();
		void uniqueJoinCollapsing();
	public:
		OverlapGraph(std::vector<std::string> reads, std::vector<overlap> overlaps);
		void runUnitigging();
};<commit_msg>expanded interface with private members and methods required to do unique join collapsing algorithm<commit_after>#include<vector>
#include<string>

struct overlap
{
	int read1;
	int read2;
	char orientation;
	int ahg;
	int bhg;
};

class Chunk{
	public: 
		int id;
		std::vector< int > members;
};

class OverlapGraph
{
	private:
		std::vector<std::string> reads;
		std::vector<overlap> overlaps;
		std::vector<int> nonContainedReads;
		std::vector< std::vector<overlap> > graph;
		std::vector< std::vector<overlap> > reducedGraph;
		std::vector< Chunk > collapsedReducedGraph;
		std::vector<int> reducedGraphVertexReferenceCounter;
		void initialize();
		void containedReadRemoval();
		void transitiveEdgeRemoval();
		void uniqueJoinCollapsing();
		void calculateChunks(int chunkStartingVertexId, int requestedChunkId);
		bool vertexAlreadyInChunk(int vertexId);
	public:
		OverlapGraph(std::vector<std::string> reads, std::vector<overlap> overlaps);
		void runUnitigging();
};
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