Fix build and some bugs

.gitignore

@@ -0,0 +1,3 @@
+bin
+src/cluster/bin
+src/cluster/meshclust

src/Makefile

@@ -1,7 +1,10 @@
-# CXX = /usr/bin/c++
-CXX ?= g++
+ifeq ($(shell uname), Darwin)
+	CXX = xcrun -sdk macosx clang++
+else
+	CXX ?= g++
+endif
 
-CXXFLAGS =	-O3 -g -fmessage-length=0 -Wall -march=native -std=c++11
+CXXFLAGS = -std=c++11 -pedantic -Wall -Wno-overloaded-virtual -O3 -flto -march=native
 
 #
 # Objects

src/cluster/Makefile

@@ -1,13 +1,19 @@
 TARGET ?= meshclust
 VERSION ?= 1.2.0
-CXX ?= g++
+
+ifeq ($(shell uname), Darwin)
+	CXX = xcrun -sdk macosx clang++
+else
+	CXX ?= g++
+endif
+
 ifeq ($(debug),yes)
-	CXXFLAGS += -ggdb  -fopenmp
+	CXXFLAGS += -ggdb
 else
-	CXXFLAGS += -fopenmp -O3 -march=native -g
+	CXXFLAGS += -O3 -flto -march=native -DNDEBUG=1
 endif
-CXXFLAGS += -std=c++11 -DVERSION=\"$(VERSION)\"
-LDFLAGS += -lm
+CXXFLAGS += -std=c++11 -pedantic -Wall -Wno-overloaded-virtual -Wno-unused-variable -DVERSION=\"$(VERSION)\"
+LDFLAGS += -flto -lm
 
 SOURCES := $(shell find ./src -name '*.cpp')
 OBJECTS = $(SOURCES:%.cpp=bin/%.o)

src/cluster/src/ClusterFactory.h

@@ -22,7 +22,7 @@
 template<class T>
 class ClusterFactory {
 public:
-	ClusterFactory(int k_len, int npp=std::numeric_limits<int>::max()) : k(k_len), num_per_partition(npp) {}
+	ClusterFactory(int k_len, int npp=std::numeric_limits<int>::max()) : num_per_partition(npp), k(k_len) {}
 	std::vector<Point<T>*> build_points(vector<string> files, std::function<Point<T>*(ChromosomeOneDigit*)> get_point);
         Point<T>* get_histogram(ChromosomeOneDigit *chrom);
 	Point<T>* get_divergence_point(ChromosomeOneDigit *chrom);

src/cluster/src/Runner.cpp

@@ -321,21 +321,13 @@ void test()
 template<class T>
 int Runner::do_run()
 {
-	using pvec = vector<Point<T> *>;
-	using pmap = map<Point<T>*, pvec*>;
-
 	ClusterFactory<T> factory(k);
-	// for (auto f : files) {
-	// 	cout << "File: " << f << endl;
-	// }
+
 	auto points = factory.build_points(files, [&](nonltr::ChromosomeOneDigit *p){ return factory.get_divergence_point(p); });
 	Trainer<T> tr(points, sample_size, largest_count, similarity, pivots, global_mat, global_sigma, global_epsilon, align ? 0 : k);
 	tr.train();
 	vector<uint64_t> lengths;
 	for (Point<T>* p : points) {
-		// if (!align) {
-		// 	p->set_data_str("");
-		// }
 		lengths.push_back(p->get_length());
 	}
 	// Initializing BVec
@@ -348,28 +340,6 @@ int Runner::do_run()
 		bv.insert(p);
 	}
 	bv.insert_finalize();
-//	cout << "bv size: " << bv.report() << endl;
-	// Point<T>* mid = points[points.size()/2];
-	// auto rng = bv.get_range(mid->get_length() * 0.99,
-	// 			mid->get_length() / 0.99);
-	// auto begin = bv.iter(rng.first);
-	// auto end = bv.iter(rng.second);
-	// size_t before = bv.report();
-	// for (int i = 0; i < 1; i++) {
-	// 		bool is_min = false;
-	// 		Point<T>* p = tr.get_close(mid, begin, end, is_min);
-	// 		size_t after = bv.report();
-	// 		if (is_min) {
-	// 			string expr = (after + 1 == before) ? "true" : "false";
-	// 			if (expr == "false") {
-	// 				throw expr;
-	// 			}
-	// 			cout << expr << endl;
-	// 			cout << "is min" << endl;
-	// 		} else {
-	// 			cout << "is not min" << endl;
-	// 		}
-	// }
 	factory.MS(bv, bandwidth, similarity, tr, output, iterations, delta);
 	return 0;
 }

src/cluster/src/SingleFeature.h

@@ -8,9 +8,9 @@ template<class T>
 class SingleFeature {
 public:
 	SingleFeature(std::function<double(Point<T>*, Point<T>*)> f, bool is_sim_=true)
-		: raw(f), is_sim(is_sim_), min_set(false), max_set(false) {}
+		: raw(f), is_sim(is_sim_), max_set(false), min_set(false) {}
 	SingleFeature(std::function<double(Point<T>*, Point<T>*, const vector<int>&, const vector<int>&)> f, vector<int> rrv, vector<int> rrc, bool is_sim_=true)
-		: rraw(f), is_sim(is_sim_), min_set(false), max_set(false), rv(rrv), rc(rrc) {}
+		: rraw(f), rv(rrv), rc(rrc), is_sim(is_sim_), max_set(false), min_set(false) {}
 	void normalize(const vector<pair<Point<T>*,Point<T>*> > &pairs);
 	double operator()(Point<T>*, Point<T>*) const;
 	double min, max;

src/cluster/src/Trainer.h

@@ -12,7 +12,7 @@
 template<class T>
 class Trainer {
 public:
-	Trainer(std::vector<Point<T>*> v, size_t num_points, int largest_count, double cutoff_, size_t max_pts_from_one_, double (&matrix)[4][4], double sig, double eps, int ksize) : points(v), n_points(num_points), cutoff(cutoff_), max_pts_from_one(max_pts_from_one_), k(ksize) {
+	Trainer(std::vector<Point<T>*> v, size_t num_points, int largest_count, double cutoff_, size_t max_pts_from_one_, double (&matrix)[4][4], double sig, double eps, int ksize) : points(v), n_points(num_points), max_pts_from_one(max_pts_from_one_), cutoff(cutoff_), k(ksize) {
 		init(matrix, sig, eps);
 		uintmax_t size = 1000 * 1000 * 10;
 		log_table = new double[size];

src/nonltr/EnrichmentMarkovView.cpp

@@ -12,7 +12,7 @@ namespace nonltr {
  */
 template<class I, class V>
 EnrichmentMarkovView<I, V>::EnrichmentMarkovView(int k, int order, int m) :
-		minObs(m), factor(10000.00), KmerHashTable<I, V>(k) {
+    KmerHashTable<I, V>(k), minObs(m), factor(10000.00) {
 	initialize(order);
 }
 

src/utility/AffineId.h

@@ -22,22 +22,14 @@ class AffineId {
 
 	int len1;
 	int len2;
-	//int lenTotal;
 	int lenCS;
 	int lenPath;
-	int * m; // Middle level
-	//int * l; // Lower level
-	int * u; // Upper level
-
-	// const int MATCH = 4; // Score of a match
-	// const int MIS = -4; // Score of a mismatch
-	// const int OPEN = -2; // Score of a gap opening
-	// const int EXT = -1; // Score of a gap extension
 
 	const int MATCH = 1;
 	const int MIS = -1;
 	const int OPEN = -2;
 	const int EXT = -1;
+
 	void align();
 
 public:

src/utility/ILocation.h

@@ -16,6 +16,7 @@ namespace utility {
 
 class ILocation {
 public:
+    inline virtual ~ILocation() {}
 	virtual int getEnd() const = 0;
 	virtual int getStart() const = 0;
 	virtual void setEnd(int) = 0;