Improved Makefile compatibility with bioconda

src/Makefile

@@ -1,48 +1,46 @@
-CXX = g++
-CXXFLAGS = -Wall -Wextra -std=c++17 -O3
-OBJS = globals.o print.o variant.o dist.o bed.o cluster.o phase.o edit.o timer.o
 TARGET = vcfdist
 INSTALLDIR = /usr/local/bin
+OBJS = globals.o print.o variant.o dist.o bed.o cluster.o phase.o edit.o timer.o
 
-LDLIBS = -lz -lhts -lpthread
-# g++ < 9.1 and llvm < 9.0 require linking to lstdc++fs
-# if using g++ >= 9.1 or llvm >= 9.0, please comment the following line
-LDLIBS += -lstdc++fs
+CXX ?= g++
+CXXFLAGS ?= -O3
+CXXFLAGS += -Wall -Wextra -std=c++17
+LDFLAGS += -lz -lhts -lpthread
 
 all: $(TARGET)
 
 install:
 	cp $(TARGET) $(INSTALLDIR)
 
 $(TARGET): $(OBJS) main.cpp
-	$(CXX) $(CXXFLAGS) $(OBJS) -o $(TARGET) main.cpp $(LDLIBS)
+	$(CXX) $(OBJS) -o $(TARGET) main.cpp $(LDFLAGS)
 
 globals.o: globals.cpp globals.h bed.h print.h defs.h timer.h
-	$(CXX) -c $(CXXFLAGS) globals.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) globals.cpp
 
 print.o: print.cpp print.h globals.h phase.h dist.h edit.h defs.h variant.h
-	$(CXX) -c $(CXXFLAGS) print.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) print.cpp
 
 timer.o: timer.cpp timer.h globals.h defs.h
-	$(CXX) -c $(CXXFLAGS) timer.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) timer.cpp
 
 variant.o: variant.cpp variant.h print.h fasta.h defs.h globals.h
-	$(CXX) -c $(CXXFLAGS) variant.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) variant.cpp
 
 dist.o: dist.cpp dist.h fasta.h variant.h cluster.h print.h edit.h defs.h globals.h
-	$(CXX) -c $(CXXFLAGS) dist.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) dist.cpp
 
 bed.o: bed.cpp bed.h print.h defs.h globals.h
-	$(CXX) -c $(CXXFLAGS) bed.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) bed.cpp
 
 edit.o: edit.cpp edit.h defs.h globals.h
-	$(CXX) -c $(CXXFLAGS) edit.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) edit.cpp
 
 cluster.o: cluster.cpp cluster.h variant.h fasta.h globals.h dist.h defs.h
-	$(CXX) -c $(CXXFLAGS) cluster.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) cluster.cpp
 
 phase.o: phase.cpp phase.h cluster.h print.h globals.h defs.h variant.h
-	$(CXX) -c $(CXXFLAGS) phase.cpp
+	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) phase.cpp
 
 clean:
 	rm -f $(TARGET) *.o