Makefile: Improve management of dependencies

The library is now built in core, where we have the list of dependencies
(dep.mk). Before dep.mk was in algo/ but the files it was refering to were in
core/. Thus the dep.mk file was useless.

algo/Makefile

 CC=g++
 OPTIM=-O2 
-CFLAGS=-W -Wall $(OPTIM) $(DEBUG) $(CONFIG)
+CXXFLAGS=-W -Wall $(OPTIM) $(DEBUG) $(CONFIG)
 LDFLAGS=-lm
 EXEC=vidjil kmer kmer_count cut count detailed_affect
-SRCCORE=$(wildcard core/*.cpp) $(wildcard core/*.h) 
 MAINCORE=$(wildcard *.cpp)
-OBJCORE=$(SRCCORE:.cpp=.o)
-LIBCORE=core.a
+LIBCORE=core/vidjil.a
 
 BINDIR=..
 
+.PHONY: all core clean forcedep
+
 v: vidjil
 
 ###
@@ -42,39 +42,26 @@ debug:
 	make clean
 	make DEBUG="-ggdb"
 
-$(EXEC): %: %.o $(LIBCORE) 
-	$(CC) -o $(BINDIR)/$@ $^ $(LDFLAGS) $(CFLAGS)
-
-core: $(LIBCORE)
-
-$(LIBCORE): $(OBJCORE)
-	rm -f $(LIBCORE)
-	ar rc $@ $^
-
-%.o: %.cpp %.h core/dynprog.h
-	$(CC) -o $@ -c $< $(CFLAGS)
-
-%.o: %.cpp 
-	$(CC) -o $@ -c $< $(CFLAGS)
+$(EXEC): %: %.o 
+	make -C core
+	$(CC) -o $(BINDIR)/$@ $^ $(LIBCORE) $(LDFLAGS) $(CXXFLAGS)
 
 clean:
-	rm -f core/*.o *.o $(LIBCORE)
+	make -C core $@
 	cd $(BINDIR) ; rm -f $(EXEC)
 	make -C tests $@
 
 forcedep:
-	g++ -M $(SRCCORE) $(MAINCORE) > dep.mk
+	g++ -M $(MAINCORE) > dep.mk
 
 DEP=$(wildcard dep.mk)
 
 ifeq (${DEP},)
-$(shell	g++ -M $(SRCCORE) $(MAINCORE) > dep.mk)
+$(shell	g++ -M $(MAINCORE) > dep.mk)
 endif
 include dep.mk
 
 
-
-
 RELEASE_H = release.h
 RELEASE_SOURCE = $(wildcard src/*.cpp) $(wildcard src/*.h)  $(wildcard src/core/*.cpp) $(wildcard src/core/*.h)  
 RELEASE_FILES = $(RELEASE_SOURCE) src/Makefile germline/get-germline doc/README doc/LICENSE

algo/core/Makefile

+CC=g++
+OPTIM=-O2 
+CXXFLAGS=-W -Wall $(OPTIM)
+SRCCORE=$(wildcard *.cpp)
+OBJCORE=$(SRCCORE:.cpp=.o)
+LIBCORE=vidjil.a
+
+all: $(LIBCORE)
+
+$(LIBCORE): $(OBJCORE)
+	ar rc $@ $^
+
+clean:
+	rm -f $(OBJCORE) $(LIBCORE)
+
+DEP=$(wildcard dep.mk)
+
+ifeq (${DEP},)
+$(shell	g++ -M $(SRCCORE) > dep.mk)
+endif
+include dep.mk

algo/tests/Makefile

 CC=g++
-CFLAGS=-W -Wall -g -O0
+CXXFLAGS=-W -Wall -g -O0
 INCLUDE=-I ..
 LDFLAGS=
 SRC= tests.cpp
 EXEC=$(SRC:.cpp=)
 OTHER_SRC=$(wildcard *.cpp)
-LIB=../core.a
+LIB=../core/vidjil.a
 SHOULD=$(wildcard *.should_get)
 SHOULD_LOG=$(SHOULD:.should_get=.log)
 
@@ -27,16 +27,16 @@ should: core $(SHOULD_LOG)
 	./should-to-tap.sh $<
 
 $(EXEC): % : %.o $(LIB) 
-	$(CC) -o $@ $< $(LIB) $(LDFLAGS) $(CFLAGS)
+	$(CC) -o $@ $< $(LIB) $(LDFLAGS) $(CXXFLAGS)
 
 
 ../core.a: core
 
 core:
-	make OPTIM="-O0 -g" -C .. core.a
+	make OPTIM="-O0 -g" -C ../core 
 
 %.o: %.cpp $(OTHER_SRC)
-	$(CC) -o $@ $(INCLUDE) -c $< $(CFLAGS)
+	$(CC) -o $@ $(INCLUDE) -c $< $(CXXFLAGS)
 
 clean:
 	rm -f *.o $(EXEC) *.tap *.log