Makefile: extract BamTools' API creating to a separate target.

Ensures the BamTools' API files are created first (before any compilation occurs).
This allows parallel builds with "make -j 4".

Makefile

@@ -101,6 +101,14 @@ print_banner:
 $(OBJ_DIR) $(BIN_DIR):
 	@mkdir -p $@
 
+
+# One special case: All (or almost all) programs requires the BamTools API files to be created first.
+.PHONY: bamtools_api
+bamtools_api:
+	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
+$(UTIL_SUBDIRS) $(SUBDIRS): bamtools_api
+
+
 # even though these are real directories, treat them as phony targets, forcing to always go in them are re-make.
 # a future improvement would be the check for the compiled object, and rebuild only if the source code is newer.
 .PHONY: $(UTIL_SUBDIRS) $(SUBDIRS)
@@ -109,13 +117,9 @@ $(UTIL_SUBDIRS) $(SUBDIRS): $(OBJ_DIR) $(BIN_DIR)
 	@$(MAKE) --no-print-directory --directory=$@
 
 clean:
-	@echo "Cleaning up."	
+	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) clean_api
+	@echo " * Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-	@rm -Rf $(BT_ROOT)/lib
-	@rm -f $(BT_ROOT)/src/api/*.o
-	@rm -f $(BT_ROOT)/src/api/internal/*/*.o
-	@rm -Rf $(BT_ROOT)/include
-
 .PHONY: clean
 
 test: all

src/utils/BamTools/Makefile

@@ -55,15 +55,6 @@ all: $(LIBRARY)
 .PHONY: all
 
 $(LIBRARY): $(OBJECTS)
-	[ -d lib ] || mkdir -p lib
-	[ -d include ] || mkdir -p include
-	[ -d include/api ] || mkdir -p include/api
-	[ -d include/shared ] || mkdir -p include/shared
-
-	@cp src/api/*.h include/api
-	@cp src/shared/*.h include/shared
-
-
 	@echo " * linking $(LIBRARY)"
 	ar cr $@ $^
 	-ranlib $@
@@ -71,3 +62,18 @@ $(LIBRARY): $(OBJECTS)
 $(OBJECTS): $(SOURCES)
 	@echo " * compiling" $(*F).cpp
 	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
+
+.PHONY: api
+api:
+	@echo " * Creating BamTools API"
+	@mkdir -p lib
+	@mkdir -p include
+	@mkdir -p include/api
+	@mkdir -p include/shared
+	@cp src/api/*.h include/api
+	@cp src/shared/*.h include/shared
+
+.PHONY: clean_api
+clean_api:
+	@echo " * Cleaning-up BamTools API"
+	@rm -rf ./lib ./src/api/*.o ./src/api/internal/*/*.o ./include