Commit 86bce5cb authored by arq5x's avatar arq5x
Browse files

t push origin masterMerge branch 'wookietreiber-wip-issue-206'

parents b1e3d8de 2d7b5503
......@@ -134,8 +134,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
@echo "- Building main bedtools binary."
@$(CXX) $(CXXFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
@$(CXX) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
@echo "done."
@echo "- Creating executables for old CLI."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -24,7 +24,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
......
......@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -51,7 +51,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -25,7 +25,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/ToolBase/ \
-I$(TOOL_DIR)/intersectFile/
# ----------------------------------
# define our source and object files
......@@ -41,7 +41,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
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