Makefile

# Determine the yaha build number
BUILDNUM := 83
# Decide if we are compiling for user mode, or internal lab usage.
# This almost exclusively determines the options available to the user when running YAHA.
# But also controls timing information.
USERMODE := TRUE

# Set up the sub-directory names.
SDIR := src
ODIR := obj
BDIR := bin

# Set up flags depending on mode
ifdef USERMODE
PROG	 := yaha
CCFLAGS  := -Wall -O3 -D COMPILE_USER_MODE -D BUILDNUM=$(BUILDNUM)
else
PROG	 := yaha$(BUILDNUM)
CCFLAGS  := -Wall -Winline -O3 -g -D BUILDNUM=$(BUILDNUM)
endif

# Auto build dependency files.
CCFLAGS  += -MMD -MP

CC	 := gcc
CPP      := g++
CFLAGS	 := $(CCFLAGS) -std=gnu99
CPPFLAGS := $(CCFLAGS)
LDFLAGS  := -pthread

# The list of object files.
OBJfiles := Main.o AlignArgs.o AlignHelpers.o AlignExtFrag.o AlignOutput.o BaseSeq.o Compress.o \
	FileHelpers.o GraphPath.o Index.o Query.o QueryMatch.o QueryState.o SW.o Math.o
# Convert to use the obj dir
OBJS := $(patsubst %,$(ODIR)/%,$(OBJfiles))

# Make everything, all of which is defined below
YAHA: $(ODIR) $(BDIR) $(BDIR)/$(PROG)

# Make the directories
$(ODIR):
	mkdir -p $(ODIR)
$(BDIR):
	mkdir -p $(BDIR)

# Link the program
$(BDIR)/$(PROG): $(OBJS)
	$(CPP) $(LDFLAGS) -o $@ $(OBJS)

# Include the dependencies.
# The actual objects will be built by the below generic rules based on these dependencies.
# The - suppresses warning messages about missing files when building from scratch.
-include $(OBJS:.o=.d)

# Make the object files.
# The built in rules will miss the subdirectories. 
$(ODIR)/%.o: $(SDIR)/%.c
	$(CC) $(CFLAGS) -c $< -o $@

$(ODIR)/%.o: $(SDIR)/%.cpp
	$(CPP) $(CPPFLAGS) -c $< -o $@

.PHONY: clean
clean:
	rm -Rf $(ODIR)
	rm -Rf $(BDIR)