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# 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
CFLAGS ?= -Wall -O3 -D COMPILE_USER_MODE
CXXFLAGS ?= -Wall -O3 -D COMPILE_USER_MODE
else
PROG := yaha$(BUILDNUM)
CFLAGS ?= -Wall -Winline -O3 -g
CXXFLAGS ?= -Wall -Winline -O3 -g
endif
CFLAGS += -D BUILDNUM=$(BUILDNUM)
# Auto build dependency files.
CFLAGS += -MMD -MP
CC ?= gcc
CXX ?= g++
LDFLAGS += -pthread
CXXFLAGS += -fpermissive
# 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)
$(CXX) $(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) $(CPPFLAGS) -c $< -o $@
$(ODIR)/%.o: $(SDIR)/%.cpp
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c $< -o $@
.PHONY: clean
clean:
rm -Rf $(ODIR)
rm -Rf $(BDIR)
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