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Makefile
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Makefile
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CPP = g++
#CPP = g++ -pg
FLAGS = -O9 -Wall
#FLAGS = -g -O0 -Wall -DNDEBUG
OBJS = ./src/basics/io.o \
./src/basics/buffer.o\
./src/basics/BitSequenceRG.o\
./src/coders/Coder.o \
./src/coders/THuff.o \
./src/coders/Huffman.o \
./src/cqual/CQualPBlock.o\
./src/cqual/CQualRBlock.o\
./src/cqual/CQualLL.o\
./src/cqual/CQualBlock.o\
./src/crps/CRPSPreMF.o\
./src/crps/CRPSPreMFAll.o\
./src/crps/CRePoSe.o\
./src/cfields/CFields.o\
./src/csam/CSAM.o\
BIN = CompressSAM DecompressSAM CompressQual DecompressQual CompressSeq DecompressSeq GetIntervalSeq GetIntervalSeqSample CountReadsSample GetIntervalSAM GetIntervalSAMSample GetIntervalSSN
%.o: %.cpp
@echo " [C++] Compiling $<"
@$(CPP) $(FLAGS) -c $< -o $@
all: clean $(OBJS) $(BIN)
IntervalTest:
$(CPP) $(FLAGS) $(OBJS) -o IntervalTest ./tests/IntervalTest.cpp -lboost_iostreams
CompressQual:
$(CPP) $(FLAGS) $(OBJS) -o CompressQual ./tests/CompressQual.cpp -lboost_iostreams
DecompressQual:
$(CPP) $(FLAGS) $(OBJS) -o DecompressQual ./tests/DecompressQual.cpp -lboost_iostreams
CompressSeq:
$(CPP) $(FLAGS) $(OBJS) -o CompressSeq ./tests/CompressSeq.cpp -lboost_iostreams
DecompressSeq:
$(CPP) $(FLAGS) $(OBJS) -o DecompressSeq ./tests/DecompressSeq.cpp -lboost_iostreams
CompressSAM:
$(CPP) $(FLAGS) $(OBJS) -o CompressSAM ./tests/CompressSAM.cpp -lboost_iostreams
DecompressSAM:
$(CPP) $(FLAGS) $(OBJS) -o DecompressSAM ./tests/DecompressSAM.cpp -lboost_iostreams
GetIntervalSeq:
$(CPP) $(FLAGS) $(OBJS) -o GetIntervalSeq ./tests/GetIntervalSeq.cpp -lboost_iostreams
GetIntervalSeqSample:
$(CPP) $(FLAGS) $(OBJS) -o GetIntervalSeqSample ./tests/GetIntervalSeqSample.cpp -lboost_iostreams
CountReadsSample:
$(CPP) $(FLAGS) $(OBJS) -o CountReadsSample ./tests/CountReadsSample.cpp -lboost_iostreams
GetIntervalSAM:
$(CPP) $(FLAGS) $(OBJS) -o GetIntervalSAM ./tests/GetIntervalSAM.cpp -lboost_iostreams
GetIntervalSAMSample:
$(CPP) $(FLAGS) $(OBJS) -o GetIntervalSAMSample ./tests/GetIntervalSAMSample.cpp -lboost_iostreams
GetIntervalSSN:
$(CPP) $(FLAGS) $(OBJS) -o GetIntervalSSN ./tests/GetIntervalSSN.cpp -lboost_iostreams
doc:
@echo " [DOC] Generating documentation"
@doxygen
clean:
@echo " [CLN] Removing object files"
@rm -f $(OBJS) $(BIN) *~