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bsmap/Makefile
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| BINDIR ?= $(PREFIX)/bin | |
| BIN = $(DESTDIR)/$(BINDIR) | |
| # With pthreads | |
| override CXXFLAGS+= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 $(EXTRA_CXXFLAGS) | |
| # Without pthreads | |
| #override CXXFLAGS+= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 $(EXTRA_CXXFLAGS) | |
| THREAD= -lpthread | |
| SOURCE = align dbseq main pairs param reads utilities | |
| OBJS1= $(patsubst %,%.o,$(SOURCE)) | |
| all: bsmap | |
| %.o:%.cpp %.h | |
| $(CXX) $(CXXFLAGS) -c $< -o $@ | |
| bsmap: $(OBJS1) | |
| $(MAKE) -C samtools | |
| $(MAKE) -C gzstream | |
| $(CXX) $(CXXFLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream | |
| clean: | |
| rm -f *.o *~ bsmap | |
| $(MAKE) -C samtools clean | |
| $(MAKE) -C gzstream clean | |
| install: | |
| install -d $(BIN) | |
| install ./bsmap $(BIN) | |
| install ./sam2bam.sh $(BIN) | |
| install ./methratio.py $(BIN) |