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Fix makefile #3

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merged 5 commits into from
Oct 9, 2017
Merged

Fix makefile #3

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5c8af88
Makefile: Remove -march=native
donald Oct 7, 2017
7650bcb
Makefile: Add EXTRA_CXXFLAGS
donald Oct 7, 2017
d36bd75
Makefile: Remove -g default
donald Oct 7, 2017
6900deb
Makefile: Do not clean up in build target
donald Oct 7, 2017
a8f3a4b
Makefile: Correct recursive usage
donald Oct 8, 2017
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13 changes: 6 additions & 7 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
BINDIR ?= $(PREFIX)/bin
BIN = $(DESTDIR)/$(BINDIR)
# With pthreads
override CXXFLAGS+= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -march=native -g
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 -march=native
#override CXXFLAGS+= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 $(EXTRA_CXXFLAGS)

THREAD= -lpthread

Expand All @@ -14,15 +14,14 @@ all: bsmap
%.o:%.cpp
$(CXX) $(CXXFLAGS) -c $< -o $@
bsmap: $(OBJS1)
(cd samtools; make)
(cd gzstream; make)
$(MAKE) -C samtools
$(MAKE) -C gzstream
$(CXX) $(CXXFLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream
rm -f *.o

clean:
rm -f *.o *~ bsmap
(cd samtools; make clean)
(cd gzstream; make clean)
$(MAKE) -C samtools clean
$(MAKE) -C gzstream clean
install:
install -d $(BIN)
install ./bsmap $(BIN)
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