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7
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1 DEBUG ?= 0
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2 PARALLEL ?= 0
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3
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4 # External Libraries
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5 BOOST_ROOT ?= /g/solexa/bin/software/boost_1_53_0/
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6 BAMTOOLS_ROOT ?= /g/solexa/bin/software/bamtools-2.3.0/
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7 SEQTK_ROOT ?= /g/solexa/bin/software/kseq/
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8
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9 # Flags
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10 CXX=g++
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11 CXXFLAGS += -isystem ${BOOST_ROOT}/include -isystem ${BAMTOOLS_ROOT}/include -isystem ${SEQTK_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
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12 LDFLAGS += -L${BOOST_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -L${BAMTOOLS_ROOT}/lib -lbamtools -lz -Wl,-rpath,${BAMTOOLS_ROOT}/lib,-rpath,${BOOST_ROOT}/lib
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13
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14 # Additional flags for release/debug
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15 ifeq (${PARALLEL}, 1)
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16 CXXFLAGS += -fopenmp -DOPENMP
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17 else
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18 CXXFLAGS += -DNOPENMP
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19 endif
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20
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21 # Additional flags for release/debug
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22 ifeq (${DEBUG}, 1)
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23 CXXFLAGS += -g -O0 -fno-inline -DDEBUG
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24 else ifeq (${DEBUG}, 2)
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25 CXXFLAGS += -g -O0 -fno-inline -DPROFILE
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26 LDFLAGS += -lprofiler -ltcmalloc
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27 else
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28 CXXFLAGS += -O9 -DNDEBUG
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29 #LDFLAGS += --static
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30 endif
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31
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32 # External sources
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33 HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h)
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34 BAMTOOLSSOURCES = $(wildcard src/bamtools/src/api/*.h) $(wildcard src/bamtools/src/api/*.cpp)
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35 DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
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36
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37 # Targets
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38 TARGETS = src/delly src/extract src/cov src/iover src/stats
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39
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40 all: $(TARGETS)
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41
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42 src/delly: $(DELLYSOURCES)
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43 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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44
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45 src/extract: $(DELLYSOURCES)
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46 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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47
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48 src/cov: $(DELLYSOURCES)
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49 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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50
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51 src/iover: $(DELLYSOURCES)
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52 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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53
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54 src/stats: $(DELLYSOURCES)
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55 $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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56
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57 clean:
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58 rm -f $(TARGETS) $(TARGETS:=.o)
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