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Makefile
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PROG= lra
PROG_EXTRA= alchemy2 qti
LIBS= -lz -lpthread -lhts
PROF=/home/cmb-16/mjc/shared/lib/
DEBUG?=""
OPT?=""
STATIC=
CXX=g++ -std=c++14
CFLAGS=-g
asan?=""
tsan?=""
ifneq ($(DEBUG), "")
CFLAGS=-g
else
CFLAGS=-O2 -DNDEBUG
endif
ifneq ($(asan), "")
CFLAGS+=-fsanitize=address
LIBS+=-fsanitize=address
endif
ifneq ($(tsan), "")
CFLAGS+=-fsanitize=thread
LIBS+=-fsanitize=thread
endif
ifneq ($(OPT), "")
#STATIC=-L $(PROF) -lprofiler
endif
HEADERS=MinCount.h \
SeqUtils.h \
CompareLists.h \
TupleOps.h \
Sorting.h \
MMIndex.h \
Options.h\
Clustering.h \
Genome.h \
Alignment.h \
Read.h \
MapRead.h \
Input.h \
Fragment.h\
BasicEndpoint.h\
PrioritySearchTree.h\
AffineOneGapAlign.h \
GlobalChain.h \
Read.h \
SparseDP.h \
Timing.h \
IndelRefine.h \
Mapping_ultility.h \
SparseDP_Forward.h \
DivideSubByCol1.h \
DivideSubByCol2.h \
DivideSubByRow1.h \
DivideSubByRow2.h \
AlignmentBlock.h \
ChainRefine.h \
Chain.h \
ClusterRefine.h \
Fragment_Info.h \
LinearExtend.h \
LocalRefineAlignment.h \
LogLookUpTable.h \
Map_highacc.h \
Map_lowacc.h \
SubRountine.h \
Types.h \
SubProblem.h \
SplitClusters.h \
RefineBreakpoint.h
all:$(PROG)
# tag: TestAffineOneGapAlign.cpp AffineOneGapAlign.h
# $(CXX) -g TestAffineOneGapAlign.cpp -o tag
# # -D _MAT_PRINT_
# tgc: TestGlobalChain.cpp GlobalChain.h Fragment.h BasicEndpoint.h PrioritySearchTree.h
# $(CXX) -g TestGlobalChain.cpp -o tgc
# tir: TestIndelRefine.cpp IndelRefine.h
# $(CXX) -g TestIndelRefine.cpp -I $(CONDA_PREFIX)/include -L $(CONDA_PREFIX)/lib -lhts -o tir -lbz2 -lz
lra: lra.o
$(CXX) $(CFLAGS) $(STATIC) $^ -I -L/usr/lib64 -L $(CONDA_PREFIX)/lib $(LIBS) -o $@ -Wl,-rpath-link=$(CONDA_PREFIX)/lib
alchemy2: Alchemy2.o
$(CXX) $(CFLAGS) $(STATIC) $^ -L $(CONDA_PREFIX)/lib $(LIBS) -o $@ -Wl,-rpath,$(CONDA_PREFIX)/lib
qti: QueryTime.o
$(CXX) $(CFLAGS) $(STATIC) $^ -L $(CONDA_PREFIX)/lib $(LIBS) -o $@
lra.o: lra.cpp $(HEADERS)
$(CXX) $(CFLAGS) -c -I $(CONDA_PREFIX)/include lra.cpp
Alchemy2.o: Alchemy2.cpp Genome.h
$(CXX) $(CFLAGS) -c -I $(CONDA_PREFIX)/include Alchemy2.cpp
QueryTime.o: QueryTime.cpp $(HEADERS) $(CONDA_PREFIX)/lib/libhts.a
$(CXX) $(CFLAGS) -c -I $(CONDA_PREFIX)/include QueryTime.cpp
clean:
rm -f $(PROG) $(PROG_EXTRA) *.o