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# Use g++
CXX=g++
CXXFLAGS=-g -O3
LIBS=-lm
# Use Intel compiler (faster!)
#CXX=icpc
#CXXFLAGS=-g -O2 -ip -align -falign-functions -Wno-deprecated -Isrc -w
#LIBS=
all: findknownsnps reassemble variety mapcontigs ungap
findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
reassemble: src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
variety: src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
mapcontigs: src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
ungap: src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
.cpp.o:
$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
clean:
rm -f *.o
rm -f src/*.o
rm -f findknownsnps
rm -f variety
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