update makefile

.gitignore

@@ -33,4 +33,5 @@ admix.*
 run.sh
 inst/include/htslib*
 src/phaseless.so
+src/libsrc.*
 *.gz

Makefile

@@ -1,13 +1,14 @@
 HTSDIR   = ./inst/include/htslib-1.18
 CXX      = g++
 
-CXXFLAGS = -std=c++17 -Wall -O3 -g -fsanitize=address
+# CXXFLAGS = -std=c++17 -Wall -O3 -g -fsanitize=address
 # CXXFLAGS = -std=c++17 -Wall -O3 -march=native -DNDEBUG
-# CXXFLAGS = -std=c++17 -Wall -O3 -DNDEBUG
+CXXFLAGS = -std=c++17 -Wall -O3 -DNDEBUG
 INC      = -I./src -I./inst/include -I$(HTSDIR)
 LDFLAGS  =  -L$(HTSDIR) -Wl,-rpath,$(HTSDIR)
 LIBS     =  -llzma -lbz2 -lm -lz -lpthread
-OBJS     = src/main.o src/phaseless.o src/fastphase.o src/admixture.o src/io.o src/utils.o
+OBJS     = src/phaseless.o src/fastphase.o src/admixture.o src/io.o src/utils.o
+libsrc   = src/libsrc.a
 BINS     = phaseless
 libhts   = $(HTSDIR)/libhts.a
 FLOAT    = 0
@@ -24,14 +25,17 @@ all: $(BINS) $(libhts)
 %.o: %.cpp
 	${CXX} ${CXXFLAGS} -o $@ -c $< ${INC}
 
-$(BINS): $(OBJS) $(libhts)
-	${CXX} ${CXXFLAGS} -o $@ $(OBJS) ${INC} $(libhts) $(LIBS) $(LDFLAGS)
+$(BINS): src/main.o $(libsrc) $(libhts)
+	${CXX} ${CXXFLAGS} -o $@ src/main.o $(libsrc) $(libhts) $(LIBS) $(LDFLAGS) $(INC)
 
 $(libhts):
 	cd $(HTSDIR) && ./configure --disable-libcurl --without-libdeflate && make -j6
 
+$(libsrc): $(OBJS)
+	ar -rcs $@ $?
+
 clean:
-	rm -f $(BINS) $(OBJS)
+	rm -f $(BINS) src/*.o src/*.a
 	cd $(HTSDIR) && make clean
 
 impute:

tests/Makefile

@@ -1,15 +1,15 @@
 HTSDIR   = ../inst/include/htslib-1.18
 CXX      = g++
 CXXFLAGS = -std=c++17 -Wall -O3
-INC      = -I. -I../src -I../inst/include -I$(HTSDIR)
-LDFLAGS  =  -L$(HTSDIR) -Wl,-rpath,$(HTSDIR)
-LIBS     = -lhts -llzma -lbz2 -lm -lz -lpthread
+INC      = -I../src -I../inst/include -I$(HTSDIR)
+# LDFLAGS  =  -L$(HTSDIR) -Wl,-rpath,$(HTSDIR)
+LIBS     = $(HTSDIR)/libhts.a -llzma -lbz2 -lm -lz -lpthread
 
 OBJS = test-main.o test-joint.o test-admixture.o test-fastphase.o test-utils.o
 
 BINS = test-joint.bin test-admixture.bin test-fastphase.bin test-utils.bin
 
-DEPS = ../src/phaseless.o ../src/fastphase.o ../src/admixture.o
+DEPS = ../src/libsrc.a
 
 UTILS = test-cli test-io
 
@@ -21,7 +21,7 @@ all: $(BINS) $(OBJS)
 	$(CXX) $(CXXFLAGS) -o $@ -c $< ${INC}
 
 %.bin: %.o test-main.o $(DEPS)
-	${CXX} ${CXXFLAGS} -o $@ $< test-main.o $(DEPS) $(LDFLAGS) $(LIBS)
+	${CXX} ${CXXFLAGS} -o $@ $< test-main.o $(DEPS) $(LDFLAGS) $(LIBS) $(INC)
 
 test: $(BINS)
 	./test-utils.bin --success

tests/test-fastphase.cpp

@@ -45,7 +45,7 @@ TEST_CASE("fastphasek4", "[test-fastphasek4]")
         llike.clear(); // clear future and renew
         faith4.updateClusterFreqPI(postProbsZ, tol);
         faith4.updateAlleleFreqWithinCluster(postProbsZandG, tol);
-        // REQUIRE(loglike > prevlike);
+        REQUIRE(loglike > prevlike);
         prevlike = loglike;
     }
 }