set refillhaps as 2 in default

Makefile

@@ -6,28 +6,29 @@ CXX      = g++
 CXXFLAGS = -std=c++17 -Wall -O3 -DNDEBUG
 INC      = -I./src -I./inst/include -I$(HTSDIR)
 LDFLAGS  =  -L$(HTSDIR) -Wl,-rpath,$(HTSDIR)
-LIBS     = $(HTSDIR)/libhts.a -llzma -lbz2 -lm -lz -lpthread
+LIBS     =  -llzma -lbz2 -lm -lz -lpthread
 OBJS     = src/main.o src/phaseless.o src/fastphase.o src/admixture.o src/utils.o
 BINS     = phaseless
+libhts   = $(HTSDIR)/libhts.a
 FLOAT    = 0
 
 ifeq ($(strip $(FLOAT)),1)
   $(info "use float in phaseless!")
   CXXFLAGS += -DUSE_FLOAT
 endif
 
-.PHONY: all clean htslib
+.PHONY: all clean 
 
-all: $(BINS)
+all: $(BINS) $(libhts)
 
 %.o: %.cpp
 	${CXX} ${CXXFLAGS} -o $@ -c $< ${INC}
 
-$(BINS): $(OBJS)
-	${CXX} ${CXXFLAGS} -o $@ $(OBJS) ${INC} $(LIBS) $(LDFLAGS)
+$(BINS): $(OBJS) $(libhts)
+	${CXX} ${CXXFLAGS} -o $@ $(OBJS) ${INC} $(libhts) $(LIBS) $(LDFLAGS)
 
-htslib:
-	cd $(HTSDIR) && ./configure --disable-libcurl --without-libdeflate && make -j10
+$(libhts):
+	cd $(HTSDIR) && ./configure --disable-libcurl --without-libdeflate && make -j6
 
 clean:
 	rm -f $(BINS) $(OBJS)

src/fastphase.cpp

@@ -310,7 +310,7 @@ int run_impute_main(Options & opts)
     for(int it = 0; SIG_COND && it <= opts.nimpute; it++)
     {
         tim.clock();
-        if(opts.refillHaps && it > 4 && it < opts.nimpute / 2 && it % 4 == 1)
+        if(opts.refillHaps && it > 4 && it < opts.nimpute / 4 && it % 4 == 1)
             faith.refillHaps(opts.refillHaps);
         faith.initIteration();
         for(int i = 0; i < faith.N; i++)

src/main.cpp

@@ -179,7 +179,7 @@ int main(int argc, char * argv[])
               "2: re-sample P by copying from haplotype with the highest probability\n"
               "3: re-sample P by copying from others with respect to their probability\n"
               "0: disable this")
-        .default_value(0)
+        .default_value(2)
         .scan<'i', int>();
     cmd_impute.add_argument("--minRecombRate")
         .help("min recombination rate to determine if a SNP should be collapsed")