update bgen

Author: Zilong-Li

Makefile

@@ -212,3 +212,7 @@ ld_tests:
 	./PCAone -B adj.residuals --match-bim adj.mbim  --ld-r2 0.8  --ld-bp 1000000 -o adj_prune_m0 -m 0
 	./PCAone -B adj.residuals --match-bim adj.mbim  --ld-r2 0.8  --ld-bp 1000000 -o adj_prune_m1 -m 2
 	diff adj_prune_m0.ld.prune.out adj_prune_m1.ld.prune.out > /dev/null
+
+bgen_tests:
+	./PCAone -g example/test.bgen -n6
+	./PCAone -g example/test.bgen -m 0.1 -n6

external/bgen/Makefile

@@ -1,13 +1,15 @@
 #
 # Makefile to compile bgen library
 #
+Platform    := $(shell uname -s)
 CXX         ?= g++
-CXXFLAGS    += -O3 -Wall -std=c++11
+CXXFLAGS     = -O2 -Wall -std=c++11
 AVX = 1
 
-ifeq ($(strip $(AVX)), 1)
-  $(info "use -mavx2 for bgen")
-  CXXFLAGS += -mavx -mavx2 -DAVX2
+ifeq ($(Platform), Darwin)
+	CXXFLAGS += -march=native
+else
+	CXXFLAGS += -mavx -mavx2
 endif
 
 OBJECTS      = $(patsubst %.cpp,%.o,$(wildcard *.cpp))