--- ext/bifrost/CMakeLists.txt.orig	2024-09-17 05:40:08 UTC
+++ ext/bifrost/CMakeLists.txt
@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX
 
 # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
 SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
-# Enable architecture optimizations
-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
-# Enable AVX2 instructions
-SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
+SET(CMAKE_VERBOSE_MAKEFILE "ON")
 
 # Set some default compile flags
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call")
 
-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
-
-
 #check if we are on arm64 and apple, if so, disable AVX2
 if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
 	message("Disabling AVX2 instructions on arm64")
@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF")
 	message("Disabling native architecture compilation (including AVX2)")
 else(COMPILATION_ARCH MATCHES "OFF")
 	message("Compilation architecture: ${COMPILATION_ARCH}")
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
 endif(COMPILATION_ARCH MATCHES "OFF")
 
 if(ENABLE_AVX2 MATCHES "OFF")
@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
 		set(CMAKE_EXE_LINKER_FLAGS "-pg")
 	else(CMAKE_BUILD_TYPE MATCHES Profile)
 		message("Build type: Release")
-		add_compile_options(-O3)
+		add_compile_options(-O2)
 	endif(CMAKE_BUILD_TYPE MATCHES Profile) 
 endif(CMAKE_BUILD_TYPE MATCHES Debug)