--- CMakeLists.txt.orig	2026-01-20 17:34:25 UTC
+++ CMakeLists.txt
@@ -60,7 +60,7 @@ else()
     include(CheckCXXCompilerFlag)
     check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17)
     if(COMPILER_SUPPORTS_CXX17)
-        set(CMAKE_CXX_STANDARD 17)
+        set(CMAKE_CXX_STANDARD 11)
     else()
         set(CMAKE_CXX_STANDARD 11)
     endif()
@@ -69,9 +69,7 @@ endif()
     set(CMAKE_CXX_EXTENSIONS OFF)
 endif()
 
-#add_compile_options(-Wall -Wno-unused-function)
-add_compile_options(-Wno-deprecated-declarations -Wno-subobject-linkage) # Suppress bifrost warning
-set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-subobject-linkage -Wno-return-type") # Suppress bifrost warning
+set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-return-type") # Suppress bifrost warning
 
 if(LINK MATCHES static)
     message("static build")
@@ -81,24 +79,13 @@ include(ExternalProject)
 
 
 include(ExternalProject)
-if (USE_BAM)
-ExternalProject_Add(htslib
-    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
-    BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND "" #autoreconf -i && autoheader &&  autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
-        #--prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
-    BUILD_COMMAND "" #make lib-static
-    INSTALL_COMMAND ""
-)
-endif(USE_BAM)
 
 ExternalProject_Add(bifrost
     PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost
     SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${MAX_KMER_SIZE} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} ${DO_ENABLE_AVX2} ${DO_ENABLE_COMPILATION_ARCH}
-    BUILD_COMMAND cd build && make
+    BUILD_COMMAND cd build && gmake
     INSTALL_COMMAND ""
 )
 
@@ -109,13 +96,13 @@ if (ZLIBNG)
     SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX}
-    BUILD_COMMAND cd zlib-ng && make
+    BUILD_COMMAND cd zlib-ng && gmake
     INSTALL_COMMAND ""
     )
 endif(ZLIBNG)
 
 if (USE_BAM)
-    include_directories(${htslib_PREFIX}/src/htslib)
+    include_directories(${LOCALBASE}/htslib)
 endif(USE_BAM)
 
 include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src)
