--- src/CMakeLists.txt.orig	2024-07-20 19:07:27 UTC
+++ src/CMakeLists.txt
@@ -3,16 +3,10 @@ list(REMOVE_ITEM sources main.cpp)
 
 list(REMOVE_ITEM sources main.cpp)
 
-if (USE_BAM)
-include_directories(../ext/htslib)
-endif(USE_BAM)
-
 if(NOT MAX_KMER_SIZE)
 set(MAX_KMER_SIZE "32")
 endif()
 
-add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
-
 add_library(kallisto_core ${sources} ${headers})
 target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
@@ -21,7 +15,7 @@ if (USE_BAM)
 find_package( Threads REQUIRED )
 ExternalProject_Get_Property(bifrost install_dir)
 if (USE_BAM)
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
+target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
 else()
 target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
 endif(USE_BAM)