$NetBSD$

# Use external htslib

--- CMakeLists.txt.orig	2024-07-20 19:07:27.000000000 +0000
+++ CMakeLists.txt
@@ -23,16 +23,12 @@ add_compile_definitions("MAX_KMER_SIZE=$
 
 
 option(USE_HDF5 "Compile with HDF5 support" OFF) #OFF by default
-option(USE_BAM "Compile with HTSLIB support" OFF) # OFF by default
+option(USE_BAM "Compile with HTSLIB support" ON)
 
 if(USE_HDF5)
     add_compile_definitions("USE_HDF5=ON")
 endif(USE_HDF5)
 
-if(NOT USE_BAM)
-    add_compile_definitions("NO_HTSLIB=ON")
-endif()
-
 set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
 set(CMAKE_CXX_FLAGS_PROFILE "-g")
 
@@ -73,42 +69,16 @@ ENDIF(LINK MATCHES static)
 
 
 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 ""
 )
 
-if (ZLIBNG)
-    message("zlib-ng enabled.")
-    ExternalProject_Add(zlib-ng
-    PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
-    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
-    INSTALL_COMMAND ""
-    )
-endif(ZLIBNG)
-
-if (USE_BAM)
-include_directories(${htslib_PREFIX}/src/htslib)
-endif(USE_BAM)
 include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src)
 
 ExternalProject_Get_Property(bifrost install_dir)