bwa-mem2 2.2.1 (#1786)

Author: YoshitakaMo

Formula/bwa-mem2.rb

@@ -2,8 +2,8 @@ class BwaMem2 < Formula
   desc "Next version of bwa-mem short read aligner"
   homepage "https://github.com/bwa-mem2/bwa-mem2"
   url "https://github.com/bwa-mem2/bwa-mem2.git",
-      tag:      "v2.0",
-      revision: "cbcc183c0843d20d45c84e066177eb8d58be2f9b"
+      tag:      "v2.2.1",
+      revision: "bf3d376e95f4321b0d37a27d7ff1c77da4d289ff"
   head "https://github.com/bwa-mem2/bwa-mem2.git"
 
   bottle do
@@ -12,16 +12,101 @@ class BwaMem2 < Formula
     sha256 cellar: :any_skip_relocation, x86_64_linux: "943583113491f963bd0e8460994ec17a95f19208a62b07a8d514d18e648ddf7d"
   end
 
+  depends_on "cmake" => :build
+  depends_on "dos2unix" => :build
   uses_from_macos "zlib"
 
+  resource "sse2neon" do
+    url "https://raw.githubusercontent.com/DLTcollab/sse2neon/v1.7.0/sse2neon.h"
+    sha256 "c36e1355c1a22d9c3357c945d1ef8bd005cb1f0f7b378e6577a45ea96931a083"
+  end
+
+  resource "safestringlib" do
+    url "https://github.com/intel/safestringlib/archive/refs/tags/v1.2.0.tar.gz"
+    sha256 "3f16492460eb6dc40fc63f4a1c018e7e32db9db65b86a1294aa6c3bf1e31310e"
+  end
+
+  resource "patch" do
+    url "https://gist.githubusercontent.com/YoshitakaMo/eb6e6df7a621a9c9737bcc9363cf9bfc/raw/5936f4884daac3c961c6c9a62d9a0c676f578bbb/fastmap.patch"
+    sha256 "cbba705412b8a1139be752759490606a988eee0483a3c0ee65aa0a03c1c9c9e8"
+  end
+
+  resource "patch2" do
+    url "https://gist.githubusercontent.com/YoshitakaMo/c4cabc8e1e4b618047507bc354dbb51e/raw/1265ecf70a976476bd3e55d06804b94f9969310e/bandedSWA.cpp.patch"
+    sha256 "cdc13b153a23beb890d258eeb41d13aa0b777c1747bdefa49c399634c176cda7"
+  end
+
   def install
-    # Fix the error: error: conflicting types for 'memset_s'
-    # See https://github.com/intel/safestringlib/issues/14
-    inreplace "ext/safestringlib/include/safe_mem_lib.h",
-      "extern errno_t memset_s",
-      "//xxx extern errno_t memset_s"
+    # patch for fastmap.cpp
+    system "dos2unix", "src/fastmap.cpp"
+    system "dos2unix", "src/bandedSWA.cpp"
+    buildpath.install resource("patch")
+    buildpath.install resource("patch2")
+    system "patch", "-p1", "src/fastmap.cpp", "fastmap.patch"
+    system "patch", "-p1", "src/bandedSWA.cpp", "bandedSWA.cpp.patch"
+    # patch for src/utils.h to fix build error
+    # https://aur.archlinux.org/cgit/aur.git/tree/gcc_rdtsc.patch?h=bwa-mem2
+    inreplace "src/utils.h", "defined(__GNUC__) && !defined(__clang__)",
+                             "defined(__GNUC__) &&  __GNUC__ < 11 && !defined(__clang__)"
+    # install safestringlib v1.2.0 first
+    (buildpath/"safestringlib-1.2.0").install resource("safestringlib")
+    cd "safestringlib-1.2.0" do
+      inreplace "makefile", "LDFLAGS=-z noexecstack -z relo -z now", "LDFLAGS="
+      inreplace "CMakeLists.txt", " -z noexecstack -z relro -z now", ""
+      inreplace "include/safe_mem_lib.h", "extern errno_t memset_s", "//xxx extern errno_t memset_s"
+      system "cmake", "-S", ".", "-B", "build", *std_cmake_args(install_prefix: buildpath/"safestringlib")
+      system "cmake", "--build", "build"
+    end
+    inreplace "Makefile" do |s|
+      s.gsub! "SAFE_STR_LIB=    ext/safestringlib/libsafestring.a",
+              "SAFE_STR_LIB= safestringlib-1.2.0/build/libsafestring_static.a"
+      s.gsub! "-Iext/safestringlib/include",
+              "-Isafestringlib-1.2.0/include"
+    end
+
+    # use sse2neon for Apple Silicon
+    if OS.mac? && Hardware::CPU.arm?
+      (buildpath/"src").install resource("sse2neon")
+      inreplace "src/sse2neon.h", "FORCE_INLINE uint64_t _rdtsc(void)", "FORCE_INLINE uint64_t __rdtsc(void)"
+      inreplace ["src/FMI_search.h", "src/kswv.h", "src/bandedSWA.h"] do |s|
+        s.gsub! "#include <immintrin.h>", "#include \"sse2neon.h\""
+      end
+      inreplace ["src/ksw.h", "src/ksw.cpp"] do |s|
+        s.gsub! "#include <emmintrin.h>", "#include \"sse2neon.h\""
+      end
+      inreplace "src/bandedSWA.h", "#include <smmintrin.h>", "#include \"sse2neon.h\""
+    end
+
+    # Use safestringlib v1.2.0 instead of the bundled version
+    inreplace "Makefile", "-Lext/safestringlib -lsafestring",
+                          "-Lsafestringlib-1.2.0/build/ -lsafestring_static"
+    inreplace "Makefile", "-Lext/safestringlib/ -lsafestring",
+                          "-Lsafestringlib-1.2.0/build/ -lsafestring_static"
+    # fix build error with latest compilers
+    inreplace "src/FMI_search.cpp" do |s|
+      s.gsub! "_mm_prefetch((const char *)", "_mm_prefetch(reinterpret_cast<const char*>"
+      s.gsub! "_mm_prefetch(&sa_ls_word[pos >> SA_COMPX]",
+              "_mm_prefetch(reinterpret_cast<const char*>(&sa_ls_word[pos >> SA_COMPX])"
+      s.gsub! "_mm_prefetch(&sa_ms_byte[pos >> SA_COMPX]",
+              "_mm_prefetch(reinterpret_cast<const char*>(&sa_ms_byte[pos >> SA_COMPX])"
+      s.gsub! "_mm_prefetch(&sa_ls_word[sp >> SA_COMPX]",
+              "_mm_prefetch(reinterpret_cast<const char*>(&sa_ls_word[sp >> SA_COMPX])"
+      s.gsub! "_mm_prefetch(&sa_ms_byte[sp >> SA_COMPX]",
+              "_mm_prefetch(reinterpret_cast<const char*>(&sa_ms_byte[sp >> SA_COMPX])"
+      s.gsub! "_mm_prefetch(&cp_occ[occ_id_pp_]",
+              "_mm_prefetch(reinterpret_cast<const char*>(&cp_occ[occ_id_pp_])"
+    end
+    inreplace "src/bwamem.cpp" do |s|
+      s.gsub! "__m512i zero512 = _mm512_setzero_si512()", "__m128i zero128 = _mm_setzero_si128();"
+      s.gsub! "_mm512_store_si512((__m512i *)(hist + i), zero512)", "_mm_store_si128((__m128i *)(hist + i), zero128)"
+    end
+    inreplace "ext/safestringlib/safeclib/safeclib_private.h",
+              "#include \"safe_lib.h\"", "#include <safe_lib.h>"
 
-    system "make"
+    cflags = "-Wno-implicit-function-declaration" if DevelopmentTools.clang_build_version >= 1403
+    # arch=avx2 for Linux, but it's not best for all CPUs.
+    arch = OS.mac? ? "native" : "avx2"
+    system "make", "arch=#{arch}", "CFLAGS=#{cflags}"
     bin.install "bwa-mem2"
   end