Merge pull request #55 from smithlabcode/andrewdavidsmith-patch-1

Preventing attempts to use SSE instruction when not supported

.github/workflows/macos-builds.yml

@@ -9,20 +9,20 @@ on:
 
 jobs:
   build:
-    runs-on: macos-12
+    runs-on: macos-14
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Update Homebrew
       run: brew update
-    - name: Install autotools
-      run: brew install autoconf automake libtool
+    - name: Install automake
+      run: brew install automake
     - name: Install dependencies
-      run: brew install htslib gsl
+      run: brew install htslib
     - name: Generate configure script
       run: ./autogen.sh
     - name: configure with g++-13
       run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
-    - name: make
-      run: make
+    - name: Build with g++
+      run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic"

src/abismal.cpp

@@ -1002,8 +1002,10 @@ check_hits(const uint32_t offset, const PackedRead::const_iterator read_st,
            vector<uint32_t>::const_iterator start_idx, result_type &res) {
   for (; start_idx != end_idx && !res.sure_ambig; ++start_idx) {
     // GS: adds the next candidate to L1d cache while current is compared
+#ifdef __SSE__
     _mm_prefetch(&(*(genome_st + ((*(start_idx + 10) - offset) >> 4))),
                  _MM_HINT_T0);
+#endif
     const uint32_t the_pos = *start_idx - offset;
     /* GS: the_pos & 15u tells if the position is a multiple of 16, in
      * which case it is aligned with the genome. Otherwise we need to