Merge pull request #4394 from vgteam/path-normalize

Fix build on Ubuntu 24.04.1 / GCC 13.2.0
vgteam · Sep 11, 2024 · 2220b91 · 2220b91 · adamnovak · Sep 11, 2024
2 parents 95bcbb4 + 3bfb4b9
commit 2220b91
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Showing 4 changed files with 13 additions and 6 deletions.
diff --git a/deps/kff-cpp-api b/deps/kff-cpp-api
diff --git a/deps/sublinear-Li-Stephens b/deps/sublinear-Li-Stephens
diff --git a/src/main.cpp b/src/main.cpp
@@ -75,7 +75,7 @@ int main(int argc, char *argv[]) {
         vg_help(argv);
         return 1;
     }
-    
+
     auto* subcommand = vg::subcommand::Subcommand::get(argc, argv);
     if (subcommand != nullptr) {
         // We found a matching subcommand, so run it
@@ -85,7 +85,12 @@ int main(int argc, char *argv[]) {
         return (*subcommand)(argc, argv);
     } else {
         // No subcommand found
-        string command = argv[1];
+        string command;
+        // note: doing argv[1] = string is producing totally bizarre "error: inlining failed in call to ‘always_inline’ ..."
+        // error when upgrading to Ubuntu 24.04.1 / GCC 13.2.  Doing the base-by-base copy seems to work around it...
+        for (size_t i = 0; i < strlen(argv[1]); ++i) {
+            command += argv[1][i];
+        }
         cerr << "error:[vg] command " << command << " not found" << endl;
         vg_help(argv);
         return 1;

diff --git a/src/multipath_mapper.cpp b/src/multipath_mapper.cpp
@@ -1836,8 +1836,10 @@ namespace vg {
                     std::swap(rescued_secondaries[i], rescued_secondaries[end - 1]);
                     std::swap(rescued_distances[i], rescued_distances[end - 1]);
                     std::swap(rescued_multiplicities[i], rescued_multiplicities[end - 1]);
-                    std::swap(duplicate[i], duplicate[end - 1]);
-
+                    // nb: cant std::swap bool vectors in new c++
+                    bool dupe_i = duplicate[i];
+                    duplicate[i] = duplicate[end - 1];
+                    duplicate[end - 1] = dupe_i;
                     end--;
                 }
                 else {