feat: Add node mask parameter to odgi similarity for selective node p…

…rocessing

src/subcommand/similarity_main.cpp

@@ -31,6 +31,7 @@ int main_similarity(int argc, char** argv) {
     args::ArgumentParser parser("Provides a sparse similarity matrix for paths or groups of paths. Each line prints in a tab-delimited format to stdout.");
     args::Group mandatory_opts(parser, "[ MANDATORY ARGUMENTS ]");
     args::ValueFlag<std::string> dg_in_file(mandatory_opts, "FILE", "Load the succinct variation graph in ODGI format from this *FILE*. The file name usually ends with *.og*. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!", {'i', "idx"});
+    args::ValueFlag<std::string> mask_file(mandatory_opts, "FILE", "Load node mask from this file. Each line contains a 0 or 1, where 0 means the node at that position should be ignored in similarity computation.", {'m', "mask"});
     args::Group path_investigation_opts(parser, "[ Path Investigation Options ]");
     args::ValueFlag<std::string> path_delim(path_investigation_opts, "CHAR", "The part of each path name before this delimiter CHAR is a group identifier.",
                                                     {'D', "delim"});
@@ -198,9 +199,37 @@ args::Group threading_opts(parser, "[ Threading ]");
     }
 
     // ska::flat_hash_map<std::pair<uint64_t, uint64_t>, uint64_t> leads to huge memory usage with deep graphs
+    // Load mask if specified
+    std::vector<bool> node_mask;
+    if (mask_file) {
+        std::ifstream mask_in(args::get(mask_file));
+        std::string line;
+        while (std::getline(mask_in, line)) {
+            if (line == "0") {
+                node_mask.push_back(false);
+            } else if (line == "1") {
+                node_mask.push_back(true);
+            } else {
+                std::cerr << "[odgi::similarity] error: mask file should contain only 0 or 1 values, found: " << line << std::endl;
+                return 1;
+            }
+        }
+        if (node_mask.size() != graph.get_node_count()) {
+            std::cerr << "[odgi::similarity] error: mask file should have exactly " << graph.get_node_count() << " lines, found: " << node_mask.size() << std::endl;
+            return 1;
+        }
+    } else {
+        // If no mask specified, include all nodes
+        node_mask.resize(graph.get_node_count(), true);
+    }
+
     ska::flat_hash_map<uint64_t, uint64_t> path_intersection_length;
     graph.for_each_handle(
         [&](const handle_t& h) {
+            // Skip masked-out nodes
+            if (!node_mask[graph.get_id(h) - 1]) {
+                return;
+            }
             ska::flat_hash_map<uint32_t, uint64_t> local_path_lengths;
             size_t l = graph.get_length(h);
             graph.for_each_step_on_handle(