Hublabel

src/multipath_alignment_graph.cpp

@@ -6505,7 +6505,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
         for (const auto& path_node : path_nodes) {
             for (const auto& edge : path_node.edges) {
                 const auto& next_node = path_nodes[edge.first];
-                shift = max<size_t>(shift, abs<int64_t>((next_node.begin - path_node.end) - edge.second));
+                shift = max<size_t>(shift, std::abs(static_cast<int64_t>((next_node.begin - path_node.end) - edge.second)));
             }
         }
         return shift;
@@ -6529,7 +6529,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
                     ++in_degree[edge.first];
 
                     const auto& next_node = path_nodes[edge.first];
-                    size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
+                    size_t shift = std::abs(static_cast<int64_t>((next_node.begin - path_node.end) - edge.second));
 
 #ifdef debug_shift_pruning
                     cerr << "shift DP reverse " << i << " <- " << edge.first << " with shift " << shift << " for total " << min_shift_rev[edge.first] + shift << endl;
@@ -6555,7 +6555,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
             else {
                 for (auto& edge : path_node.edges) {
                     const auto& next_node = path_nodes[edge.first];
-                    size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
+                    size_t shift = std::abs(static_cast<int64_t>((next_node.begin - path_node.end) - edge.second));
 #ifdef debug_shift_pruning
                     cerr << "shift DP forward " << i << " -> " << edge.first << " with shift " << shift << " for total " << min_shift_fwd[i] + shift << endl;
 #endif
@@ -6577,7 +6577,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
             for (size_t j = 0; j < path_node.edges.size(); ++j) {
                 auto& edge = path_node.edges[j];
                 const auto& next_node = path_nodes[edge.first];
-                size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
+                size_t shift = std::abs(static_cast<int64_t>((next_node.begin - path_node.end) - edge.second));
 
                 size_t min_edge_shift = min_shift_fwd[i] + shift + min_shift_rev[edge.first];
 

src/multipath_mapper.cpp

@@ -2448,7 +2448,7 @@ namespace vg {
                     // in the left_idxs and right_idxs vectors
                     int64_t target_len = 2 * seq_len - left_side.clip_length - right_side.clip_length;
                     auto distance_diff = [&](size_t l, size_t r) {
-                        return abs<int64_t>(get<2>(left_sites[left_idxs[l]]) + get<2>(right_sites[right_idxs[r]]) - target_len);
+                        return std::abs(static_cast<int64_t>(get<2>(left_sites[left_idxs[l]]) + get<2>(right_sites[right_idxs[r]]) - target_len));
                     };
 
                     // sweep to identify pairs that most nearly align

src/recombinator.cpp

@@ -1585,7 +1585,7 @@ void add_path(const gbwt::GBWT& source, gbwt::size_type path_id, gbwt::GBWTBuild
     gbwt::PathName path_name = source.metadata.path(path_id);
     std::string sample_name = source.metadata.sample(path_name.sample);
     std::string contig_name = source.metadata.contig(path_name.contig);
-    if (sample_name == gbwtgraph::REFERENCE_PATH_SAMPLE_NAME) {
+    if (sample_name == gbwtgraph::GENERIC_PATH_SAMPLE_NAME) {
         metadata.add_generic_path(contig_name);
     } else {
         // Reference samples will be copied later.

src/subcommand/gampcompare_main.cpp

@@ -216,7 +216,7 @@ int main_gampcompare(int argc, char** argv) {
                             if (path_true_positions[i].second == path_mapped_positions[j].second) {
                                 // there is a pair of positions on the same strand of the same path
                                 abs_dist = min<int64_t>(abs_dist,
-                                                        abs<int64_t>(path_true_positions[i].first - path_mapped_positions[j].first));
+                                                        std::abs(static_cast<int64_t>(path_true_positions[i].first - path_mapped_positions[j].first)));
                             }
                         }
                     }