From d4407e817fd4024c9305b42be2567a9bd5691298 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Fri, 7 Feb 2025 14:49:50 -0800
Subject: [PATCH] Fix build

---
 src/algorithms/chain_items.cpp       | 14 ++++++++------
 src/minimizer_mapper_from_chains.cpp | 13 +++++++++----
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/algorithms/chain_items.cpp b/src/algorithms/chain_items.cpp
index d1fc9400cb..3d55c8e9d8 100644
--- a/src/algorithms/chain_items.cpp
+++ b/src/algorithms/chain_items.cpp
@@ -197,12 +197,14 @@ transition_iterator zip_tree_transition_iterator(const std::vector<SnarlDistance
                                                  size_t max_read_lookback_bases) {
     
     // TODO: Remove seeds because we only bring it here for debugging and it complicates the dependency relationships
-    return [&seeds, &zip_code_tree, max_lookback_bases](const VectorView<Anchor>& to_chain,
-                                                        const SnarlDistanceIndex& distance_index,
-                                                        const HandleGraph& graph,
-                                                        size_t max_indel_bases,
-                                                        const transition_iteratee& callback) {
-                            
+    return [&seeds, &zip_code_tree, max_graph_lookback_bases, max_read_lookback_bases](
+        const VectorView<Anchor>& to_chain,
+        const SnarlDistanceIndex& distance_index,
+        const HandleGraph& graph,
+        size_t max_indel_bases,
+        const transition_iteratee& callback
+    ) {
+
         // We need a way to map from the seeds that zip tree thinks about to the anchors that we think about. So we need to index the anchors by leading/trailing seed.
         // TODO: Should we make someone else do the indexing so we can make the Anchor not need to remember the seed?
         std::unordered_map<size_t, size_t> seed_to_starting;
diff --git a/src/minimizer_mapper_from_chains.cpp b/src/minimizer_mapper_from_chains.cpp
index 4366e94643..24932b3652 100644
--- a/src/minimizer_mapper_from_chains.cpp
+++ b/src/minimizer_mapper_from_chains.cpp
@@ -632,7 +632,7 @@ vector<Alignment> MinimizerMapper::map_from_chains(Alignment& aln) {
     ZipCodeForest zip_code_forest;
     crash_unless(distance_index);
     zip_code_forest.fill_in_forest(seeds, minimizers, *distance_index, 
-                                   max_lookback_bases, aln.sequence().size() * zipcode_tree_scale);
+                                   max_graph_lookback_bases, aln.sequence().size() * zipcode_tree_scale);
 
 #ifdef debug_print_forest
     if (show_work) {
@@ -3195,6 +3195,8 @@ Alignment MinimizerMapper::find_chain_alignment(
         // We will measure the graph distance on the link path actually found, for work-showing.
         // This gets filled from either the WFA alignment we have already, or the BGA alignment we are about to compute.
         size_t link_graph_path_length;
+        // We also measure the score for work-showing.
+        int link_score;
 
         if (link_alignment) {
             // We found a link alignment
@@ -3224,7 +3226,9 @@ Alignment MinimizerMapper::find_chain_alignment(
                 link_graph_path_length = path_from_length(link_path);
                 append_path(composed_path, std::move(link_path));
             }
-            composed_score += link_alignment.score;
+
+            link_score = link_alignment.score;
+            composed_score += link_score;
         } else {
             // The sequence to the next thing is too long, or we couldn't reach it doing connect().
             // Fall back to another alignment method
@@ -3289,13 +3293,14 @@ Alignment MinimizerMapper::find_chain_alignment(
             Path link_path(link_aln.path());
             link_graph_path_length = path_from_length(link_path);
             append_path(composed_path, std::move(link_path));
-            composed_score += link_aln.score();
+            link_score = link_aln.score();
+            composed_score += link_score;
         }
 
         if (show_work) {
             #pragma omp critical (cerr)
             {
-                cerr << log_name() << "Aligned and added link of " << link_length << " bp read and " << link_graph_path_length << " bp graph via " << link_alignment_source << " with score of " << link_aln.score() << std::endl;
+                cerr << log_name() << "Aligned and added link of " << link_length << " bp read and " << link_graph_path_length << " bp graph via " << link_alignment_source << " with score of " << link_score << std::endl;
             }
         }