Make sure to adopt the node offset when adopting the initial node

src/gbwt_extender.cpp

@@ -888,10 +888,14 @@ void WFAAlignment::join(const WFAAlignment& second) {
     if (second.edits.empty()) {
         throw std::runtime_error("Cannot join alignments because second alignment has no edits");
     }
-
+    
     if (!second.unlocalized_insertion()) {
         // The second alignment has a path
-        if (second.node_offset == 0 || unlocalized_insertion()) {
+        if (unlocalized_insertion()) {
+            // We don't, so include the first handle and copy the offset on it.
+            node_offset = second.node_offset
+            path.push_back(second.path.front());
+        } else if (second.node_offset == 0) {
             // Include the first handle from the second alignment because it can't be shared
             path.push_back(second.path.front());
         } else {

src/gbwt_extender.hpp

@@ -247,6 +247,7 @@ struct WFAAlignment {
     std::vector<std::pair<Edit, uint32_t>> edits;
 
     /// Starting offset in the initial node.
+    /// If there is no initial node, the value stored is undefined.
     uint32_t node_offset = 0;
 
     /// Starting offset in the sequence.

src/minimizer_mapper.hpp

@@ -983,7 +983,7 @@ Alignment MinimizerMapper::find_chain_alignment(
     } else {
         // No left tail to start with.
         // Just use an empty starting alignment, which is OK.
-        aligned = WFAAlignment::make_empty(); 
+        aligned = WFAAlignment::make_empty();
     }
 
     while(next_it != chain.end()) {