also update frequency property on nucleotide nodes

src/main/java/nl/wur/bif/pantools/construction/build_pangenome/GenomeLayer.java

@@ -1341,8 +1341,6 @@ public class GenomeLayer {
             targetNode = createNewNodeGfa(edge.getTarget(), new int[]{genomeNr, sequenceNr, pathPosition}, index, nodeCache);
             createNewRelationshipGfa(sourceNode, edge.getType(), edge.getSourceEndOnTarget(), targetNode, origin, pathPosition, trsc);
             sourceNode = targetNode;
-
-            //TODO: update the localization information in the edge to the next node
         }
 
         // connect the last node to the sequence node with FF
@@ -1374,6 +1372,7 @@ public class GenomeLayer {
             newNode.setProperty("address", address);
             newNode.setProperty("length", node.getLength());
             newNode.setProperty("frequencies", new long[GENOME_DB.num_genomes + 1]);
+            newNode.setProperty("frequency", 0);
             newNode.setProperty("sequence", node.getSequence());
             num_bases += node.getLength();
 
@@ -1438,6 +1437,15 @@ public class GenomeLayer {
         frequencies[address[0]]++;
         newNode.setProperty("frequencies", frequencies);
 
+        // update the frequency property of the node
+        final long frequency = Arrays.stream(frequencies).sum();
+        newNode.setProperty("frequency", frequency);
+
+        // update global highest_frequency integer
+        if (frequency > highest_frequency) {
+            highest_frequency = frequency;
+        }
+
         // return the new node
         return newNode;
     }