Draft: construct pangenome database from GFA

Related to !147, I would like to not only go from pantools_DB -> GFA but also vice versa. This merge request collects my tries of doing that. It's marked as draft for now because I'm not sure if I'll use this code in the end.

TODO:

• Fix kmer index
• Make working on cyclic graphs
• Find out what happens with degenerate nodes
• Don't require genome locations file if GFA is provided (if GFA contains sequences)
• Get it to run on any valid GFA
• Ensure neo4j -> GFA -> neo4j gives identical database
• Ensure GFA -> neo4j -> GFA gives identical GFA file
• Update documentation accordingly

src/main/java/nl/wur/bif/pantools/utils/graph/GfaReader.java

@@ -11,11 +11,12 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
+import java.util.stream.Collectors;
 
 public class GfaReader {
     private final Path gfaFile;
     private final Map<Long, GraphNode> vertices = new HashMap<>();
-    private final Map<Long, GraphEdge> edges = new HashMap<>();
+    private final Map<EdgeKey, GraphEdge> edges = new HashMap<>();
     private final List<GraphPath> paths = new ArrayList<>();
 
     public GfaReader(Path gfaFile) throws IOException {
@@ -96,8 +97,7 @@ public class GfaReader {
                     final GraphNode source = this.vertices.get(sourceId);
                     final char sourceOrientation = steps[j - 1].charAt(steps[j - 1].length() - 1);
                     final char orientation = step.charAt(step.length() - 1);
-                    final GraphEdge edgeId = findGraphEdge(source, sourceOrientation, vertex, orientation);
-                    final GraphEdge pathGraphEdge = this.edges.get(edgeId.getId());
+                    final GraphEdge pathGraphEdge = findGraphEdge(source, sourceOrientation, vertex, orientation);
                     pathGraphEdges.add(pathGraphEdge);
                 }
             }
@@ -121,7 +121,8 @@ public class GfaReader {
             final char targetOrientation = fields[4].charAt(0);
             final String overlap = fields[5];
             final GraphEdge edge = new GraphEdge(i, this.vertices.get(sourceId), sourceOrientation, this.vertices.get(targetId), targetOrientation, overlap);
-            this.edges.put(edge.getId(), edge);
+            EdgeKey key = new EdgeKey(sourceId, sourceOrientation, targetId, targetOrientation);
+            this.edges.put(key, edge);
             i++;
         }
     }
@@ -141,7 +142,7 @@ public class GfaReader {
     }
 
     /**
-     * Find an edge in the graph.
+     * Find an edge in the graph using an EdgeKey
      * @param source source vertex
      * @param sourceOrientation orientation of the source vertex
      * @param target target vertex
@@ -149,16 +150,43 @@ public class GfaReader {
      * @return the edge
      */
     public GraphEdge findGraphEdge(GraphNode source, char sourceOrientation, GraphNode target, char targetOrientation) {
-        for (GraphEdge edge : this.edges.values()) {
-            if (edge.getSource().equals(source) &&
-                    edge.getSourceOrientation() == sourceOrientation &&
-                    edge.getTarget().equals(target) &&
-                    edge.getTargetOrientation() == targetOrientation) {
-                return edge;
-            }
+        EdgeKey key = new EdgeKey(source.getId(), sourceOrientation, target.getId(), targetOrientation);
+        GraphEdge edge = this.edges.get(key);
+        if (edge == null) {
+            Pantools.logger.error("GraphEdge {}{} -> {}{} does not exist.", source.getId(), sourceOrientation, target.getId(), targetOrientation);
+            throw new RuntimeException("GraphEdge " + source.getId() + sourceOrientation + " -> " + target.getId() + targetOrientation + " does not exist");
+        }
+        return edge;
+    }
+
+    private static class EdgeKey {
+        private final long sourceId;
+        private final char sourceOrientation;
+        private final long targetId;
+        private final char targetOrientation;
+
+        public EdgeKey(long sourceId, char sourceOrientation, long targetId, char targetOrientation) {
+            this.sourceId = sourceId;
+            this.sourceOrientation = sourceOrientation;
+            this.targetId = targetId;
+            this.targetOrientation = targetOrientation;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+            if (this == o) return true;
+            if (o == null || getClass() != o.getClass()) return false;
+            EdgeKey edgeKey = (EdgeKey) o;
+            return sourceId == edgeKey.sourceId &&
+                    sourceOrientation == edgeKey.sourceOrientation &&
+                    targetId == edgeKey.targetId &&
+                    targetOrientation == edgeKey.targetOrientation;
+        }
+
+        @Override
+        public int hashCode() {
+            return Objects.hash(sourceId, sourceOrientation, targetId, targetOrientation);
         }
-        Pantools.logger.error("GraphEdge {}{} -> {}{} does not exist.", source.getId(), sourceOrientation, target.getId(), targetOrientation);
-        throw new RuntimeException("GraphEdge " + source.getId() + sourceOrientation + " -> " + target.getId() + targetOrientation + " does not exist");
     }
 
     /**
@@ -184,14 +212,6 @@ public class GfaReader {
         throw new RuntimeException("Invalid GFA header");
     }
 
-    public Map<Long, GraphNode> getVertices() {
-        return this.vertices;
-    }
-
-    public Map<Long, GraphEdge> getGraphEdges() {
-        return this.edges;
-    }
-
     public List<GraphPath> getGraphPaths() {
         return this.paths;
     }
@@ -205,6 +225,11 @@ public class GfaReader {
     }
 
     public Graph getGraph() {
-        return new Graph(this.vertices, this.edges, new HashSet<>(this.paths));
+        return new Graph(this.vertices,
+                this.edges.values()
+                        .stream()
+                        .collect(Collectors.toMap(GraphEdge::getId,
+                                edge -> edge)),
+                new HashSet<>(this.paths));
     }
 }