sclass LineComp_PairIndex {
  bool verbose;
  bool inOrder = true;
  MultiSetMap<IntPair, Node> nodes;
  MultiSetMap<Int, IntPair> byCount
    //= multiSetMap_innerHashSet_outerRevTreeMap(); // makes a difference in selecting a pair if there are multiple with the same count
    = multiSetMap_innerCompactHashSet_outerRevTreeMap(); // same but more compact
    //= multiSetMap_innerTreeSet_outerRevTreeMap(); // initial version that kind of pointlessly sorts the same-count nodes lexicographically
  new LinkedHashMap<S, Ch> chains;
  
  void init {
    nodes = inOrder
      ? multiSetMap_innerLinkedHashSet_outerHashMap()
      : multiSetMap_innerHashSet_outerHashMap();
  }
  
  // a "chain" of nodes (one input file)
  sclass Ch {
    Node tail;
    
    *(LineComp_PairIndex pi, L<Int> l) {
      fOr (int i : l) add(pi, i);
    }
    
    L<Int> toList() {
      new L<Int> l;
      Node node = tail;
      while (node != null) {
        l.add(node.value);
        node = node.prev;
      }
      ret reverseInPlace(l);
    }
    
    void add(LineComp_PairIndex pi, int i) {
      new Node n;
      n.ch = this;
      n.value = i;
      n.prev = tail;
      if (tail != null) tail.next = n;
      tail = n;
      pi.addToIndex(n.prev);
    }
  }
  
  sclass Node {
    Ch ch;
    int value;
    Node prev, next;
    
    int a() { ret value; }
    int b() { ret next == null ? -1 : next.value; }
    IntPair pair() { ret next == null ? null : IntPair(a(), b()); }
  }
  
  IntPair nodeToPair(Node n) {
    ret n?.pair();
  }
  
  // add node to pair index
  void addToIndex(Node n) {
    IntPair p = nodeToPair(n);
    if (p == null) ret;
    int count = nodes.getSize(p);
    nodes.add(p, n);
    if (count != 0) byCount.remove(count, p);
    byCount.put(count+1, p);
  }
  
  // remove node from pair index
  void removeFromIndex(Node n) {
    IntPair p = nodeToPair(n);
    if (p == null) ret;
    int count = nodes.getSize(p);
    if (count == 0) fail("Can't remove pair " + p);
    nodes.remove(p, n);
    byCount.remove(count, p);
    if (--count > 0) byCount.put(count, p);
  }
  
  IntPair mostPopularDuplicate() {
    ret toInt(firstKey(byCount)) < 2 ? null : firstValue(byCount);
  }
  
  int numberOfDuplicates() {
    ret byCount.size()-l(byCount.get(1));
  }
  
  int getCount(IntPair p) {
    ret nodes.getSize(p);
  }
  
  void replacePair(int pa, int pb, int replaceWith) {
    IntPair p = IntPair(pa, pb);
    Set<Node> set = nodes.get(p);
    for (Node n : cloneList(set)) {
      continue if n.a() != pa || n.b() != pb; // nodes might have been deleted or changed
      replacePair(n, replaceWith);
    }
  }
  
  void replacePair(Node node, int replaceWith) {
    removeFromIndex(node.prev);
    removeFromIndex(node);
    removeFromIndex(node.next);
    node.value = replaceWith;
    deleteNode(node.next);
    addToIndex(node.prev);
    addToIndex(node);
  }
  
  void deleteNode(Node node) {
    if (node.next != null) node.next.prev = node.prev; else node.ch.tail = node.prev;
    if (node.prev != null) node.prev.next = node.next;
    node.value = -1; // mark invalid
  }
  
  void newChain(S version, L<Int> encoding) {
    chains.put(version, new Ch(this, encoding));
  }
}

Began life as a copy of #1028247