3 files changed, 18 insertions, 7 deletions
diff --git a/utils/atools.cc b/utils/atools.cc
index 1726c4ac..559eadef 100644
--- a/utils/atools.cc
+++ b/utils/atools.cc
@@ -203,14 +203,16 @@ struct RefineCommand : public Command {
     bool keep_going = !p.empty();
     while (keep_going) {
       keep_going = false;
-      for (set<pair<int, int> >::iterator pi = p.begin();
-           pi != p.end(); ++pi) {
+      set<pair<int, int> > added;
+      for (set<pair<int, int> >::iterator pi = p.begin(); pi != p.end(); ++pi) {
         if ((this->*pred)(pi->first, pi->second)) {
           Align(pi->first, pi->second);
-          p.erase(pi);
+          added.insert(make_pair(pi->first, pi->second));
           keep_going = true;
         }
       }
+      for (set<pair<int, int> >::iterator ai = added.begin(); ai != added.end(); ++ai)
+        p.erase(*ai);
     }
   }
   Array2D<bool> res_;  // refined alignment
diff --git a/utils/filelib.h b/utils/filelib.h
index b9ea3940..4fa69760 100644
--- a/utils/filelib.h
+++ b/utils/filelib.h
@@ -75,7 +75,10 @@ class ReadFile : public BaseFile<std::istream> {
       }
     }
   }
-
+  void ReadAll(std::string& s) {
+    getline(*stream(), s, (char) EOF);
+    if (s.size() > 0) s.resize(s.size()-1);
+  }
 };
 
 class WriteFile : public BaseFile<std::ostream> {
diff --git a/utils/hash.h b/utils/hash.h
index 189ed1ae..e1426ffb 100644
--- a/utils/hash.h
+++ b/utils/hash.h
@@ -20,11 +20,17 @@
 # define HASH_MAP_RESERVED(h,empty,deleted) do { (h).set_empty_key(empty); (h).set_deleted_key(deleted); } while(0)
 # define HASH_MAP_EMPTY(h,empty) do { (h).set_empty_key(empty); } while(0)
 #else
+#ifndef HAVE_OLD_CPP
+# include <unordered_map>
+# include <unordered_set>
+#else
 # include <tr1/unordered_map>
 # include <tr1/unordered_set>
-# define SPARSE_HASH_MAP std::tr1::unordered_map
-# define HASH_MAP std::tr1::unordered_map
-# define HASH_SET std::tr1::unordered_set
+namespace std { using std::tr1::unordered_map; using std::tr1::unordered_set; }
+#endif
+# define SPARSE_HASH_MAP std::unordered_map
+# define HASH_MAP std::unordered_map
+# define HASH_SET std::unordered_set
 # define HASH_MAP_DELETED(h,deleted)
 # define HASH_MAP_RESERVED(h,empty,deleted)
 # define HASH_MAP_EMPTY(h,empty)