set neff value when generating sub-profile

modules/seq/base/doc/seq.rst

@@ -755,7 +755,8 @@ probabilities between Match, Insertion or Deletion states or neff values
     :type to:  :class:`int`
 
     :returns: sub-profile as defined by given indices
-              (:attr:`null_model` is copied)
+              (:attr:`null_model` and :attr:`neff` are copied,
+              you might want to manually reset neff)
     :rtype: :class:`ProfileHandle`
 
     :raises: :exc:`~exceptions.Error` if *to* <= *from* or

modules/seq/base/src/profile_handle.cc

@@ -149,6 +149,7 @@ ProfileHandlePtr ProfileHandle::Extract(uint from, uint to) const {
   // get subset to return
   ProfileHandlePtr return_prof(new ProfileHandle);
   return_prof->SetNullModel(null_model_);
+  return_prof->SetNeff(neff_);
   for (uint i = from; i < to; ++i) {
     return_prof->AddColumn(columns_[i], seq_[i]);
   }