fix: sync filter_mod.dopplerfold with filter_mod

fixes: #565

assimilation_code/modules/assimilation/filter_mod.dopplerfold.f90

@@ -385,7 +385,6 @@ subroutine filter_main()
 write(msgstring, '(A,I5)') 'running with an ensemble size of ', ens_size
 call error_handler(E_MSG,'filter_main:', msgstring, source)
 
-
 call set_missing_ok_status(allow_missing_clm)
 allow_missing = get_missing_ok_status()
 
@@ -982,6 +981,7 @@ subroutine filter_main()
       call timestamp_message('After  computing posterior observation values')
       call     trace_message('After  computing posterior observation values')
 
+
       call trace_message('Before posterior obs space diagnostics')
 
       ! Write posterior observation space diagnostics
@@ -995,6 +995,10 @@ subroutine filter_main()
 
       call trace_message('After  posterior obs space diagnostics')
    else
+      ! call this alternate routine to collect any updated QC values that may
+      ! have been set in the assimilation loop and copy them to the outgoing obs seq
+      call obs_space_sync_QCs(obs_fwd_op_ens_handle, seq, keys, num_obs_in_set, &
+                              OBS_GLOBAL_QC_COPY, DART_qc_index)
       call deallocate_single_copy(obs_fwd_op_ens_handle, prior_qc_copy)
    endif
 
@@ -1593,7 +1597,7 @@ subroutine obs_space_diagnostics(obs_fwd_op_ens_handle, qc_ens_handle, ens_size,
    OBS_MEAN_START, OBS_VAR_START, OBS_GLOBAL_QC_COPY, OBS_VAL_COPY, &
    OBS_ERR_VAR_COPY, DART_qc_index, do_post)
 
-! Do prior observation space diagnostics on the set of obs corresponding to keys
+! Do observation space diagnostics on the set of obs corresponding to keys
 
 type(ensemble_type),     intent(inout) :: obs_fwd_op_ens_handle, qc_ens_handle
 integer,                 intent(in)    :: ens_size
@@ -1701,6 +1705,52 @@ end subroutine obs_space_diagnostics
 
 !-------------------------------------------------------------------------
 
+subroutine obs_space_sync_QCs(obs_fwd_op_ens_handle,  &
+   seq, keys, num_obs_in_set, OBS_GLOBAL_QC_COPY, DART_qc_index)
+
+
+type(ensemble_type),     intent(inout) :: obs_fwd_op_ens_handle
+integer,                 intent(in)    :: num_obs_in_set
+integer,                 intent(in)    :: keys(num_obs_in_set)
+type(obs_sequence_type), intent(inout) :: seq
+integer,                 intent(in)    :: OBS_GLOBAL_QC_COPY
+integer,                 intent(in)    :: DART_qc_index
+
+integer               :: j
+integer               :: io_task, my_task
+real(r8), allocatable :: obs_temp(:)
+real(r8)              :: rvalue(1)
+
+! this is a query routine to return which task has 
+! logical processing element 0 in this ensemble.
+io_task = map_pe_to_task(obs_fwd_op_ens_handle, 0)
+my_task = my_task_id()
+
+! create temp space for QC values
+if (my_task == io_task) then
+   allocate(obs_temp(num_obs_in_set))
+else 
+   allocate(obs_temp(1))
+endif
+
+! Optimize: Could we use a gather instead of a transpose and get copy?
+call all_copies_to_all_vars(obs_fwd_op_ens_handle)
+
+! Update the qc global value
+call get_copy(io_task, obs_fwd_op_ens_handle, OBS_GLOBAL_QC_COPY, obs_temp)
+if(my_task == io_task) then
+   do j = 1, obs_fwd_op_ens_handle%num_vars
+      rvalue(1) = obs_temp(j)
+      call replace_qc(seq, keys(j), rvalue, DART_qc_index)
+   end do
+endif
+
+deallocate(obs_temp)
+
+end subroutine obs_space_sync_QCs
+
+!-------------------------------------------------------------------------
+
 subroutine filter_sync_keys_time(ens_handle, key_bounds, num_obs_in_set, time1, time2)
 
 integer,             intent(inout)  :: key_bounds(2), num_obs_in_set