Update windows.py

raiss/windows.py

@@ -164,7 +164,10 @@ def impg_like_imputation(ld_file, ref_panel, zscore, window_size, buffer, lamb,
         unknown_in_LD_reg_n_window =  in_region(all_unknowns.pos, start_pos, end_pos)
 
         known = zscore.loc[in_LD_reg_n_window].index
+        known = known.intersection(LD_mat.index)
+
         unknowns = all_unknowns.loc[unknown_in_LD_reg_n_window].index
+        unknowns = unknowns.intersection(LD_mat.index)
 
         sig_t = LD_mat.loc[known, known]
         sig_i_t = LD_mat.loc[unknowns, known]