Added ld_score to the output

impute_jass/impute_jass/windows.py

@@ -43,8 +43,9 @@ def prepare_zscore_for_imputation(ref_panel, zscore):
     the snps that are not present in the ref panel are filtered
     """
     zscore = realigned_zfiles_on_panel(ref_panel, zscore)
-    zscore['Var'] = 1
+    zscore['Var'] = -1
     zscore['Nsnp_to_impute'] = -1
+    zscore['ld_score'] = -1
     zscore = zscore.loc[zscore.index.intersection(ref_panel.index)]
     return zscore
 
@@ -138,8 +139,8 @@ def impg_like_imputation(ld_file, ref_panel, zscore, window_size, buffer, lamb,
             in_core_window = in_region(batch_df.pos, start_core_window, end_core_window)
 
             # keep only SNP with non negligible explained variance
-            snp_well_predicted = batch_df.Var < 0.5
-            batch_df_filt = batch_df_filt.loc[in_core_window & snp_well_predicted, zscore_results.columns]
+            snp_well_predicted = (batch_df.Var < 0.4)
+            batch_df_filt = batch_df.loc[in_core_window & snp_well_predicted, zscore_results.columns]
             zscore_results = pd.concat([zscore_results, batch_df_filt])
         i = i+1
         print_progression(i, Nwindows)