fixed realigned window

impute_jass/impute_jass/windows.py

@@ -31,10 +31,11 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
     If not, the coded and other allele are inverted and the zscore sign
     is inverted also.
     """
-    allele_inverted = (ref_panel.loc[zscore.index, 'Ref_all'] != zscore.A0)
+    sub_ref_panel = ref_panel.loc[zscore.index]
+    allele_inverted = (sub_ref_panel['Ref_all'] != zscore.A0)
 
-    zscore.loc[allele_inverted, "A0"] = ref_panel.alt_all
-    zscore.loc[allele_inverted, "A1"] = ref_panel.Ref_all
+    zscore.loc[allele_inverted, "A0"] = sub_ref_panel.loc[allele_inverted].Ref_all
+    zscore.loc[allele_inverted, "A1"] = sub_ref_panel.loc[allele_inverted].alt_all
     zscore.loc[allele_inverted, "Z"] = - zscore.loc[allele_inverted, "Z"]
 
     return zscore