remove duplicated index in imputed SNPs

raiss/windows.py

@@ -32,8 +32,15 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
         - ref_panel (pd.dataframe) : snp of reference on the imputed chromosome
         - zscore (pd.dataframe):
     """
-    zscore.drop_duplicates(keep='first', inplace=True)
-    ref_panel.drop_duplicates(keep='first', inplace=True)
+    
+    # Remove SNPs with duplicated index
+    print("Duplicated SNPs to be removed")
+    print(ref_panel[ref_panel.index.duplicated(keep='first')])
+    print(zscore[zscore.index.duplicated(keep='first')])
+
+    zscore = zscore[~zscore.index.duplicated(keep='first')]
+    ref_panel = ref_panel[~ref_panel.index.duplicated(keep='first')]
+
     inter_id = zscore.index.intersection(ref_panel.index).drop_duplicates(keep='first')
 
     zscore = zscore.loc[inter_id]
@@ -41,7 +48,6 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
 
     zscore.sort_index(inplace=True)
     sub_ref_panel.sort_index(inplace=True)
-
     allele_inverted = (sub_ref_panel.Ref_all != zscore.A0)
 
     zscore.loc[allele_inverted, "A0"] = sub_ref_panel.loc[allele_inverted].Ref_all