treat exception when missing position

jass_preprocessing/map_reference.py

@@ -21,8 +21,10 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
     """
     ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t",
                       names =[ 'chr', "snp_id", "MAF","pos",  "ref", "alt"],
-                      dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.int64, "ref":str, "alt":str},
+                      dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.double, "ref":str, "alt":str},
                        index_col="snp_id")
+    ref = ref.loc[~ref.pos.isnull()]
+    ref.pos = ref.pos.astype('int')
 
     def sorted_alleles(x):
         return "".join(sorted(x))