corrected column mix up when snpid is not first

jass_preprocessing/map_gwas.py

@@ -152,13 +152,13 @@ def read_gwas( gwas_internal_link, column_map):
                                compression=compression,
                                 #column_dict['label_position'].keys(),
                                names= column_map.index,
-                                index_col=0,
                                  header=0, na_values= ['', '#N/A', '#N/A', 'N/A','#NA', '-1.#IND', '-1.#QNAN',
                                                  '-NaN', '-nan', '1.#IND', '1.#QNAN', 'N/A',
                                                  'NA', 'NULL', 'NaN',
-                                                 'nan', 'na', '.'])
-
-
+                                                 'nan', 'na', '.', '-'], dtype={"snpid":str, "a1":str,"a2":str,"freq":float, "z":float,"se":float, "pval":float})
+    print(fullGWAS.head())
+    fullGWAS.set_index("snpid", inplace=True)
+    print(fullGWAS.head())
     fullGWAS = fullGWAS[~fullGWAS.index.duplicated(keep='first')]
     #fullGWAS = convert_missing_values(fullGWAS)