test(preprocessor): strict test to make sure pharmcat_position.vcf an…

…d pharmcat_position.uniallelic.vcf have the same content

preprocessor/tests/test_utilities.py

@@ -411,16 +411,11 @@ def test_prep_pharmcat_positions():
         assert tmp_uniallelic.is_file()
         assert uniallelic_mtime == tmp_uniallelic.stat().st_mtime
 
-        # check whether the uniallelic position file has the same number of positions as the position file
-        uniallelic_file_lines = helpers.read_vcf(helpers.uniallelic_pharmcat_positions_file, bgzipped=True).split('\n')
-        n_uniallelic_file_lines: int = len(uniallelic_file_lines)
-        # note that tmp_uniallelic is the equivalent uniallelic file generated from the pharmcat position file
-        tmp_uniallelic_lines = helpers.read_vcf(tmp_uniallelic, bgzipped=True).split('\n')
-        n_tmp_uniallelic_lines: int = len(tmp_uniallelic_lines)
-        # uniallelic_pharmcat_positions_file should
-        # have the same number of lines as its equivalent file generated from the pharmcat position file
-        assert n_uniallelic_file_lines == n_tmp_uniallelic_lines, \
-            'mismatching numbers of positions between %s and %s' % \
+        # check whether the uniallelic position file has the same file content as the position file
+        uniallelic_file_lines = helpers.read_vcf(helpers.uniallelic_pharmcat_positions_file, bgzipped=True)
+        tmp_uniallelic_lines = helpers.read_vcf(tmp_uniallelic, bgzipped=True)
+        assert uniallelic_file_lines == tmp_uniallelic_lines, \
+            'mismatching positions between %s and %s' % \
             (helpers.uniallelic_pharmcat_positions_file.name, helpers.pharmcat_positions_file.name)