ex-273 (jebene/dkriti) added guard against having both untranslated and

translated input VCFs

jacquard/merge.py

@@ -653,6 +653,26 @@ def _validate_consistent_samples(file_readers):
         msg = "Some samples appear to be missing VCF(s)"
         logger.warning(msg)
 
+def _validate_consistent_input(vcf_readers, include_all):
+    if not include_all:
+        untranslated_readers = []
+        translated = False
+        untranslated = False
+
+        for vcf_reader in vcf_readers:
+            if '##jacquard.translate.caller' in vcf_reader.metaheaders:
+                translated = True
+            else:
+                untranslated = True
+                untranslated_readers.append(vcf_reader)
+
+        if translated and untranslated:
+            msg = ("Some input VCFs [{}] were not translated by Jacquard. Review "
+                   "input and/or use --included_all flag")\
+                   .format(untranslated_readers)
+            raise utils.UsageError(msg)
+
+
 def _merge_records(vcf_readers,
                    coordinates,
                    filter_strategy,
@@ -771,6 +791,7 @@ def execute(args, execution_context):
 #signatures of these methods more similar or even combine some methods to
 #reduce excess iterations over the coordinates/vcf_readers
         merge_vcf_readers = _create_vcf_readers(file_readers)
+        _validate_consistent_input(merge_vcf_readers, args.include_all)
         merge_vcf_readers = _sort_readers(merge_vcf_readers, output_path)
         format_tags = _get_format_tags(merge_vcf_readers)
         _disambiguate_format_tags(merge_vcf_readers, format_tags)

test/merge_test.py

@@ -463,6 +463,53 @@ def test_validate_consistent_samples_allMissingCallers(self):
                                  "Some samples appear to be missing VCF(s)"]
         self.assertEquals(expected_log_warnings, actual_log_warnings)
 
+    def test_validate_consistent_input_allTranslatedOkay(self):
+        metaheaders1 = ["##metaheader1", "##metaheader2", "##jacquard.translate.caller"]
+        vcf_reader1 = MockVcfReader(metaheaders=metaheaders1)
+
+        metaheaders2 = ["##metaheader3", "##jacquard.translate.caller", "##metaheader4"]
+        vcf_reader2 = MockVcfReader(metaheaders=metaheaders2)
+
+        merge._validate_consistent_input([vcf_reader1, vcf_reader2], False)
+        actual_log_errors = test.utils.mock_logger.messages["ERROR"]
+        self.assertEquals([], actual_log_errors)
+
+    def test_validate_consistent_input_allUntranslatedOkay(self):
+        metaheaders1 = ["##metaheader1", "##metaheader2"]
+        vcf_reader1 = MockVcfReader(metaheaders=metaheaders1)
+
+        metaheaders2 = ["##metaheader3", "##metaheader4"]
+        vcf_reader2 = MockVcfReader(metaheaders=metaheaders2)
+
+        merge._validate_consistent_input([vcf_reader1, vcf_reader2], False)
+        actual_log_errors = test.utils.mock_logger.messages["ERROR"]
+        self.assertEquals([], actual_log_errors)
+
+    def test_validate_consistent_input_errorIfMixed(self):
+        metaheaders1 = ["##metaheader1", "##metaheader2", "##jacquard.translate.caller"]
+        vcf_reader1 = MockVcfReader(metaheaders=metaheaders1)
+
+        metaheaders2 = ["##metaheader3", "##metaheader4"]
+        vcf_reader2 = MockVcfReader(metaheaders=metaheaders2)
+
+        self.assertRaisesRegexp(utils.UsageError,
+                                r"Some input VCFs \[.*\] were not translated by Jacquard. Review input and/or use --included_all flag",
+                                merge._validate_consistent_input,
+                                [vcf_reader1, vcf_reader2],
+                                False)
+
+    def test_validate_consistent_input_okayIfIncludeAll(self):
+        metaheaders1 = ["##metaheader1", "##metaheader2", "##jacquard.translate.caller"]
+        vcf_reader1 = MockVcfReader(metaheaders=metaheaders1)
+
+        metaheaders2 = ["##metaheader3", "##metaheader4"]
+        vcf_reader2 = MockVcfReader(metaheaders=metaheaders2)
+
+        merge._validate_consistent_input([vcf_reader1, vcf_reader2], True)
+        actual_log_errors = test.utils.mock_logger.messages["ERROR"]
+        self.assertEquals([], actual_log_errors)
+
+
     def test_predict_output(self):
         with TempDirectory() as input_dir, TempDirectory() as output_dir:
             input_dir.write("A.normalized.jacquardTags.HCsomatic.vcf", b"##source=strelka\n#colHeader")