Added test cases for missing meta-data of reference and contig

EBIvariation · Apr 6, 2018 · 49624f6 · 49624f6
1 parent 1dd5910
commit 49624f6
Showing 1 changed file with 76 additions and 4 deletions.
diff --git a/test/vcf/optional_policy_test.cpp b/test/vcf/optional_policy_test.cpp
@@ -392,6 +392,79 @@ namespace ebi
 
     TEST_CASE("Meta-data warnings", "[warnings]")
     {
+        SECTION("Reference not in meta section")
+        {
+            std::shared_ptr<vcf::Source> source{
+                new vcf::Source{
+                    "Example VCF source",
+                    vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
+                    vcf::Version::v43}};
+
+            vcf::ParsingState parsing_state{source};
+
+            vcf::ValidateOptionalPolicy optional_policy;
+
+            CHECK_THROWS_AS( (optional_policy.optional_check_meta_section(parsing_state)), vcf::MetaSectionError*);
+        }
+
+        SECTION("Contig not in meta section")
+        {
+            std::shared_ptr<vcf::Source> source{
+                new vcf::Source{
+                    "Example VCF source",
+                    vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
+                    vcf::Version::v43}};
+
+            source->meta_entries.emplace(vcf::REFERENCE,
+                vcf::MetaEntry{
+                    1,
+                    vcf::REFERENCE,
+                    "file",
+                    source
+            });
+
+            source->meta_entries.emplace(vcf::CONTIG,
+                vcf::MetaEntry{
+                    1,
+                    vcf::CONTIG,
+                    { { vcf::ID, "chr1" } },
+                    source
+            });
+
+            vcf::ParsingState parsing_state{source};
+
+            vcf::ValidateOptionalPolicy optional_policy;
+
+            CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
+                                1,
+                                "chr1",
+                                123456,
+                                { vcf::MISSING_VALUE },
+                                "A",
+                                { "AC" },
+                                1.0,
+                                { vcf::PASS },
+                                { { vcf::MISSING_VALUE, "" } },
+                                { },
+                                { },
+                                source})) );
+
+            CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
+                                1,
+                                "chr2",
+                                123456,
+                                { vcf::MISSING_VALUE },
+                                "A",
+                                { "AC" },
+                                1.0,
+                                { vcf::PASS },
+                                { { vcf::MISSING_VALUE, "" } },
+                                { },
+                                { },
+                                source})),
+                            vcf::NoMetaDefinitionError*); 
+        }
+
         SECTION("Alternate Allele not in meta section")
         {
             std::shared_ptr<vcf::Source> source{
@@ -435,7 +508,7 @@ namespace ebi
                                 1,
                                 "chr1",
                                 123456,
-                                { vcf::PASS },
+                                { vcf::MISSING_VALUE },
                                 "A",
                                 { "AC" },
                                 1.0,
@@ -453,7 +526,7 @@ namespace ebi
                                 "A",
                                 { "<DEL>" },
                                 1.0,
-                                { vcf::MISSING_VALUE },
+                                { vcf::PASS },
                                 { { vcf::MISSING_VALUE, "" } },
                                 { },
                                 { },
@@ -467,13 +540,12 @@ namespace ebi
                                 "A",
                                 { "<INS>" },
                                 1.0,
-                                { "q10" },
+                                { vcf::PASS },
                                 { { vcf::MISSING_VALUE, "" } },
                                 { },
                                 { },
                                 source})),
                             vcf::NoMetaDefinitionError*);
-
         }
 
         SECTION("FILTER not in meta section")