Merge pull request #119 from srbcheema1/test_cases

Added test cases for SVLEN
EBIvariation · Apr 6, 2018 · e38e5d3 · e38e5d3
2 parents 15dd67b + 4a5c3b0
commit e38e5d3
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diff --git a/src/vcf/validate_optional_policy.cpp b/src/vcf/validate_optional_policy.cpp
@@ -175,7 +175,7 @@ namespace ebi
             util::string_split(it->second, ",", values);
             if (values.size() != record.alternate_alleles.size()) {
                 throw new InfoBodyError{state.n_lines,
-                        "INFO SVLEN should have same number of values as ALT ", "Expected " + std::to_string(record.alternate_alleles.size())
+                        "INFO SVLEN should have same number of values as ALT", "Expected " + std::to_string(record.alternate_alleles.size())
                         + ", found " + std::to_string(values.size())};
             }
         }

diff --git a/test/vcf/optional_policy_test.cpp b/test/vcf/optional_policy_test.cpp
@@ -135,6 +135,51 @@ namespace ebi
                                 vcf::InfoBodyError*);
             }
         }
+
+        SECTION("SVLEN test")
+        {
+            source->meta_entries.emplace(vcf::INFO,
+                vcf::MetaEntry{
+                    1,
+                    vcf::INFO,
+                    {
+                        { vcf::ID, vcf::SVLEN },
+                        { vcf::NUMBER, "2" },
+                        { vcf::TYPE, vcf::INTEGER },
+                        { vcf::DESCRIPTION, "Difference in length between REF and ALT alleles" }
+                    },
+                    source
+            });
+
+            CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
+                                1,
+                                "chr1",
+                                123456,
+                                { "id123" },
+                                "A",
+                                { "AC", "ACT" },
+                                1.0,
+                                { vcf::PASS },
+                                { { vcf::SVLEN, "1,2" } },
+                                { vcf::GT },
+                                { "1|0" },
+                                source})) );
+
+            CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
+                                1,
+                                "chr1",
+                                123456,
+                                { "id123" },
+                                "A",
+                                { "AC" },
+                                1.0,
+                                { vcf::PASS },
+                                { { vcf::SVLEN, "1,2" } },
+                                { vcf::GT },
+                                { "0|1" },
+                                source})),
+                            vcf::InfoBodyError*);
+        }
     }
 
     TEST_CASE("Alternate allele warnings", "[body alt warnings]")