[TEST] Add tests

Author: eseiler

test/unit/io/sam_file/format_bam_test.cpp

@@ -37,6 +37,13 @@ struct sam_file_read<seqan3::format_bam> : public sam_file_data
                                '\x33', '\x34', '\x0a', '\x01', '\x00', '\x00', '\x00', '\x04', '\x00', '\x00', '\x00',
                                '\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00'};
 
+    std::string unknown_tag_header{
+        '\x42', '\x41', '\x4d', '\x01', '\x25', '\x00', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56',
+        '\x4e', '\x3a', '\x31', '\x2e', '\x36', '\x09', '\x70', '\x62', '\x3a', '\x35', '\x2e', '\x30', '\x2e',
+        '\x30', '\x0a', '\x40', '\x53', '\x51', '\x09', '\x53', '\x4e', '\x3a', '\x72', '\x65', '\x66', '\x09',
+        '\x4c', '\x4e', '\x3a', '\x33', '\x34', '\x0a', '\x01', '\x00', '\x00', '\x00', '\x04', '\x00', '\x00',
+        '\x00', '\x72', '\x65', '\x66', '\x00', '\x22', '\x00', '\x00', '\x00'};
+
     std::string big_header_input{
         '\x42', '\x41', '\x4D', '\x01', '\xB7', '\x01', '\x00', '\x00', '\x40', '\x48', '\x44', '\x09', '\x56', '\x4E',
         '\x3A', '\x31', '\x2E', '\x36', '\x09', '\x53', '\x4F', '\x3A', '\x63', '\x6F', '\x6F', '\x72', '\x64', '\x69',

test/unit/io/sam_file/format_sam_test.cpp

@@ -18,6 +18,11 @@ struct sam_file_read<seqan3::format_sam> : public sam_file_data
     std::string minimal_header{
         R"(@HD	VN:1.6
 @SQ	SN:ref	LN:34
+)"};
+
+    std::string unknown_tag_header{
+        R"(@HD	VN:1.6	pb:5.0.0
+@SQ	SN:ref	LN:34
 )"};
 
     std::string big_header_input{

test/unit/io/sam_file/sam_file_format_test_template.hpp

@@ -19,6 +19,7 @@
 #include <seqan3/test/expect_range_eq.hpp>
 #include <seqan3/test/pretty_printing.hpp>
 #include <seqan3/test/streambuf.hpp>
+#include <seqan3/test/tmp_directory.hpp>
 
 using seqan3::operator""_cigar_operation;
 using seqan3::operator""_dna5;
@@ -356,6 +357,67 @@ TYPED_TEST_P(sam_file_read, issue2423)
     EXPECT_EQ(fin.header().ref_dict.size(), 64u);
 }
 
+TYPED_TEST_P(sam_file_read, unknown_header_tag)
+{
+    // Default: Warnings to cerr
+    {
+        typename TestFixture::stream_type istream{this->unknown_tag_header};
+        seqan3::sam_file_input fin{istream, TypeParam{}};
+        testing::internal::CaptureStdout();
+        testing::internal::CaptureStderr();
+        EXPECT_NO_THROW(fin.begin());
+        EXPECT_EQ(testing::internal::GetCapturedStdout(), "");
+        EXPECT_EQ(testing::internal::GetCapturedStderr(), "Unsupported SAM header tag in @HD: pb\n");
+    }
+    // Redirect to cout
+    {
+        typename TestFixture::stream_type istream{this->unknown_tag_header};
+        seqan3::sam_file_input fin{istream, TypeParam{}};
+        fin.options.warning_stream = std::addressof(std::cout);
+        testing::internal::CaptureStdout();
+        testing::internal::CaptureStderr();
+        EXPECT_NO_THROW(fin.begin());
+        EXPECT_EQ(testing::internal::GetCapturedStdout(), "Unsupported SAM header tag in @HD: pb\n");
+        EXPECT_EQ(testing::internal::GetCapturedStderr(), "");
+    }
+    // Redirect to file
+    {
+        seqan3::test::tmp_directory tmp{};
+        auto filename = tmp.path() / "warnings.txt";
+
+        // Scope for ofstream-RAII
+        {
+            std::ofstream warning_file{filename};
+            ASSERT_TRUE(warning_file.good());
+
+            typename TestFixture::stream_type istream{this->unknown_tag_header};
+            seqan3::sam_file_input fin{istream, TypeParam{}};
+            fin.options.warning_stream = std::addressof(warning_file);
+            testing::internal::CaptureStdout();
+            testing::internal::CaptureStderr();
+            EXPECT_NO_THROW(fin.begin());
+            EXPECT_EQ(testing::internal::GetCapturedStdout(), "");
+            EXPECT_EQ(testing::internal::GetCapturedStderr(), "");
+        }
+
+        std::ifstream warning_file{filename};
+        ASSERT_TRUE(warning_file.good());
+        std::string content{std::istreambuf_iterator<char>(warning_file), std::istreambuf_iterator<char>()};
+        EXPECT_EQ(content, "Unsupported SAM header tag in @HD: pb\n");
+    }
+    // Silence
+    {
+        typename TestFixture::stream_type istream{this->unknown_tag_header};
+        seqan3::sam_file_input fin{istream, TypeParam{}};
+        fin.options.warning_stream = nullptr;
+        testing::internal::CaptureStdout();
+        testing::internal::CaptureStderr();
+        EXPECT_NO_THROW(fin.begin());
+        EXPECT_EQ(testing::internal::GetCapturedStdout(), "");
+        EXPECT_EQ(testing::internal::GetCapturedStderr(), "");
+    }
+}
+
 // ----------------------------------------------------------------------------
 // sam_file_write
 // ----------------------------------------------------------------------------
@@ -703,7 +765,8 @@ REGISTER_TYPED_TEST_SUITE_P(sam_file_read,
                             cigar_vector,
                             format_error_ref_id_not_in_reference_information,
                             format_error_uneven_hexadecimal_tag,
-                            issue2423);
+                            issue2423,
+                            unknown_header_tag);
 
 REGISTER_TYPED_TEST_SUITE_P(sam_file_write,
                             no_records,