[FIX] compression streams writing wrong format

include/seqan3/io/detail/misc_input.hpp

@@ -21,7 +21,6 @@
 #include <string>
 #include <tuple>
 
-
 #ifdef SEQAN3_HAS_BZIP2
     #include <seqan3/contrib/stream/bz2_istream.hpp>
 #endif
@@ -31,6 +30,7 @@
     #include <seqan3/contrib/stream/gz_istream.hpp>
 #endif
 #include <seqan3/io/detail/magic_header.hpp>
+#include <seqan3/io/exception.hpp>
 #include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::detail

include/seqan3/io/detail/misc_output.hpp

@@ -12,19 +12,20 @@
 
 #pragma once
 
+#include <seqan3/std/filesystem>
 #include <iostream>
 #include <string>
 #include <tuple>
 
-#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #ifdef SEQAN3_HAS_BZIP2
     #include <seqan3/contrib/stream/bz2_ostream.hpp>
 #endif
 #ifdef SEQAN3_HAS_ZLIB
     #include <seqan3/contrib/stream/bgzf_ostream.hpp>
     #include <seqan3/contrib/stream/gz_ostream.hpp>
 #endif
-#include <seqan3/std/filesystem>
+#include <seqan3/io/exception.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::detail
 {
@@ -46,16 +47,24 @@ inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream,
 
     std::string extension = filename.extension().string();
 
-    if ((extension == ".gz") || (extension == ".bgzf") || (extension == ".bam"))
+    if (extension == ".gz")
+    {
+    #ifdef SEQAN3_HAS_ZLIB
+        filename.replace_extension("");
+        return {new contrib::basic_gz_ostream<char_t>{primary_stream}, stream_deleter_default};
+    #else
+        throw file_open_error{"Trying to write a gzipped file, but no ZLIB available."};
+    #endif
+    }
+    else if ((extension == ".bgzf") || (extension == ".bam"))
     {
     #ifdef SEQAN3_HAS_ZLIB
         if (extension != ".bam") // remove extension except for bam
             filename.replace_extension("");
 
-        return {new contrib::basic_bgzf_ostream<char_t>{primary_stream},
-                stream_deleter_default};
+        return {new contrib::basic_bgzf_ostream<char_t>{primary_stream}, stream_deleter_default};
     #else
-        throw file_open_error{"Trying to write a gzipped file, but no ZLIB available."};
+        throw file_open_error{"Trying to write a bgzf'ed file, but no ZLIB available."};
     #endif
     }
     else if (extension == ".bz2")

test/unit/io/detail/misc_test.cpp

@@ -7,12 +7,16 @@
 
 #include <gtest/gtest.h>
 
+#include <fstream>
+#include <seqan3/std/ranges>
 #include <string>
 #include <vector>
 
 #include <seqan3/io/detail/magic_header.hpp>
 #include <seqan3/io/detail/misc.hpp>
-#include <seqan3/std/ranges>
+#include <seqan3/io/detail/misc_input.hpp>
+#include <seqan3/io/detail/misc_output.hpp>
+#include <seqan3/test/expect_same_type.hpp>
 #include <seqan3/test/tmp_filename.hpp>
 
 struct dummy_file
@@ -70,3 +74,52 @@ TEST(misc, valid_compression_extensions)
         EXPECT_TRUE(std::find(valid_compression.begin(), valid_compression.end(), "zst") != valid_compression.end());
     #endif
 }
+
+template <typename compression_t>
+class misc : public ::testing::Test
+{
+public:
+    static inline std::string const compression_extension = "." + compression_t::file_extensions[0];
+    static constexpr auto expected_magic_header = compression_t::magic_header;
+    static constexpr size_t biggest_magic_header_size = seqan3::detail::bgzf_compression::magic_header.size();
+
+    std::filesystem::path file_path() const
+    {
+        return tmp_file.get_path();
+    }
+
+private:
+    std::string const tmp_file_name = "io_misc_test.txt" + compression_extension;
+    seqan3::test::tmp_filename const tmp_file{tmp_file_name.c_str()};
+};
+
+using compression_types = ::testing::Types<seqan3::detail::gz_compression,
+                                           seqan3::detail::bgzf_compression,
+                                           seqan3::detail::bz2_compression>;
+
+TYPED_TEST_SUITE(misc, compression_types, );
+
+// https://github.com/seqan/seqan3/issues/2455
+TYPED_TEST(misc, issue2455)
+{
+    {
+        auto file_path = this->file_path();
+        std::ofstream filestream{file_path};
+        auto stream_ptr = seqan3::detail::make_secondary_ostream(filestream, file_path);
+        *stream_ptr << std::string(this->biggest_magic_header_size, 'a') << '\n';
+    }
+
+    std::ifstream filestream{this->file_path()};
+    std::array<char, this->biggest_magic_header_size> magic_header{};
+    std::copy_n(std::istreambuf_iterator{filestream}, this->biggest_magic_header_size, magic_header.begin());
+
+    if constexpr (std::same_as<TypeParam, seqan3::detail::bgzf_compression>)
+    {
+        EXPECT_TRUE(TypeParam::validate_header(std::span{magic_header}));
+    }
+    else
+    {
+        EXPECT_TRUE(seqan3::detail::starts_with(magic_header, this->expected_magic_header));
+        EXPECT_FALSE(seqan3::detail::bgzf_compression::validate_header(std::span{magic_header}));
+    }
+}

test/unit/io/sam_file/sam_file_output_test.cpp

@@ -650,7 +650,7 @@ TEST(compression, by_filename_gz)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte.
-    EXPECT_EQ(buffer, expected_bgzf);
+    EXPECT_EQ(buffer, expected_gz);
 }
 
 TEST(compression, by_stream_gz)

test/unit/io/sequence_file/sequence_file_output_test.cpp

@@ -528,7 +528,7 @@ TEST(compression, by_filename_gz)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
-    EXPECT_EQ(buffer, expected_bgzf);
+    EXPECT_EQ(buffer, expected_gz);
 }
 
 TEST(compression, by_stream_gz)

test/unit/io/structure_file/structure_file_output_test.cpp

@@ -481,7 +481,7 @@ TEST_F(structure_file_output_compression, by_filename_gz)
     seqan3::test::tmp_filename filename{"structure_file_output_test.dbn.gz"};
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
-    EXPECT_EQ(buffer, expected_bgzf);
+    EXPECT_EQ(buffer, expected_gz);
 }
 
 TEST_F(structure_file_output_compression, by_stream_gz)