update on current main

Author: smehringer

include/bio/format/sam_input_handler.hpp

@@ -51,7 +51,7 @@ class format_input_handler<sam> : public format_input_handler_base<format_input_
 
     /* RAW RECORD HANDLING*/
     using format_fields = decltype(map_io::default_field_ids);
-    using raw_record_type = detail::record_from_typelist<format_fields,
+    using raw_record_type = bio::record<format_fields,
                   seqan3::list_traits::repeat<format_fields::size, std::string_view>>;
 
     //!\brief Type of the low-level iterator.

test/unit/format/sam_file_format_test_template.hpp

@@ -30,8 +30,7 @@ using seqan3::operator""_phred42;
 using seqan3::operator""_tag;
 
 // global variables for reuse
-seqan3::sam_file_input_options<seqan3::dna5> input_options;
-seqan3::sam_file_output_options output_options;
+bio::map_io::reader_options default_options{};
 
 struct sam_file_data : public ::testing::Test
 {
@@ -175,10 +174,7 @@ TYPED_TEST_P(sam_file_read, full_data_set)
 
     // read data
     typename TestFixture::stream_type istream{this->verbose_reads_input};
-    using record_t =
-      bio::detail::record_from_typelist<std::remove_cvref_t<decltype(bio::map_io::default_field_ids)>,
-                                        std::remove_cvref_t<decltype(bio::map_io::field_types_sam<>)>>;
-    bio::map_io::reader_options default_options{};
+    using record_t = bio::record<decltype(default_options.field_ids), decltype(default_options.field_types)>;
     bio::format_input_handler<bio::sam> input_handler{istream, default_options};
     record_t rec;
 
@@ -205,10 +201,7 @@ TYPED_TEST_P(sam_file_read, all_missing_data)
 {
     typename TestFixture::stream_type istream{this->empty_input};
 
-    using record_t =
-      bio::detail::record_from_typelist<std::remove_cvref_t<decltype(bio::map_io::default_field_ids)>,
-                                        std::remove_cvref_t<decltype(bio::map_io::field_types_sam<>)>>;
-    bio::map_io::reader_options default_options{};
+    using record_t = bio::record<decltype(default_options.field_ids), decltype(default_options.field_types)>;
     bio::format_input_handler<bio::sam> input_handler{istream, default_options};
     record_t rec;
 
@@ -236,9 +229,7 @@ TYPED_TEST_P(sam_file_read, select_fields)
     constexpr auto fid = bio::vtag<bio::field::rname, bio::field::pos>;
     constexpr auto ftype = bio::ttag<std::string_view, int64_t>;
 
-    using record_t =
-      bio::detail::record_from_typelist<std::remove_cvref_t<decltype(fid)>, std::remove_cvref_t<decltype(ftype)>>;
-    bio::map_io::reader_options default_options{};
+    using record_t = bio::record<std::remove_cvref_t<decltype(fid)>, std::remove_cvref_t<decltype(ftype)>>;
     bio::format_input_handler<bio::sam> input_handler{istream, default_options};
     record_t rec;