[MISC] Update and extend prefixes.

include/hibf/detail/layout/layout.hpp

@@ -27,7 +27,7 @@ struct layout
             requires std::derived_from<stream_type, std::ostream>
         friend stream_type & operator<<(stream_type & stream, max_bin const & object)
         {
-            stream << prefix::header << prefix::merged_bin << '_';
+            stream << prefix::layout_header << prefix::layout_lower_level << '_';
             auto it = object.previous_TB_indices.begin();
             auto end = object.previous_TB_indices.end();
             // If not empty, we join with ';'
@@ -37,7 +37,7 @@ struct layout
                 while (++it != end)
                     stream << ';' << *it;
             }
-            stream << " max_bin_id:" << object.id;
+            stream << " " << prefix::layout_fullest_technical_bin_idx << object.id;
 
             return stream;
         }

include/hibf/detail/prefixes.hpp

@@ -6,21 +6,55 @@
 
 namespace hibf::prefix
 {
-
-constexpr std::string_view chopper{"chopper"};
-
-constexpr std::string_view header{"#"};
-
-constexpr std::string_view header_config{"#"};
-
-constexpr std::string_view high_level{"HIGH_LEVEL_IBF"};
-
-constexpr std::string_view first_header_line{"#HIGH_LEVEL_IBF"};
-static_assert(first_header_line.starts_with(header));
-static_assert(first_header_line.ends_with(high_level));
-
-constexpr std::string_view merged_bin{"MERGED_BIN"};
-
-constexpr std::string_view split_bin{"SPLIT_BIN"};
+/* These prefixes are for writing the layout file
+
+ * It is structured like this:
+ *
+ * [0) Possibly metadata added by chopper/raptor-layout]
+ * 1) Metadata: the hibf config
+ * 2) Layout header: max bin ids for the merged bins
+ * 3) Layout content: Assignment of user bin idx to technical bin idx
+ *
+ * And marked like this:
+ * [0) First character is @; Start and End of meta data should be marked accordingly to (1)]
+ * 1) First character is @; Start and End are marked by @HIBF_CONFIG and @HIBF_CONFIG_END respectively
+ * 2) First character is #;
+ * 3) No mark, plain content.
+ *
+ * Example:
+ *
+ * ```
+ * @CHOPPER_USER_BINS
+ * @0 /path/to/file1.fa
+ * @CHOPPER_USER_BINS_END
+ * @CHOPPER_CONFIG
+ * @0 k = 20
+ * @CHOPPER_CONFIG_END
+ *
+ * ``
+ */
+
+constexpr std::string_view meta_header{"@"};
+
+constexpr std::string_view meta_hibf_config_start{"@HIBF_CONFIG"};
+static_assert(meta_hibf_config_start.starts_with(meta_header));
+
+constexpr std::string_view meta_hibf_config_end{"@HIBF_CONFIG_END"};
+static_assert(meta_hibf_config_end.starts_with(meta_header));
+
+constexpr std::string_view layout_header{"#"};
+
+constexpr std::string_view layout_top_level{"TOP_LEVEL_IBF"};
+
+constexpr std::string_view layout_lower_level{"LOWER_LEVEL_IBF"};
+
+constexpr std::string_view layout_fullest_technical_bin_idx{"fullest_technical_bin_idx:"};
+
+constexpr std::string_view layout_first_header_line{"#TOP_LEVEL_IBF"};
+static_assert(layout_first_header_line.starts_with(layout_header));
+static_assert(layout_first_header_line.ends_with(layout_top_level));
+
+constexpr std::string_view layout_column_names{"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS"};
+static_assert(layout_column_names.starts_with(layout_header));
 
 } // namespace hibf::prefix

test/unit/hibf/detail/layout/layout_test.cpp

@@ -21,9 +21,9 @@ TEST(layout_test, printing_max_bins)
     for (auto const & mb : layout.max_bins)
         ss << mb << "\n";
 
-    std::string expected = R"mb(#MERGED_BIN_ max_bin_id:0
-#MERGED_BIN_2 max_bin_id:2
-#MERGED_BIN_1;2;3;4 max_bin_id:22
+    std::string expected = R"mb(#LOWER_LEVEL_IBF_ fullest_technical_bin_idx:0
+#LOWER_LEVEL_IBF_2 fullest_technical_bin_idx:2
+#LOWER_LEVEL_IBF_1;2;3;4 fullest_technical_bin_idx:22
 )mb";
 
     EXPECT_EQ(ss.str(), expected);