From e836084013ec68674e40e24f56335c69674b7a1d Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Mon, 3 Jun 2024 11:50:57 +0200
Subject: [PATCH] [FIX] Make it throw

---
 src/util/display_layout/general.cpp   | 10 +++---
 test/cli/util_display_layout_test.cpp | 44 +++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/src/util/display_layout/general.cpp b/src/util/display_layout/general.cpp
index 9761559a..50e98a23 100644
--- a/src/util/display_layout/general.cpp
+++ b/src/util/display_layout/general.cpp
@@ -285,9 +285,10 @@ int execute(config const & cfg)
         std::vector<uint64_t> current_kmers{};
         // How many user bins are stored in the current technical bin? Always 1 for split bins.
         size_t const ub_count{chunk.size()};
-        // The current technical bin is a merged bin if it contains more than one user bin or if the (only) user bin
-        // has previous technical bins.
-        bool const is_merged{ub_count > 1u || hibf_layout.user_bins[chunk[0]].previous_TB_indices.size() != 0};
+        bool const is_merged{ub_count > 1u};
+        bool const has_lower_level = hibf_layout.user_bins[chunk[0]].previous_TB_indices.size() != 0;
+        if (!(is_merged ^ has_lower_level))
+            throw std::logic_error{"Invalid Layout: There is a merged bin that only consists of a single user bin."};
 
         for (size_t const ub_index : chunk)
         {
@@ -328,8 +329,7 @@ int execute(config const & cfg)
             progress.report();
         }
 
-        // Into how many techincal bins is the user bin split? Always 1 for merged bins. If it is a split bin,
-        // there is only one user bin.
+        // Into how many techincal bins is the user bin split? Always 1 for merged bins.
         size_t const split_count{is_merged ? 1u : hibf_layout.user_bins[chunk[0]].number_of_technical_bins};
         size_t const avg_kmer_count = (current_kmer_set.size() + split_count - 1u) / split_count;
         size_t const sketch_estimate = (sketch.estimate() + split_count - 1u) / split_count;
diff --git a/test/cli/util_display_layout_test.cpp b/test/cli/util_display_layout_test.cpp
index 2e1a86dc..fe4b3edc 100644
--- a/test/cli/util_display_layout_test.cpp
+++ b/test/cli/util_display_layout_test.cpp
@@ -132,6 +132,50 @@ TEST_F(cli_test, display_layout_general)
     EXPECT_EQ(expected_general_file, actual_file);
 }
 
+TEST_F(cli_test, display_layout_general_throw_invalid_layout)
+{
+    std::string const seq1_filename = data("seq1.fa");
+    std::string const seq2_filename = data("seq2.fa");
+    std::string const seq3_filename = data("seq3.fa");
+    std::string const small_filename = data("small.fa");
+    seqan3::test::tmp_directory tmp_dir{};
+    std::filesystem::path const layout_filename{tmp_dir.path() / "small.layout"};
+    std::filesystem::path const general_filename{tmp_dir.path() / "small.layout.general"};
+
+    {
+        std::ofstream fout{layout_filename};
+        std::string content = get_layout_with_correct_filenames(seq1_filename,
+                                                                seq2_filename,
+                                                                seq3_filename,
+                                                                small_filename,
+                                                                layout_filename.string());
+        size_t const last_header_line_start = content.rfind('#');
+        size_t const last_header_line_end = content.find('\n', last_header_line_start);
+        ASSERT_GT(content.size(), last_header_line_end);
+        content.erase(last_header_line_end + 1u);
+        content += "0\t0\t1\n"
+                   "1\t1;0\t1;64\n"
+                   "2\t2\t1\n"
+                   "3\t3\t2\n";
+        fout << content;
+    }
+
+    ASSERT_TRUE(std::filesystem::exists(layout_filename));
+
+    cli_test_result result = execute_app("display_layout",
+                                         "general",
+                                         "--input",
+                                         layout_filename.c_str(),
+                                         "--output",
+                                         general_filename.c_str());
+
+    ASSERT_NE(result.exit_code, 0) << "PWD: " << result.pwd << "\nCMD: " << result.command;
+    EXPECT_EQ(result.out, std::string{});
+    EXPECT_TRUE(result.err.find("Invalid Layout: There is a merged bin that only consists of a single user bin.")
+                != std::string::npos)
+        << result.err;
+}
+
 TEST_F(cli_test, display_layout_general_with_shared_kmers)
 {
     std::string const seq1_filename = data("seq1.fa");