[MISC] read_layouts_file

Author: eseiler

src/util/display_layout/general.cpp

@@ -186,14 +186,16 @@ int execute(config const & cfg)
 
 // https://godbolt.org/z/PeKnxzjn1
 #if defined(__clang__)
-    auto tuple = chopper::layout::read_layout_file(layout_file);
+    auto tuple = chopper::layout::read_layouts_file(layout_file);
     // https://godbolt.org/z/WoWf55KPb
     auto filenames = std::move(std::get<0>(tuple));
     auto chopper_config = std::move(std::get<1>(tuple));
-    auto hibf_layout = std::move(std::get<2>(tuple));
+    auto hibf_layouts = std::move(std::get<2>(tuple));
 #else
-    auto [filenames, chopper_config, hibf_layouts] = chopper::layout::read_layouts_file(layout_file);
+    auto [filenames, chopper_config, hibf_layouts] = chopper::layout::read_layouts_file(layouts_file);
 #endif
+
+    auto const & hibf_layout = hibf_layouts[0];
     auto const & hibf_config = chopper_config.hibf_config;
 
     layout_file.close();
@@ -223,7 +225,7 @@ int execute(config const & cfg)
     // If the index is the same, sort by file sizes (happens for merged bins).
     // Using the smallest file to initialise the shared k-mers later will be less work.
     std::ranges::sort(
-        hibf_layouts[0].user_bins,
+        hibf_layout[0].user_bins,
         [&filesizes](seqan::hibf::layout::layout::user_bin const & lhs,
                      seqan::hibf::layout::layout::user_bin const & rhs)
         {
@@ -232,7 +234,7 @@ int execute(config const & cfg)
             return first_idx < second_idx || (first_idx == second_idx && filesizes[lhs.idx] < filesizes[rhs.idx]);
         });
 
-    size_t const total_ub_count = hibf_layouts[0].user_bins.size();
+    size_t const total_ub_count = hibf_layout[0].user_bins.size();
     progress_bar progress{total_ub_count};
 
     // Create chunks containing user bin indices for one technical bin.
@@ -249,8 +251,8 @@ int execute(config const & cfg)
         // Two user bins belong to the same chunk if they are in the same technical bin.
         auto predicate = [&](size_t const lhs, size_t const rhs)
         {
-            auto const & lhs_ub = hibf_layouts[0].user_bins[lhs];
-            auto const & rhs_ub = hibf_layouts[0].user_bins[rhs];
+            auto const & lhs_ub = hibf_layout[0].user_bins[lhs];
+            auto const & rhs_ub = hibf_layout[0].user_bins[rhs];
             // The top-level technical bin index for the current user bin.
             // user_bin.previous_TB_indices.size() == 0: true for split bins, false for merged bins
             // user_bin.storage_TB_id: technical bin index on the lowest level
@@ -289,7 +291,7 @@ int execute(config const & cfg)
 
         for (size_t const ub_index : chunk)
         {
-            auto const & user_bin = hibf_layouts[0].user_bins[ub_index];
+            auto const & user_bin = hibf_layout[0].user_bins[ub_index];
             current_kmers.clear();
 
             // We don't need to keep the current_kmers if there are no shared k-mers to merge them with.
@@ -325,7 +327,7 @@ int execute(config const & cfg)
         }
 
         // Into how many techincal bins is the user bin split? Always 1 for merged bins.
-        size_t const split_count{is_merged ? 1u : hibf_layouts[0].user_bins[chunk[0]].number_of_technical_bins};
+        size_t const split_count{is_merged ? 1u : hibf_layout[0].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;
 

src/util/display_layout/sizes.cpp

@@ -284,7 +284,7 @@ void execute_general_stats(config const & cfg)
 
 // https://godbolt.org/z/PeKnxzjn1
 #if defined(__clang__)
-    auto tuple = chopper::layout::read_layout_file(layout_file);
+    auto tuple = chopper::layout::read_layouts_file(layout_file);
     // https://godbolt.org/z/WoWf55KPb
     auto filenames = std::move(std::get<0>(tuple));
     auto chopper_config = std::move(std::get<1>(tuple));
@@ -293,6 +293,8 @@ void execute_general_stats(config const & cfg)
     auto [filenames, chopper_config, hibf_layouts] = chopper::layout::read_layouts_file(layout_file);
 #endif
 
+    auto const & hibf_layout = hibf_layouts[0];
+
     // Prepare configs
     chopper_config.hibf_config.threads = cfg.threads;
     auto input_lambda = [&filenames, &chopper_config](size_t const user_bin_id, seqan::hibf::insert_iterator it)
@@ -311,9 +313,9 @@ void execute_general_stats(config const & cfg)
     auto const & hibf_config = chopper_config.hibf_config;
 
     // Prepare stats
-    assert(hibf_layouts.size() > 0);
-    size_t part = (hibf_layouts.size() == 1) ? 0 : 1;
-    for (auto const & hibf_layout : hibf_layouts)
+    assert(hibf_layout.size() > 0);
+    size_t part = (hibf_layout.size() == 1) ? 0 : 1;
+    for (auto const & hibf_layout : hibf_layout)
     {
         size_t const number_of_ibfs = hibf_layout.max_bins.size() + 1u;
         std::vector<ibf_stats> stats(number_of_ibfs);

test/api/config_test.cpp

@@ -149,7 +149,7 @@ TEST(config_test, read_from_with_more_meta)
 }
 
 // Easier to do in the config_test because of existing helper functions
-TEST(input, read_layout_file)
+TEST(input, read_layouts_file)
 {
     std::string config_string{"@CHOPPER_USER_BINS\n"
                               "@0 file1.fa\n"
@@ -169,7 +169,9 @@ TEST(input, read_layout_file)
 
     std::stringstream ss{config_string};
 
-    auto [filenames, config, layout] = chopper::layout::read_layout_file(ss);
+    auto [filenames, config, layouts] = chopper::layout::read_layouts_file(ss);
+
+    auto const & layout = layouts[0];
 
     std::vector<std::vector<std::string>> const expected_filenames{{"file1.fa"},
                                                                    {"file2.fa"},

test/api/layout/input_test.cpp

@@ -71,7 +71,7 @@ TEST(layout_test, read_single_layout)
 5	1;2;3;4;22	1;1;1;1;21
 )layout_file"};
 
-    auto [filenames, chopper_config, layouts] = chopper::layout::read_layout_file(ss);
+    auto [filenames, chopper_config, layouts] = chopper::layout::read_layouts_file(ss);
 
     auto const & layout = layouts[0];