[INFRA] Update submodules

src/display_layout/process_file.cpp

@@ -40,14 +40,14 @@ void process_file(std::string const & filename,
             while (infile.read(hash_data, hash_bytes))
             {
                 current_kmers.push_back(hash);
-                sketch.add(hash_data, hash_bytes);
+                sketch.add(hash);
             }
         }
         else
         {
             while (infile.read(hash_data, hash_bytes))
             {
-                sketch.add(hash_data, hash_bytes);
+                sketch.add(hash);
             }
         }
     }
@@ -66,7 +66,7 @@ void process_file(std::string const & filename,
                 for (uint64_t hash_value : seq | minimizer_view)
                 {
                     current_kmers.push_back(hash_value);
-                    sketch.add(reinterpret_cast<char *>(&hash_value), sizeof(hash_value));
+                    sketch.add(hash_value);
                 }
             }
         }
@@ -76,7 +76,7 @@ void process_file(std::string const & filename,
             {
                 for (uint64_t hash_value : seq | minimizer_view)
                 {
-                    sketch.add(reinterpret_cast<char *>(&hash_value), sizeof(hash_value));
+                    sketch.add(hash_value);
                 }
             }
         }

src/measure_hyperloglog.cpp

@@ -97,7 +97,7 @@ int main(int argc, char const * argv[])
             control.insert(hash);
             for (auto & sketch : sketches)
             {
-                sketch.add(reinterpret_cast<char *>(&hash), sizeof(hash));
+                sketch.add(hash);
             }
         }
 

test/api/layout/hibf_statistics_test.cpp

@@ -64,8 +64,8 @@ TEST(hibf_statistics, only_merged_on_top_level)
         stats.hibf_layout.max_bins.emplace_back(std::vector<size_t>{0u}, 0u);
         stats.hibf_layout.max_bins.emplace_back(std::vector<size_t>{1u}, 0u);
 
-        stats.hibf_layout.user_bins.emplace_back(0u, std::vector<size_t>{0u}, 2u, 0u);
-        stats.hibf_layout.user_bins.emplace_back(1u, std::vector<size_t>{1u}, 2u, 0u);
+        stats.hibf_layout.user_bins.emplace_back(std::vector<size_t>{0u}, 0u, 2u, 0u);
+        stats.hibf_layout.user_bins.emplace_back(std::vector<size_t>{1u}, 0u, 2u, 1u);
     }
 
     testing::internal::CaptureStdout();

test/api/sketch/read_hll_files_into_test.cpp

@@ -36,7 +36,7 @@ struct read_hll_files_into_test : public ::testing::Test
 
 TEST_F(read_hll_files_into_test, basic)
 {
-    size_t const k{16};
+    size_t const kmer_size{16};
     size_t const b{5};
     seqan::hibf::sketch::hyperloglog expected{b};
 
@@ -46,14 +46,14 @@ TEST_F(read_hll_files_into_test, basic)
     sequence_file_type seq_file{input_file};
 
     // put every sequence in this file into the sketch
-    for (auto && [seq] : seq_file)
+    for (auto && [seq_vec] : seq_file)
     {
-        // we have to go C-style here for the seqan::hibf::sketch::hyperloglog Interface
-        char const * it = &(*seq.begin());
-        char const * const end = it + seq.size() - k + 1;
+        std::string_view const seq{seq_vec.begin(), seq_vec.end()};
 
-        for (; it != end; ++it)
-            expected.add(it, k);
+        for (size_t pos = 0; pos + kmer_size <= seq.size(); ++pos) // substr is [pos, pos + len)
+        {
+            expected.add(seq.substr(pos, kmer_size));
+        }
     }
 
     chopper::sketch::read_hll_files_into(data(""), test_filenames, target);