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seqan · Aug 20, 2024 · 2917b40 · 2917b40
1 parent 61907ec
commit 2917b40
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Showing 3 changed files with 30 additions and 10 deletions.
diff --git a/include/chopper/sketch/sketch_file.hpp b/include/chopper/sketch/sketch_file.hpp
@@ -19,7 +19,7 @@ struct sketch_file
     chopper::configuration chopper_config{};
     std::vector<std::vector<std::string>> filenames{};
     std::vector<seqan::hibf::sketch::hyperloglog> hll_sketches{};
-    std::vector<seqan::hibf::sketch::minhashes> minHash_sketches;
+    std::vector<seqan::hibf::sketch::minhashes> minHash_sketches{};
 
 private:
     friend class cereal::access;

diff --git a/test/api/layout/execute_with_estimation_test.cpp b/test/api/layout/execute_with_estimation_test.cpp
@@ -21,7 +21,6 @@
 
 #include <chopper/configuration.hpp>
 #include <chopper/layout/execute.hpp>
-#include <chopper/sketch/read_hll_files_into.hpp>
 
 #include <hibf/sketch/compute_sketches.hpp>
 #include <hibf/sketch/hyperloglog.hpp>

diff --git a/test/cli/cli_output_sketches.cpp b/test/cli/cli_output_sketches.cpp
@@ -13,14 +13,16 @@
 
 #include <seqan3/test/tmp_directory.hpp>
 
+#include <chopper/sketch/sketch_file.hpp>
+
 #include "cli_test.hpp"
 
 TEST_F(cli_test, chopper_layout)
 {
     seqan3::test::tmp_directory tmp_dir{};
     std::filesystem::path const input_filename{tmp_dir.path() / "data.filenames"};
     std::filesystem::path const layout_filename{tmp_dir.path() / "output.binning"};
-    std::filesystem::path const sketches_dir{tmp_dir.path() / "sketches"};
+    std::filesystem::path const sketches_filename{tmp_dir.path() / "out.sketches"};
 
     {
         std::ofstream fout{input_filename};
@@ -29,15 +31,18 @@ TEST_F(cli_test, chopper_layout)
              << data("seq3.fa").string() << '\n';
     }
 
+    size_t kmer_size{15};
+    size_t tmax{64};
+
     cli_test_result result = execute_app("chopper",
                                          "--kmer",
-                                         "15",
+                                         std::to_string(kmer_size).c_str(),
                                          "--input",
                                          input_filename.c_str(),
                                          "--tmax",
-                                         "64",
+                                         std::to_string(tmax).c_str(),
                                          "--output-sketches-to",
-                                         sketches_dir.c_str(),
+                                         sketches_filename.c_str(),
                                          "--output",
                                          layout_filename.c_str());
 
@@ -48,8 +53,24 @@ TEST_F(cli_test, chopper_layout)
     // Layout file should exist. Content is checked in other test.
     EXPECT_TRUE(std::filesystem::exists(layout_filename));
 
-    EXPECT_TRUE(std::filesystem::exists(sketches_dir)); // directory exists
-    EXPECT_TRUE(std::filesystem::exists(sketches_dir / "seq1.hll"));
-    EXPECT_TRUE(std::filesystem::exists(sketches_dir / "seq2.hll"));
-    EXPECT_TRUE(std::filesystem::exists(sketches_dir / "seq3.hll"));
+    ASSERT_TRUE(std::filesystem::exists(sketches_filename));
+
+    sketch_file sin{};
+
+    std::ifstream is{sketches_filename};
+    cereal::BinaryInputArchive iarchive{is};
+    iarchive(sin);
+
+    EXPECT_EQ(sin.chopper_config.k, kmer_size);
+    EXPECT_EQ(sin.chopper_config.data_file, input_filename);
+    EXPECT_EQ(sin.chopper_config.output_filename, layout_filename);
+    EXPECT_EQ(sin.chopper_config.hibf_config.tmax, tmax);
+
+    EXPECT_EQ(sin.filenames.size(), 3);
+    EXPECT_EQ(sin.hll_sketches.size(), 3);
+    EXPECT_EQ(sin.minHash_sketches.size(), 0); // currently, no minhash sketches are needed in chopper layout
+
+    EXPECT_EQ(sin.filenames[0][0], data("seq1.fa").string());
+    EXPECT_EQ(sin.filenames[1][0], data("seq2.fa").string());
+    EXPECT_EQ(sin.filenames[2][0], data("seq3.fa").string());
 }