Merge pull request #297 from smehringer/preparations

[INFRA] Update chopper
seqan · May 3, 2023 · a948d0b · a948d0b · vercel · May 3, 2023
2 parents af8df1f + 6237c75
commit a948d0b
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Showing 3 changed files with 14 additions and 6 deletions.
diff --git a/lib/chopper b/lib/chopper
diff --git a/src/layout/raptor_layout.cpp b/src/layout/raptor_layout.cpp
@@ -35,12 +35,21 @@ void chopper_layout(sharg::parser & parser)
     config.disable_sketch_output = !parser.is_option_set("output-sketches-to");
 
     chopper::layout::layout hibf_layout{};
+    std::vector<std::string> filenames{};
+    std::vector<size_t> kmer_counts{};
+    std::vector<chopper::sketch::hyperloglog> sketches{};
 
-    chopper::data_store store{.false_positive_rate = config.false_positive_rate, .hibf_layout = &hibf_layout};
+    chopper::sketch::read_data_file(config, filenames);
 
-    chopper::sketch::execute(config, store);
-    chopper::sketch::estimate_kmer_counts(store.sketches, store.kmer_counts);
-    chopper::layout::execute(config, store);
+    chopper::sketch::execute(config, filenames, sketches);
+    chopper::sketch::estimate_kmer_counts(sketches, kmer_counts);
+
+    chopper::data_store store{.false_positive_rate = config.false_positive_rate,
+                              .hibf_layout = &hibf_layout,
+                              .kmer_counts = kmer_counts,
+                              .sketches = sketches};
+
+    chopper::layout::execute(config, filenames, store);
 }
 
 } // namespace raptor
diff --git a/test/unit/cli/build/build_hibf_chopper_test.cpp b/test/unit/cli/build/build_hibf_chopper_test.cpp
@@ -32,7 +32,6 @@ TEST_F(build_hibf_layout, pipeline)
         cli_test_result const result = execute_app("raptor",
                                                    "layout",
                                                    "--kmer-size 19",
-                                                   "--column-index 2",
                                                    "--threads 1",
                                                    "--input-file",
                                                    data_filename,