Fix missing include from symbol_test and added missing else clause if…

… no barcoding kit specified
nanoporetech · Mar 21, 2024 · cc328db · cc328db
1 parent 3f2bc41
commit cc328db
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/dorado/cli/basecaller.cpp b/dorado/cli/basecaller.cpp
@@ -55,7 +55,8 @@ const barcode_kits::KitInfo& get_barcode_kit_info(const std::string& kit_name) {
     if (!kit_info) {
         spdlog::error(
                 "{} is not a valid barcode kit name. Please run the help "
-                "command to find out available barcode kits.");
+                "command to find out available barcode kits.",
+                kit_name);
         std::exit(EXIT_FAILURE);
     }
     return *kit_info;
@@ -103,7 +104,7 @@ void setup(std::vector<std::string> args,
            const std::string& dump_stats_file,
            const std::string& dump_stats_filter,
            const std::string& resume_from_file,
-           const std::vector<std::string>& barcode_kits,
+           const std::string& barcode_kit,
            bool barcode_both_ends,
            bool barcode_no_trim,
            bool adapter_no_trim,
@@ -161,7 +162,7 @@ void setup(std::vector<std::string> args,
                                                     recursive_file_loading);
 
     const bool adapter_trimming_enabled = (!adapter_no_trim || !primer_no_trim);
-    const bool barcode_enabled = !barcode_kits.empty() || custom_kit;
+    const bool barcode_enabled = !barcode_kit.empty() || custom_kit;
     const auto thread_allocations = utils::default_thread_allocations(
             int(num_devices), !remora_runners.empty() ? int(num_remora_threads) : 0, enable_aligner,
             barcode_enabled, adapter_trimming_enabled);
@@ -179,10 +180,12 @@ void setup(std::vector<std::string> args,
         auto [kit_name, kit_info] = get_custom_barcode_kit_info(*custom_kit);
         utils::add_rg_headers_with_barcode_kit(hdr.get(), read_groups, kit_name, kit_info,
                                                sample_sheet.get());
-    } else {
-        const auto kit_info = get_barcode_kit_info(barcode_kits[0]);
-        utils::add_rg_headers_with_barcode_kit(hdr.get(), read_groups, barcode_kits[0], kit_info,
+    } else if (!barcode_kit.empty()) {
+        const auto kit_info = get_barcode_kit_info(barcode_kit);
+        utils::add_rg_headers_with_barcode_kit(hdr.get(), read_groups, barcode_kit, kit_info,
                                                sample_sheet.get());
+    } else {
+        utils::add_rg_headers(hdr.get(), read_groups);
     }
 
     utils::HtsFile hts_file("-", output_mode, thread_allocations.writer_threads);
@@ -212,8 +215,9 @@ void setup(std::vector<std::string> args,
                 !primer_no_trim, std::move(custom_primer_file));
     }
     if (barcode_enabled) {
+        std::vector<std::string> kit_as_vector{barcode_kit};
         current_sink_node = pipeline_desc.add_node<BarcodeClassifierNode>(
-                {current_sink_node}, thread_allocations.barcoder_threads, barcode_kits,
+                {current_sink_node}, thread_allocations.barcoder_threads, kit_as_vector,
                 barcode_both_ends, barcode_no_trim, std::move(allowed_barcodes),
                 std::move(custom_kit), std::move(custom_barcode_file));
     }
@@ -434,7 +438,8 @@ int basecaller(int argc, char* argv[]) {
 
     parser.visible.add_argument("--kit-name")
             .help("Enable barcoding with the provided kit name. Choose from: " +
-                  dorado::barcode_kits::barcode_kits_list_str() + ".");
+                  dorado::barcode_kits::barcode_kits_list_str() + ".")
+            .default_value(std::string{});
     parser.visible.add_argument("--barcode-both-ends")
             .help("Require both ends of a read to be barcoded for a double ended barcode.")
             .default_value(false)
@@ -640,7 +645,6 @@ int basecaller(int argc, char* argv[]) {
     spdlog::info("> Creating basecall pipeline");
 
     try {
-        /* clang format off */
         setup(args, model_path, data, mods_model_paths, parser.visible.get<std::string>("-x"),
               parser.visible.get<std::string>("--reference"), parser.visible.get<int>("-c"),
               parser.visible.get<int>("-o"), parser.visible.get<int>("-b"),
@@ -654,13 +658,12 @@ int basecaller(int argc, char* argv[]) {
               parser.hidden.get<std::string>("--dump_stats_file"),
               parser.hidden.get<std::string>("--dump_stats_filter"),
               parser.visible.get<std::string>("--resume-from"),
-              parser.visible.get<std::vector<std::string>>("--kit-name"),
+              parser.visible.get<std::string>("--kit-name"),
               parser.visible.get<bool>("--barcode-both-ends"), no_trim_barcodes, no_trim_adapters,
               no_trim_primers, parser.visible.get<std::string>("--sample-sheet"),
               std::move(custom_kit), std::move(custom_barcode_seqs), std::move(custom_primer_file),
               resume_parser, parser.visible.get<bool>("--estimate-poly-a"),
               polya_config.empty() ? nullptr : &polya_config, model_selection);
-        /* clang format on */
     } catch (const std::exception& e) {
         spdlog::error("{}", e.what());
         utils::clean_temporary_models(temp_download_paths);

diff --git a/tests/symbol_test.cpp b/tests/symbol_test.cpp
@@ -7,7 +7,6 @@
 #include "api/runner_creation.h"
 #include "basecall/CRFModelConfig.h"
 #include "basecall/ModelRunner.h"
-#include "demux/parse_custom_kit.h"
 #include "demux/parse_custom_sequences.h"
 #include "modbase/ModBaseModelConfig.h"
 #include "modbase/ModBaseRunner.h"
@@ -23,6 +22,7 @@
 #include "utils/barcode_kits.h"
 #include "utils/gpu_monitor.h"
 #include "utils/parameters.h"
+#include "utils/parse_custom_kit.h"
 #include "utils/sequence_utils.h"
 #include "utils/string_utils.h"
 #include "utils/time_utils.h"