Merge branch 'jdaw/fix-barcode-documentation' into 'master'

fix custom barcode documentation

See merge request machine-learning/dorado!801

(cherry picked from commit 12329e5)

8e33c0c fix custom barcode documentation
64fa1cd add read filename to debug log

documentation/CustomBarcodes.md

@@ -28,10 +28,10 @@ The following are all the options that can be defined in the arrangement file.
 name = "custom_barcode"
 kit = "BC"
 
-mask_1_front = "ATCG"
-mask_1_rear = "ATCG"
-mask_2_front = "TTAA"
-mask_2_rear = "GGCC"
+mask1_front = "ATCG"
+mask1_rear = "ATCG"
+mask2_front = "TTAA"
+mask2_rear = "GGCC"
 
 # Barcode sequences
 barcode1_pattern = "BC%02i"
@@ -44,7 +44,7 @@ last_index = 96
 min_soft_barcode_threshold = 0.2
 min_hard_barcode_threshold = 0.2
 min_soft_flank_threshold = 0.3
-min_hard_barcode_threshold = 0.3
+min_hard_flank_threshold = 0.3
 min_barcode_score_dist = 0.1
 ```
 

dorado/data_loader/DataLoader.cpp

@@ -342,6 +342,7 @@ void DataLoader::load_reads(const std::string& path,
                 if (m_loaded_read_count == m_max_reads) {
                     break;
                 }
+                spdlog::debug("Load reads from file {}", entry.path().string());
                 std::string ext = std::filesystem::path(entry).extension().string();
                 std::transform(ext.begin(), ext.end(), ext.begin(),
                                [](unsigned char c) { return std::tolower(c); });