Only warn the users when whitelist is NA. (ff8fb17e) · Commits · github_fork / Chromap

src/chromap.cc

+21 −5

Original line number	Diff line number	Diff line
		@@ -1393,7 +1393,13 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		barcode_batch_for_loading);
		read_batch1_for_loading.SwapSequenceBatch(read_batch1);
		read_batch2_for_loading.SwapSequenceBatch(read_batch2);
		if (!is_bulk_data_) {
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		// TODO(Haowen): simplify this condition check.
		if (num_loaded_pairs > 0) {
		output_tools_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		}
		}

		// Setup thread private vectors to save mapping results.
		std::vector<std::vector<std::vector<MappingRecord>>>
		@@ -2790,7 +2796,15 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		uint32_t num_loaded_reads = LoadSingleEndReadsWithBarcodes(
		&read_batch_for_loading, &barcode_batch_for_loading);
		read_batch_for_loading.SwapSequenceBatch(read_batch);

		if (!is_bulk_data_) {
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		// TODO(Haowen): simplify this condition check.
		if (num_loaded_reads > 0) {
		output_tools_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		}
		}

		std::vector<std::vector<std::vector<MappingRecord>>>
		mappings_on_diff_ref_seqs_for_diff_threads;
		std::vector<std::vector<std::vector<MappingRecord>>>
		@@ -6159,16 +6173,17 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		mapping_parameters.read_file2_paths =
		result["read2"].as<std::vector<std::string>>();
		}

		if (result.count("b")) {
		mapping_parameters.is_bulk_data = false;
		mapping_parameters.barcode_file_paths =
		result["barcode"].as<std::vector<std::string>>();
		if (result.count("barcode-whitelist") == 0) {
		chromap::Chromap<>::ExitWithMessage(
		"There are input barcode files but a barcode whitelist file is "
		"missing!");
		std::cerr << "WARNING: there are input barcode files but a barcode "
		"whitelist file is missing!\n";
		}
		}

		if (result.count("barcode-whitelist")) {
		if (mapping_parameters.is_bulk_data) {
		chromap::Chromap<>::ExitWithMessage(
		@@ -6178,6 +6193,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		mapping_parameters.barcode_whitelist_file_path =
		result["barcode-whitelist"].as<std::string>();
		}

		if (result.count("p")) {
		mapping_parameters.matrix_output_prefix =
		result["matrix-output-prefix"].as<std::string>();

src/output_tools.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -70,6 +70,10 @@ class OutputTools {
		mapping_output_format_ = format;
		}

		inline void SetBarcodeLength(uint32_t cell_barcode_length) {
		cell_barcode_length_ = cell_barcode_length;
		}

		inline void FinalizeMappingOutput() { fclose(mapping_output_file_); }

		inline void AppendMappingOutput(const std::string &line) {

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