Format code. (c5c4994b) · Commits · github_fork / Chromap

src/chromap.cc

+23 −17

Original line number	Diff line number	Diff line
		@@ -750,10 +750,16 @@ void Chromap<MappingRecord>::ComputeBarcodeAbundance(
		}
		}

		if (!skip_barcode_check_
		&& num_sample_barcodes_ * 20 < num_loaded_barcodes) {
		// Since num_loaded_pairs is a constant, this if is actuaclly only effective in the first iteration
		Chromap<>::ExitWithMessage("Less than 5\% barcodes can be found or corrected based on the barcode whitelist.\nPlease check whether the barcode whitelist matches the data, e.g. length, reverse-complement. If this is a false positive warning, please run Chromap with the option --skip-barcode-check.");
		if (!skip_barcode_check_ &&
		num_sample_barcodes_ * 20 < num_loaded_barcodes) {
		// Since num_loaded_pairs is a constant, this if is actuaclly only
		// effective in the first iteration
		Chromap<>::ExitWithMessage(
		"Less than 5\% barcodes can be found or corrected based on the "
		"barcode whitelist.\nPlease check whether the barcode whitelist "
		"matches the data, e.g. length, reverse-complement. If this is a "
		"false positive warning, please run Chromap with the option "
		"--skip-barcode-check.");
		}

		if (num_sample_barcodes_ >= max_num_sample_barcodes) {
		@@ -1828,8 +1834,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		// }
		// }
		//}
		// Update cache
		#pragma omp taskwait
		// Update cache
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs;
		++pair_index) {
		if (num_reads_ > 5000000 &&
		@@ -5976,8 +5982,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		//("p,matrix-output-prefix", "Prefix of matrix output files",
		// cxxopts::value<std::string>(), "FILE")
		("output-mappings-not-in-whitelist",
		"Output mappings with barcode not in the whitelist")
		("chr-order", "custom chromsome order", cxxopts::value<std::string>(),
		"Output mappings with barcode not in the whitelist")(
		"chr-order", "custom chromsome order", cxxopts::value<std::string>(),
		"FILE")("BED", "Output mappings in BED/BEDPE format")(
		"TagAlign", "Output mappings in TagAlign/PairedTagAlign format")(
		"SAM", "Output mappings in SAM format")(
		@@ -6007,9 +6013,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"drop-repetitive-reads",
		"Drop reads with too many best mappings [500000]", cxxopts::value<int>(),
		"INT")("allocate-multi-mappings", "Allocate multi-mappings")(
		"PAF", "Output mappings in PAF format (only for test)")
		("skip-barcode-check", "Do not check whether too few barcodes are in the whitelist")
		;
		"PAF", "Output mappings in PAF format (only for test)")(
		"skip-barcode-check",
		"Do not check whether too few barcodes are in the whitelist");

		auto result = options.parse(argc, argv);
		if (result.count("h")) {

src/chromap.h

+2 −2

File changed.

Contains only whitespace changes.

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