Changed default parameters (491e13c5) · Commits · github_fork / Chromap

src/chromap.cc

+18 −7

Original line number	Diff line number	Diff line
		@@ -4160,12 +4160,13 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		//("drop-repetitive-reads", "Drop reads with too many best mappings [500000]", cxxopts::value<int>(), "INT")
		("trim-adapters", "Try to trim adapters on 3'")
		("remove-pcr-duplicates", "Remove PCR duplicates")
		("remove-pcr-duplicates-at-bulk-level", "Remove PCR duplicates at bulk level for single cell data")
		("remove-pcr-duplicates-at-cell-level", "Remove PCR duplicates at cell level for single cell data")
		//("allocate-multi-mappings", "Allocate multi-mappings")
		("Tn5-shift", "Perform Tn5 shift")
		("low-mem", "Use low memory mode")
		("bc-error-threshold", "Max Hamming distance allowed to correct a barcode [2]", cxxopts::value<int>(), "INT")
		("bc-probability-threshold", "Min probability to correct a barcode [0.975]", cxxopts::value<double>(), "FLT")
		("bc-error-threshold", "Max Hamming distance allowed to correct a barcode [1]", cxxopts::value<int>(), "INT")
		("bc-probability-threshold", "Min probability to correct a barcode [0.9]", cxxopts::value<double>(), "FLT")
		("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>(), "INT");
		//options.add_options("Peak")
		// ("cell-by-bin", "Generate cell-by-bin matrix")
		@@ -4222,8 +4223,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		uint8_t mapq_threshold = 30;
		int num_threads = 1;
		int min_read_length = 30;
		int barcode_correction_error_threshold = 2;
		double barcode_correction_probability_threshold = 0.975;
		int barcode_correction_error_threshold = 1;
		double barcode_correction_probability_threshold = 0.9;
		int multi_mapping_allocation_distance = 0;
		int multi_mapping_allocation_seed = 11;
		int drop_repetitive_reads = 500000;
		@@ -4250,11 +4251,13 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		max_insert_size = 2000;
		trim_adapters = true;
		remove_pcr_duplicates = true;
		remove_pcr_duplicates_at_bulk_level = false;
		Tn5_shift = true;
		output_mapping_in_BED = true;
		low_memory_mode = true;
		} else if (read_type == "chip") {
		std::cerr << "Preset parameters for ChIP-seq are used.\n";
		max_insert_size = 2000;
		remove_pcr_duplicates = true;
		low_memory_mode = true;
		output_mapping_in_BED = true;
		@@ -4272,14 +4275,14 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		// Optional parameters
		if (result.count("min-frag-length")) {
		min_fragment_length = result["min-frag-length"].as<int>();
		if (min_fragment_length <= 75) {
		if (min_fragment_length <= 60) {
		kmer_size = 17;
		window_size = 7;
		} else if (min_fragment_length <= 125) {
		} else if (min_fragment_length <= 80) {
		kmer_size = 19;
		window_size = 10;
		} else {
		kmer_size = 21;
		kmer_size = 23;
		window_size = 11;
		}
		}
		@@ -4346,6 +4349,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (result.count("remove-pcr-duplicates")) {
		remove_pcr_duplicates = true;
		}
		if (result.count("remove-pcr-duplicates-at-bulk-level")) {
		remove_pcr_duplicates_at_bulk_level = true;
		}
		if (result.count("remove-pcr-duplicates-at-cell-level")) {
		remove_pcr_duplicates_at_bulk_level = false;
		}
		@@ -4533,6 +4539,11 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (only_output_unique_mappings) {
		std::cerr << "Only output unique mappings after mapping.\n";
		}
		if (!output_mappings_not_in_whitelist) {
		std::cerr << "Only output mappings of which barcodes are in whitelist.\n";
		} else {
		std::cerr << "No filtering of mappings based on whether their barcodes are in whitelist.\n";
		}
		//if (allocate_multi_mappings && only_output_unique_mappings) {
		// std::cerr << "WARNING: you want to output unique mappings only but you ask to allocate multi-mappings! In this case, it won't allocate multi-mappings and will only output unique mappings.\n";
		// allocate_multi_mappings = false;

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -282,7 +282,7 @@ class Chromap {
		uint64_t num_reads_ = 0;
		uint64_t num_duplicated_reads_ = 0; // # identical reads
		// For barcode stats
		uint64_t initial_num_sample_barcodes_ = 500000000000;
		uint64_t initial_num_sample_barcodes_ = 20000000;
		uint64_t num_sample_barcodes_ = 0;
		uint64_t num_barcode_in_whitelist_ = 0;
		uint64_t num_corrected_barcode_ = 0;

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