removed the --use-all-reads option (d2335ebd) · Commits · github_fork / Chromap

src/chromap.h

+0 −3

Original line number	Diff line number	Diff line
		@@ -375,7 +375,6 @@ void Chromap::MapSingleEndReads() {
		mm_to_candidates_cache.GetUpdateThreshold(num_loaded_reads,
		num_reads_,
		false,
		false,
		0.01);
		// int grain_size = 10000;
		//#pragma omp taskloop grainsize(grain_size) //num_tasks(num_threads_* 50)
		@@ -673,7 +672,6 @@ void Chromap::MapPairedEndReads() {

		// Check cache-related parameters
		std::cerr << "Cache Size: " << mapping_parameters_.cache_size << std::endl;
		std::cerr << "Use All Reads for Cache: " << mapping_parameters_.use_all_reads << std::endl;
		std::cerr << "Cache Update Param: " << mapping_parameters_.cache_update_param << std::endl;

		std::vector<uint64_t> seeds_for_batch(500000, 0);
		@@ -865,7 +863,6 @@ void Chromap::MapPairedEndReads() {
		mm_to_candidates_cache.GetUpdateThreshold(num_loaded_pairs,
		num_reads_,
		true,
		mapping_parameters_.use_all_reads,
		mapping_parameters_.cache_update_param
		);
		int cache_hits_for_batch = 0;

+0 −4

Original line number	Diff line number	Diff line
		@@ -79,7 +79,6 @@ void AddMappingOptions(cxxopts::Options &options) {
		cxxopts::value<int>(), "INT")
		("cache-size", "number of cache entries [4000003]", cxxopts::value<int>(), "INT")
		("cache-update-param", "value used to control number of reads sampled [0.01]", cxxopts::value<double>(), "FLT")
		("use-all-reads", "use all reads for cache (it will slow down execution)")
		("debug-cache", "verbose output for debugging cache used in chromap")
		("frip-est-params", "coefficients used for frip est calculation, separated by semi-colons",
		cxxopts::value<std::string>(), "STR")
		@@ -347,9 +346,6 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		chromap::ExitWithMessage("cache size is not in appropriate range\n");
		}
		}
		if (result.count("use-all-reads")) {
		mapping_parameters.use_all_reads = true;
		}
		if (result.count("debug-cache")) {
		mapping_parameters.debug_cache = true;
		}

+0 −1

Original line number	Diff line number	Diff line
		@@ -26,7 +26,6 @@ struct MappingParameters {

		double cache_update_param = 0.01;
		int cache_size = 4000003;
		bool use_all_reads = false;
		bool debug_cache = false;
		std::string frip_est_params = "0.2809;0.8921;7.490e-06;-1.893e-05;-2.178e-05";
		bool output_num_uniq_cache_slots = true;

+0 −2

Original line number	Diff line number	Diff line
		@@ -358,11 +358,9 @@ class mm_cache {
		uint32_t GetUpdateThreshold(uint32_t num_loaded_reads,
		uint64_t num_reads,
		bool paired,
		bool use_all_reads,
		double cache_update_param
		) {
		const uint32_t block = paired ? 2500000 : 5000000;
		if (use_all_reads) {return num_loaded_reads;}

		if (num_reads <= block)
		return num_loaded_reads;