Adjust cache update threshold. (450e04df) · Commits · github_fork / Chromap

src/chromap.h

+8 −6

Original line number	Diff line number	Diff line
		@@ -314,6 +314,8 @@ void Chromap::MapSingleEndReads() {
		num_loaded_reads_for_loading = LoadSingleEndReadsWithBarcodes(
		read_batch_for_loading, barcode_batch_for_loading);
		} // end of openmp loading task
		uint32_t history_update_threshold =
		mm_to_candidates_cache.GetUpdateThreshold(num_loaded_reads, num_reads_, false);
		// int grain_size = 10000;
		//#pragma omp taskloop grainsize(grain_size) //num_tasks(num_threads_* 50)
		#pragma omp taskloop num_tasks( \
		@@ -353,7 +355,7 @@ void Chromap::MapSingleEndReads() {
		mapping_metadata);
		}

		if (read_index < mm_to_candidates_cache.GetUpdateThreshold(num_loaded_reads, num_reads_, false)) {
		if (read_index < history_update_threshold) {
		mm_history[read_index].timestamp = num_reads_;
		mm_history[read_index].minimizers =
		mapping_metadata.minimizers_;
		@@ -396,8 +398,7 @@ void Chromap::MapSingleEndReads() {
		}
		}
		#pragma omp taskwait
		for (uint32_t read_index = 0;
		read_index < mm_to_candidates_cache.GetUpdateThreshold(num_loaded_reads, num_reads_, false);
		for (uint32_t read_index = 0; read_index < history_update_threshold;
		++read_index) {
		if (mm_history[read_index].timestamp != num_reads_) continue;
		mm_to_candidates_cache.Update(
		@@ -707,6 +708,8 @@ void Chromap::MapPairedEndReads() {
		} // end of openmp loading task

		int grain_size = 5000;
		uint32_t history_update_threshold =
		mm_to_candidates_cache.GetUpdateThreshold(num_loaded_pairs, num_reads_, true);
		#pragma omp taskloop grainsize(grain_size)
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs;
		++pair_index) {
		@@ -763,7 +766,7 @@ void Chromap::MapPairedEndReads() {
		paired_end_mapping_metadata.mapping_metadata2_
		.GetNumCandidates();

		if (pair_index < mm_to_candidates_cache.GetUpdateThreshold(num_loaded_pairs, num_reads_, true)) {
		if (pair_index < history_update_threshold) {
		mm_history1[pair_index].timestamp =
		mm_history2[pair_index].timestamp = num_reads_;
		mm_history1[pair_index].minimizers =
		@@ -921,8 +924,7 @@ void Chromap::MapPairedEndReads() {
		//}
		#pragma omp taskwait
		// Update cache
		for (uint32_t pair_index = 0;
		pair_index < mm_to_candidates_cache.GetUpdateThreshold(num_loaded_pairs, num_reads_, true);
		for (uint32_t pair_index = 0; pair_index < history_update_threshold ;
		++pair_index) {
		if (mm_history1[pair_index].timestamp != num_reads_) continue;

src/mmcache.hpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -310,7 +310,7 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
		if (num_reads <= block)
		return num_loaded_reads;
		else
		return num_loaded_reads / (8 * (num_reads / block));
		return num_loaded_reads / (1 + (num_reads / block));
		}

		void PrintStats() {

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