Add the cache hit information in summary (c79d2649) · Commits · github_fork / Chromap

src/chromap.h

+44 −5

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.5-r478"
		#define CHROMAP_VERSION "0.2.5-r473"

		namespace chromap {

		@@ -244,6 +244,9 @@ void Chromap::MapSingleEndReads() {
		mm_cache mm_to_candidates_cache(2000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size);
		struct _mm_history *mm_history = new struct _mm_history[read_batch_size_];
		bool *mm_cache_hit = NULL ;
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		mm_cache_hit = new bool[read_batch_size_];
		static uint64_t thread_num_candidates = 0;
		static uint64_t thread_num_mappings = 0;
		static uint64_t thread_num_mapped_reads = 0;
		@@ -328,6 +331,7 @@ void Chromap::MapSingleEndReads() {
		for (uint32_t read_index = 0; read_index < num_loaded_reads;
		++read_index) {
		bool current_barcode_is_whitelisted = true;
		int cache_miss = 0;
		if (!mapping_parameters_.barcode_whitelist_file_path.empty()) {
		current_barcode_is_whitelisted = CorrectBarcodeAt(
		read_index, barcode_batch, thread_num_barcode_in_whitelist,
		@@ -358,6 +362,7 @@ void Chromap::MapSingleEndReads() {
		candidate_processor.GenerateCandidates(
		mapping_parameters_.error_threshold, index,
		mapping_metadata);
		++cache_miss;
		}

		if (read_index < history_update_threshold) {
		@@ -396,6 +401,9 @@ void Chromap::MapSingleEndReads() {
		mapping_parameters_.max_num_best_mappings);
		++thread_num_mapped_reads;

		if (mm_cache_hit != NULL && mapping_metadata.GetNumBestMappings() > 0)
		mm_cache_hit[read_index] = (cache_miss == 0) ;

		if (mapping_metadata.GetNumBestMappings() == 1) {
		++thread_num_uniquely_mapped_reads;
		}
		@@ -436,6 +444,15 @@ void Chromap::MapSingleEndReads() {
		barcode_batch.GenerateSeedFromSequenceAt(read_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		}

		// Update cache hit
		for (uint32_t read_index = 0; read_index < num_loaded_reads; ++read_index)
		if (mm_cache_hit[read_index]) {
		mapping_writer.UpdateSummaryMetadata(
		mapping_parameters_.is_bulk_data ? 0 :
		barcode_batch.GenerateSeedFromSequenceAt(read_index, 0, barcode_length_),
		SUMMARY_METADATA_CACHEHIT, 1);
		}
		}
		num_loaded_reads = num_loaded_reads_for_loading;
		read_batch_for_loading.SwapSequenceBatch(read_batch);
		@@ -483,6 +500,8 @@ void Chromap::MapSingleEndReads() {
		<< "s.\n";

		delete[] mm_history;
		if (mm_cache_hit != NULL)
		delete[] mm_cache_hit;

		OutputMappingStatistics();
		if (!mapping_parameters_.is_bulk_data) {
		@@ -590,6 +609,9 @@ void Chromap::MapPairedEndReads() {
		mm_to_candidates_cache.SetKmerLength(kmer_size);
		struct _mm_history *mm_history1 = new struct _mm_history[read_batch_size_];
		struct _mm_history *mm_history2 = new struct _mm_history[read_batch_size_];
		bool *mm_cache_hit = NULL ;
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		mm_cache_hit = new bool[read_batch_size_];

		std::vector<std::vector<MappingRecord>> mappings_on_diff_ref_seqs;
		// Initialize mapping container
		@@ -760,12 +782,14 @@ void Chromap::MapPairedEndReads() {

		if (paired_end_mapping_metadata.BothEndsHaveMinimizers()) {
		// Generate candidates
		int cache_miss = 0;
		if (mm_to_candidates_cache.Query(
		paired_end_mapping_metadata.mapping_metadata1_,
		read_batch1.GetSequenceLengthAt(pair_index)) == -1) {
		candidate_processor.GenerateCandidates(
		mapping_parameters_.error_threshold, index,
		paired_end_mapping_metadata.mapping_metadata1_);
		++cache_miss;
		}

		size_t current_num_candidates1 =
		@@ -778,6 +802,7 @@ void Chromap::MapPairedEndReads() {
		candidate_processor.GenerateCandidates(
		mapping_parameters_.error_threshold, index,
		paired_end_mapping_metadata.mapping_metadata2_);
		++cache_miss;
		}

		size_t current_num_candidates2 =
		@@ -927,6 +952,9 @@ void Chromap::MapPairedEndReads() {
		if (paired_end_mapping_metadata.GetNumBestMappings() > 0) {
		++thread_num_mapped_reads;
		++thread_num_mapped_reads;

		if (mm_cache_hit != NULL)
		mm_cache_hit[pair_index] = (cache_miss < 2) ;
		}
		}
		} // verify candidate
		@@ -977,16 +1005,25 @@ void Chromap::MapPairedEndReads() {
		}

		if (!mapping_parameters_.summary_metadata_file_path.empty()) {
		// Update total read count
		if (mapping_parameters_.is_bulk_data)
		mapping_writer.UpdateSummaryMetadata(0, SUMMARY_METADATA_TOTAL,
		num_loaded_pairs) ;
		else
		{
		else {
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index)
		mapping_writer.UpdateSummaryMetadata(
		barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		}

		// Update cache hit
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index)
		if (mm_cache_hit[pair_index]) {
		mapping_writer.UpdateSummaryMetadata(
		mapping_parameters_.is_bulk_data ? 0 :
		barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_length_),
		SUMMARY_METADATA_CACHEHIT, 1);
		}
		}

		std::cerr << "Mapped " << num_loaded_pairs << " read pairs in "
		@@ -1043,6 +1080,8 @@ void Chromap::MapPairedEndReads() {

		delete[] mm_history1;
		delete[] mm_history2;
		if (mm_cache_hit != NULL)
		delete[] mm_cache_hit;

		OutputMappingStatistics();
		if (!mapping_parameters_.is_bulk_data) {

src/summary_metadata.h

+6 −2

Original line number	Diff line number	Diff line
		@@ -18,6 +18,8 @@ enum SummaryMetadataField {
		SUMMARY_METADATA_DUP,
		SUMMARY_METADATA_MAPPED,
		SUMMARY_METADATA_LOWMAPQ,
		SUMMARY_METADATA_CACHEHIT,
		//SUMMARY_METADATA_CACHEHIT_FWD,
		SUMMARY_METADATA_FIELDS
		};

		@@ -43,7 +45,7 @@ class SummaryMetadata {

		void Output(const char *filename) {
		FILE *fp = fopen(filename, "w");
		fprintf(fp, "barcode,total,duplicate,unmapped,lowmapq\n");
		fprintf(fp, "barcode,total,duplicate,unmapped,lowmapq,cachehit,fric\n");
		khiter_t k;
		for (k = kh_begin(barcode_metadata_); k != kh_end(barcode_metadata_); ++k)
		if (kh_exist(barcode_metadata_, k)) {
		@@ -52,10 +54,12 @@ class SummaryMetadata {
		for (i = 0; i < SUMMARY_METADATA_FIELDS; ++i) {
		if (i != SUMMARY_METADATA_MAPPED)
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[i]);
		else
		else // the print is for unmapped
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_TOTAL]
		- kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_MAPPED]);
		}
		// fric: fraction in cache
		fprintf(fp, ",%lf", (double)kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_CACHEHIT] / (double)kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_MAPPED]);
		fprintf(fp, "\n");
		}
		fclose(fp);

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