Make static functions free. (32ae269d) · Commits · github_fork / Chromap

src/chromap.cc

+56 −63

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@
		#include "cxxopts.hpp"
		#include "ksw.h"
		#include "mmcache.hpp"
		#include "utils.h"

		namespace chromap {
		template <typename MappingRecord>
		@@ -394,8 +395,7 @@ uint32_t Chromap<PairedEndMappingWithBarcode>::CallPeaks(
		}
		}
		}
		std::cerr << "Built pileup in " << Chromap<>::GetRealTime() - real_start_time
		<< "s.\n";
		std::cerr << "Built pileup in " << GetRealTime() - real_start_time << "s.\n";
		real_start_time = GetRealTime();
		// Call and save peaks
		tree_extras_on_diff_ref_seqs_.clear();
		@@ -430,7 +430,7 @@ uint32_t Chromap<PairedEndMappingWithBarcode>::CallPeaks(
		BuildAugmentedTreeForPeaks(ri);
		}
		std::cerr << "Call peaks and built peak augmented tree in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< GetRealTime() - real_start_time << "s.\n";
		// Output feature matrix
		return peak_count;
		}
		@@ -482,7 +482,7 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix(
		}
		}
		std::cerr << "Index and output barcodes in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< GetRealTime() - real_start_time << "s.\n";
		real_start_time = GetRealTime();
		// Second pass to generate matrix
		khash_t(kmatrix) *matrix = kh_init(kmatrix);
		@@ -520,8 +520,8 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix(
		}
		}
		}
		std::cerr << "Generate feature matrix in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		std::cerr << "Generate feature matrix in " << GetRealTime() - real_start_time
		<< "s.\n";
		// Output matrix
		real_start_time = GetRealTime();
		feature_barcode_matrix_writer_.WriteMatrixOutputHead(
		@@ -541,8 +541,8 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix(
		(uint32_t)feature_matrix[i].first,
		(uint32_t)(feature_matrix[i].first >> 32), feature_matrix[i].second);
		}
		std::cerr << "Output feature matrix in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		std::cerr << "Output feature matrix in " << GetRealTime() - real_start_time
		<< "s.\n";
		}

		template <typename MappingRecord>
		@@ -711,7 +711,7 @@ uint32_t Chromap<MappingRecord>::LoadPairedEndReadsWithBarcodes(
		} else if (no_more_read1 && no_more_read2 && no_more_barcode) {
		break;
		} else {
		Chromap<>::ExitWithMessage("Numbers of reads and barcodes don't match!");
		ExitWithMessage("Numbers of reads and barcodes don't match!");
		}
		++num_loaded_pairs;
		}
		@@ -727,7 +727,7 @@ uint32_t Chromap<MappingRecord>::LoadPairedEndReadsWithBarcodes(
		template <typename MappingRecord>
		void Chromap<MappingRecord>::ComputeBarcodeAbundance(
		uint64_t max_num_sample_barcodes) {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		SequenceBatch barcode_batch(read_batch_size_);
		for (size_t read_file_index = 0; read_file_index < read_file1_paths_.size();
		++read_file_index) {
		@@ -755,7 +755,7 @@ void Chromap<MappingRecord>::ComputeBarcodeAbundance(
		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(
		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 "
		@@ -775,13 +775,13 @@ void Chromap<MappingRecord>::ComputeBarcodeAbundance(
		}

		std::cerr << "Compute barcode abundance using " << num_sample_barcodes_
		<< " in " << Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< " in " << GetRealTime() - real_start_time << "s.\n";
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::UpdateBarcodeAbundance(
		uint32_t num_loaded_barcodes, const SequenceBatch &barcode_batch) {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		for (uint32_t barcode_index = 0; barcode_index < num_loaded_barcodes;
		++barcode_index) {
		uint32_t barcode_length = barcode_batch.GetSequenceLengthAt(barcode_index);
		@@ -798,7 +798,7 @@ void Chromap<MappingRecord>::UpdateBarcodeAbundance(
		}
		}
		std::cerr << "Update barcode abundance using " << num_sample_barcodes_
		<< " in " << Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< " in " << GetRealTime() - real_start_time << "s.\n";
		}

		template <typename MappingRecord>
		@@ -829,7 +829,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		return;
		}

		double sort_and_dedupe_start_time = Chromap<>::GetRealTime();
		double sort_and_dedupe_start_time = GetRealTime();

		// Calculate block size and initialize
		uint64_t max_mem_size = 10 * ((uint64_t)1 << 30);
		@@ -1041,12 +1041,10 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(

		if (remove_pcr_duplicates_) {
		std::cerr << "Sorted, deduped and outputed mappings in "
		<< Chromap<>::GetRealTime() - sort_and_dedupe_start_time
		<< "s.\n";
		<< GetRealTime() - sort_and_dedupe_start_time << "s.\n";
		} else {
		std::cerr << "Sorted and outputed mappings in "
		<< Chromap<>::GetRealTime() - sort_and_dedupe_start_time
		<< "s.\n";
		<< GetRealTime() - sort_and_dedupe_start_time << "s.\n";
		}
		std::cerr << "# uni-mappings: " << num_uni_mappings
		<< ", # multi-mappings: " << num_multi_mappings
		@@ -1102,7 +1100,7 @@ void Chromap<MappingRecord>::GenerateCustomizedRidRank(
		}

		if (k > ref_size) {
		chromap::Chromap<>::ExitWithMessage(
		chromap::ExitWithMessage(
		"Unknown chromsome names found in chromosome order file");
		}

		@@ -1126,7 +1124,7 @@ void Chromap<MappingRecord>::RerankCandidatesRid(

		template <typename MappingRecord>
		void Chromap<MappingRecord>::MapPairedEndReads() {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();

		// Load reference
		SequenceBatch reference;
		@@ -1222,7 +1220,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		thread_num_candidates, thread_num_mappings, thread_num_mapped_reads, \
		thread_num_uniquely_mapped_reads, thread_num_barcode_in_whitelist, \
		thread_num_corrected_barcode)
		double real_start_mapping_time = Chromap<>::GetRealTime();
		double real_start_mapping_time = GetRealTime();
		for (size_t read_file_index = 0; read_file_index < read_file1_paths_.size();
		++read_file_index) {
		// Set read batches to the current read files.
		@@ -1289,7 +1287,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		std::mt19937 generator(11);
		#pragma omp single
		{
		double real_batch_start_time = Chromap<>::GetRealTime();
		double real_batch_start_time = GetRealTime();
		while (num_loaded_pairs > 0) {
		num_reads_ += num_loaded_pairs;
		num_reads_ += num_loaded_pairs;
		@@ -1551,9 +1549,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		}

		std::cerr << "Mapped " << num_loaded_pairs << " read pairs in "
		<< Chromap<>::GetRealTime() - real_batch_start_time
		<< "s.\n";
		real_batch_start_time = Chromap<>::GetRealTime();
		<< GetRealTime() - real_batch_start_time << "s.\n";
		real_batch_start_time = GetRealTime();

		// Swap to next batch
		num_loaded_pairs = num_loaded_pairs_for_loading;
		@@ -1605,8 +1602,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		}
		} // end of for read_file_index

		std::cerr << "Mapped all reads in "
		<< Chromap<>::GetRealTime() - real_start_mapping_time << "s.\n";
		std::cerr << "Mapped all reads in " << GetRealTime() - real_start_mapping_time
		<< "s.\n";

		delete[] mm_history1;
		delete[] mm_history2;
		@@ -1668,8 +1665,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {

		reference.FinalizeLoading();

		std::cerr << "Total time: " << Chromap<>::GetRealTime() - real_start_time
		<< "s.\n";
		std::cerr << "Total time: " << GetRealTime() - real_start_time << "s.\n";
		}

		template <typename MappingRecord>
		@@ -2575,7 +2571,7 @@ void Chromap<MappingRecord>::ApplyTn5ShiftOnPairedEndMapping(

		template <typename MappingRecord>
		void Chromap<MappingRecord>::MapSingleEndReads() {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();

		SequenceBatch reference;
		reference.InitializeLoading(reference_file_path_);
		@@ -2637,7 +2633,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		thread_num_candidates, thread_num_mappings, thread_num_mapped_reads, \
		thread_num_uniquely_mapped_reads, thread_num_barcode_in_whitelist, \
		thread_num_corrected_barcode)
		double real_start_mapping_time = Chromap<>::GetRealTime();
		double real_start_mapping_time = GetRealTime();
		for (size_t read_file_index = 0; read_file_index < read_file1_paths_.size();
		++read_file_index) {
		read_batch_for_loading.InitializeLoading(
		@@ -2698,7 +2694,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		#pragma omp single
		{
		while (num_loaded_reads > 0) {
		double real_batch_start_time = Chromap<>::GetRealTime();
		double real_batch_start_time = GetRealTime();
		num_reads_ += num_loaded_reads;
		#pragma omp task
		{
		@@ -2823,8 +2819,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		num_reference_sequences,
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		}
		std::cerr << "Mapped in "
		<< Chromap<>::GetRealTime() - real_batch_start_time
		std::cerr << "Mapped in " << GetRealTime() - real_batch_start_time
		<< "s.\n";
		}
		} // end of openmp single
		@@ -2843,8 +2838,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		}
		}

		std::cerr << "Mapped all reads in "
		<< Chromap<>::GetRealTime() - real_start_mapping_time << "s.\n";
		std::cerr << "Mapped all reads in " << GetRealTime() - real_start_mapping_time
		<< "s.\n";

		delete[] mm_history;

		@@ -2889,8 +2884,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {

		output_tools_.FinalizeMappingOutput();
		reference.FinalizeLoading();
		std::cerr << "Total time: " << Chromap<>::GetRealTime() - real_start_time
		<< "s.\n";
		std::cerr << "Total time: " << GetRealTime() - real_start_time << "s.\n";
		}

		template <typename MappingRecord>
		@@ -3486,7 +3480,7 @@ void Chromap<MappingRecord>::ApplyTn5ShiftOnSingleEndMapping(
		template <typename MappingRecord>
		uint32_t Chromap<MappingRecord>::LoadSingleEndReadsWithBarcodes(
		SequenceBatch read_batch, SequenceBatch barcode_batch) {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		uint32_t num_loaded_reads = 0;
		while (num_loaded_reads < read_batch_size_) {
		bool no_more_read = read_batch->LoadOneSequenceAndSaveAt(num_loaded_reads);
		@@ -3508,13 +3502,13 @@ uint32_t Chromap<MappingRecord>::LoadSingleEndReadsWithBarcodes(
		} else if (no_more_read && no_more_barcode) {
		break;
		} else {
		Chromap<>::ExitWithMessage("Numbers of reads and barcodes don't match!");
		ExitWithMessage("Numbers of reads and barcodes don't match!");
		}
		++num_loaded_reads;
		}
		if (num_loaded_reads > 0) {
		std::cerr << "Loaded " << num_loaded_reads << " reads in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< GetRealTime() - real_start_time << "s.\n";
		} else {
		std::cerr << "No more reads.\n";
		}
		@@ -3581,7 +3575,7 @@ template <typename MappingRecord>
		void Chromap<MappingRecord>::RemovePCRDuplicate(
		uint32_t num_reference_sequences) {
		uint32_t num_mappings = 0;
		double real_dedupe_start_time = Chromap<>::GetRealTime();
		double real_dedupe_start_time = GetRealTime();
		for (uint32_t ri = 0; ri < num_reference_sequences; ++ri) {
		// double real_start_time = Chromap<>::GetRealTime();
		// radix_sort_with_barcode(mappings_on_diff_ref_seqs_[ri].data(),
		@@ -3595,7 +3589,7 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(
		// real_start_time << "s.\n";
		}
		std::cerr << "Sorted " << num_mappings << " elements in "
		<< Chromap<>::GetRealTime() - real_dedupe_start_time << "s.\n";
		<< GetRealTime() - real_dedupe_start_time << "s.\n";
		num_mappings = 0;
		for (uint32_t ri = 0; ri < num_reference_sequences; ++ri) {
		if (mappings_on_diff_ref_seqs_[ri].size() != 0) {
		@@ -3630,7 +3624,7 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(
		}
		}
		std::cerr << num_mappings << " mappings left after dedupe in "
		<< Chromap<>::GetRealTime() - real_dedupe_start_time << "s.\n";
		<< GetRealTime() - real_dedupe_start_time << "s.\n";
		}

		template <typename MappingRecord>
		@@ -3747,7 +3741,7 @@ uint32_t Chromap<MappingRecord>::GetNumOverlappedMappings(
		template <typename MappingRecord>
		void Chromap<MappingRecord>::AllocateMultiMappings(
		uint32_t num_reference_sequences) {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		std::vector<std::vector<MappingRecord>> &mappings =
		remove_pcr_duplicates_ ? deduped_mappings_on_diff_ref_seqs_
		: mappings_on_diff_ref_seqs_;
		@@ -3850,8 +3844,8 @@ void Chromap<MappingRecord>::AllocateMultiMappings(
		}
		}
		std::cerr << "Allocated " << num_allocated_multi_mappings
		<< " multi-mappings in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< " multi-mappings in " << GetRealTime() - real_start_time
		<< "s.\n";
		std::cerr << "# multi-mappings that have no uni-mapping overlaps: "
		<< num_multi_mappings_without_overlapping_unique_mappings << ".\n";
		}
		@@ -5806,8 +5800,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		mapping_parameters.low_memory_mode = true;
		mapping_parameters.mapping_output_format = MAPPINGFORMAT_PAIRS;
		} else {
		chromap::Chromap<>::ExitWithMessage("Unrecognized preset parameters " +
		read_type + "\n");
		chromap::ExitWithMessage("Unrecognized preset parameters " + read_type +
		"\n");
		}
		}
		// Optional parameters
		@@ -5957,13 +5951,13 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (result.count("r")) {
		index_parameters.reference_file_path = result["ref"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No reference specified!");
		chromap::ExitWithMessage("No reference specified!");
		}
		if (result.count("o")) {
		index_parameters.index_output_file_path =
		result["output"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No output file specified!");
		chromap::ExitWithMessage("No output file specified!");
		}
		std::cerr << "Build index for the reference.\n";
		std::cerr << "Kmer length: " << index_parameters.kmer_size
		@@ -5979,24 +5973,24 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (result.count("r")) {
		mapping_parameters.reference_file_path = result["ref"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No reference specified!");
		chromap::ExitWithMessage("No reference specified!");
		}
		if (result.count("o")) {
		mapping_parameters.mapping_output_file_path =
		result["output"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No output file specified!");
		chromap::ExitWithMessage("No output file specified!");
		}
		if (result.count("x")) {
		mapping_parameters.index_file_path = result["index"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No index file specified!");
		chromap::ExitWithMessage("No index file specified!");
		}
		if (result.count("1")) {
		mapping_parameters.read_file1_paths =
		result["read1"].as<std::vector<std::string>>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No read file specified!");
		chromap::ExitWithMessage("No read file specified!");
		}
		if (result.count("2")) {
		mapping_parameters.read_file2_paths =
		@@ -6015,7 +6009,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {

		if (result.count("barcode-whitelist")) {
		if (mapping_parameters.is_bulk_data) {
		chromap::Chromap<>::ExitWithMessage(
		chromap::ExitWithMessage(
		"No barcode file specified but the barcode whitelist file is "
		"given!");
		}
		@@ -6027,7 +6021,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		mapping_parameters.matrix_output_prefix =
		result["matrix-output-prefix"].as<std::string>();
		if (mapping_parameters.is_bulk_data) {
		chromap::Chromap<>::ExitWithMessage(
		chromap::ExitWithMessage(
		"No barcode file specified but asked to output matrix files!");
		}
		}
		@@ -6163,7 +6157,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		std::cerr << "Output mappings in pairs format.\n";
		break;
		default:
		chromap::Chromap<>::ExitWithMessage("Unknown mapping output format!");
		chromap::ExitWithMessage("Unknown mapping output format!");
		break;
		}

		@@ -6215,8 +6209,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		break;
		}
		case MAPPINGFORMAT_PAIRS:
		chromap::Chromap<>::ExitWithMessage(
		"No support for single-end HiC yet!");
		chromap::ExitWithMessage("No support for single-end HiC yet!");
		break;
		case MAPPINGFORMAT_BED:
		case MAPPINGFORMAT_TAGALIGN:
		@@ -6231,7 +6224,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}
		break;
		default:
		chromap::Chromap<>::ExitWithMessage("Unknown mapping output format!");
		chromap::ExitWithMessage("Unknown mapping output format!");
		break;
		}
		} else {
		@@ -6268,7 +6261,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}
		break;
		default:
		chromap::Chromap<>::ExitWithMessage("Unknown mapping output format!");
		chromap::ExitWithMessage("Unknown mapping output format!");
		break;
		}
		}

src/chromap.h

+0 −17

Original line number	Diff line number	Diff line
		@@ -521,23 +521,6 @@ class Chromap {
		void RerankCandidatesRid(std::vector<Candidate> &candidates);
		void ParseReadFormat(const std::string &read_format);

		inline static double GetRealTime() {
		struct timeval tp;
		struct timezone tzp;
		gettimeofday(&tp, &tzp);
		return tp.tv_sec + tp.tv_usec * 1e-6;
		}
		inline static double GetCPUTime() {
		struct rusage r;
		getrusage(RUSAGE_SELF, &r);
		return r.ru_utime.tv_sec + r.ru_stime.tv_sec +
		1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
		}
		inline static void ExitWithMessage(const std::string &message) {
		std::cerr << message << std::endl;
		exit(-1);
		}

		private:
		// Parameters
		int kmer_size_;

src/index.cc

+11 −11

Original line number	Diff line number	Diff line
		@@ -6,12 +6,13 @@
		#include <iostream>

		#include "chromap.h"
		#include "utils.h"

		namespace chromap {

		void Index::Statistics(uint32_t num_sequences,
		const SequenceBatch &reference) const {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		int n = 0, n1 = 0;
		uint32_t i;
		uint64_t sum = 0, len = 0;
		@@ -34,8 +35,8 @@ void Index::Statistics(uint32_t num_sequences,
		fprintf(stderr,
		"[M::%s::%.3f] distinct minimizers: %d (%.2f%% are singletons); "
		"average occurrences: %.3lf; average spacing: %.3lf\n",
		__func__, Chromap<>::GetRealTime() - real_start_time, n,
		100.0 * n1 / n, (double)sum / n, (double)len / sum);
		__func__, GetRealTime() - real_start_time, n, 100.0 * n1 / n,
		(double)sum / n, (double)len / sum);
		}

		// always reserve space for minimizers in other functions
		@@ -163,7 +164,7 @@ void Index::GenerateMinimizerSketch(
		}

		void Index::Construct(uint32_t num_sequences, const SequenceBatch &reference) {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		// tmp_table stores (minimizer, position)
		std::vector<std::pair<uint64_t, uint64_t> > tmp_table;
		tmp_table.reserve(reference.GetNumBases() / window_size_ * 2);
		@@ -230,8 +231,8 @@ void Index::Construct(uint32_t num_sequences, const SequenceBatch &reference) {
		<< ", # buckets: " << kh_n_buckets(lookup_table_)
		<< ", occurrence table size: " << occurrence_table_.size()
		<< ", # singletons: " << num_singletons << ".\n";
		std::cerr << "Built index successfully in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		std::cerr << "Built index successfully in " << GetRealTime() - real_start_time
		<< "s.\n";
		}

		void Index::CheckIndex(uint32_t num_sequences,
		@@ -269,7 +270,7 @@ void Index::CheckIndex(uint32_t num_sequences,
		}

		void Index::Save() const {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		FILE *index_file = fopen(index_file_path_.c_str(), "wb");
		assert(index_file != NULL);
		uint64_t num_bytes = 0;
		@@ -299,12 +300,11 @@ void Index::Save() const {
		fclose(index_file);
		// std::cerr << "Index size: " << num_bytes / (1024.0 * 1024 * 1024) << "GB,
		// saved in " << Chromap<>::GetRealTime() - real_start_time << "s.\n";
		std::cerr << "Saved in " << Chromap<>::GetRealTime() - real_start_time
		<< "s.\n";
		std::cerr << "Saved in " << GetRealTime() - real_start_time << "s.\n";
		}

		void Index::Load() {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		FILE *index_file = fopen(index_file_path_.c_str(), "rb");
		assert(index_file != NULL);
		int err = 0;
		@@ -331,7 +331,7 @@ void Index::Load() {
		std::cerr << "Lookup table size: " << kh_size(lookup_table_)
		<< ", occurrence table size: " << occurrence_table_.size() << ".\n";
		std::cerr << "Loaded index successfully in "
		<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		<< GetRealTime() - real_start_time << "s.\n";
		}

		// Return the number of repetitive seeds.

src/sequence_batch.cc

+9 −9

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@
		#include <tuple>

		#include "chromap.h"
		#include "utils.h"

		namespace chromap {
		constexpr uint8_t SequenceBatch::char_to_uint8_table_[256];
		@@ -12,14 +13,13 @@ void SequenceBatch::InitializeLoading(const std::string &sequence_file_path) {
		sequence_file_path_ = sequence_file_path;
		sequence_file_ = gzopen(sequence_file_path_.c_str(), "r");
		if (sequence_file_ == NULL) {
		Chromap<>::ExitWithMessage("Cannot find sequence file" +
		sequence_file_path);
		ExitWithMessage("Cannot find sequence file" + sequence_file_path);
		}
		sequence_kseq_ = kseq_init(sequence_file_);
		}

		uint32_t SequenceBatch::LoadBatch() {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		uint32_t num_sequences = 0;
		num_bases_ = 0;
		for (uint32_t sequence_index = 0; sequence_index < max_num_sequences_;
		@@ -44,7 +44,7 @@ uint32_t SequenceBatch::LoadBatch() {
		num_bases_ += length;
		} else {
		if (length != -1) {
		Chromap<>::ExitWithMessage(
		ExitWithMessage(
		"Didn't reach the end of sequence file, which might be corrupted!");
		}
		// make sure to reach the end of file rather than meet an error
		@@ -53,7 +53,7 @@ uint32_t SequenceBatch::LoadBatch() {
		}
		if (num_sequences != 0) {
		std::cerr << "Loaded sequence batch successfully in "
		<< Chromap<>::GetRealTime() - real_start_time << "s, ";
		<< GetRealTime() - real_start_time << "s, ";
		std::cerr << "number of sequences: " << num_sequences << ", ";
		std::cerr << "number of bases: " << num_bases_ << ".\n";
		} else {
		@@ -83,7 +83,7 @@ bool SequenceBatch::LoadOneSequenceAndSaveAt(uint32_t sequence_index) {
		}
		} else {
		if (length != -1) {
		Chromap<>::ExitWithMessage(
		ExitWithMessage(
		"Didn't reach the end of sequence file, which might be corrupted!");
		}
		// make sure to reach the end of file rather than meet an error
		@@ -93,7 +93,7 @@ bool SequenceBatch::LoadOneSequenceAndSaveAt(uint32_t sequence_index) {
		}

		uint32_t SequenceBatch::LoadAllSequences() {
		double real_start_time = Chromap<>::GetRealTime();
		double real_start_time = GetRealTime();
		sequence_batch_.reserve(200);
		uint32_t num_sequences = 0;
		num_bases_ = 0;
		@@ -118,7 +118,7 @@ uint32_t SequenceBatch::LoadAllSequences() {
		num_bases_ += length;
		} else {
		if (length != -1) {
		Chromap<>::ExitWithMessage(
		ExitWithMessage(
		"Didn't reach the end of sequence file, which might be corrupted!");
		}
		// make sure to reach the end of file rather than meet an error
		@@ -127,7 +127,7 @@ uint32_t SequenceBatch::LoadAllSequences() {
		length = kseq_read(sequence_kseq_);
		}
		std::cerr << "Loaded all sequences successfully in "
		<< Chromap<>::GetRealTime() - real_start_time << "s, ";
		<< GetRealTime() - real_start_time << "s, ";
		std::cerr << "number of sequences: " << num_sequences << ", ";
		std::cerr << "number of bases: " << num_bases_ << ".\n";
		return num_sequences;

src/utils.h

0 → 100644

+27 −0

Original line number	Diff line number	Diff line
		#ifndef UTILS_H_
		#define UTILS_H_

		namespace chromap {

		inline static double GetRealTime() {
		struct timeval tp;
		struct timezone tzp;
		gettimeofday(&tp, &tzp);
		return tp.tv_sec + tp.tv_usec * 1e-6;
		}

		inline static double GetCPUTime() {
		struct rusage r;
		getrusage(RUSAGE_SELF, &r);
		return r.ru_utime.tv_sec + r.ru_stime.tv_sec +
		1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
		}

		inline static void ExitWithMessage(const std::string &message) {
		std::cerr << message << std::endl;
		exit(-1);
		}

		} // namespace chromap

		#endif // UTILS_H_

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