Fix a bug causing cache store empty entries. (077b2e50) · Commits · github_fork / Chromap

src/chromap.cc

+8 −1

Original line number	Diff line number	Diff line
		@@ -1175,6 +1175,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		//std::cerr << "After generation, #pc1: " << positive_candidates1.size() << ", #nc1: " << negative_candidates1.size() << ", #pc2: " << positive_candidates2.size() << ", #nc2: " << negative_candidates2.size() << "\n";
		uint32_t current_num_candidates2 = positive_candidates2.size() + negative_candidates2.size();
		if (pair_index < num_loaded_pairs && (pair_index < num_loaded_pairs / num_threads_ \|\| num_reads_ <= 5000000)) {
		mm_history1[pair_index].timestamp = mm_history2[pair_index].timestamp = num_reads_;
		mm_history1[pair_index].minimizers = minimizers1;
		mm_history1[pair_index].positive_candidates = positive_candidates1;
		mm_history1[pair_index].negative_candidates = negative_candidates1;
		@@ -1333,6 +1334,9 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		if (num_reads_ > 5000000 && pair_index >= num_loaded_pairs / num_threads_) {
		break;
		}
		if (mm_history1[pair_index].timestamp != num_reads_)
		continue ;

		mm_to_candidates_cache.Update(mm_history1[pair_index].minimizers, mm_history1[pair_index].positive_candidates, mm_history1[pair_index].negative_candidates, mm_history1[pair_index].repetitive_seed_length);
		mm_to_candidates_cache.Update(mm_history2[pair_index].minimizers, mm_history2[pair_index].positive_candidates, mm_history2[pair_index].negative_candidates, mm_history2[pair_index].repetitive_seed_length);
		/*if (mm_history1[pair_index].positive_candidates.size() < mm_history1[pair_index].positive_candidates.capacity() / 50) {
		@@ -2048,6 +2052,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		index.GenerateCandidates(error_threshold_, minimizers, &repetitive_seed_length, &positive_hits, &negative_hits, &positive_candidates, &negative_candidates);
		}
		if (read_index < num_loaded_reads && (read_index < num_loaded_reads / num_threads_ \|\| num_reads_ <= 2500000)) {
		mm_history[read_index].timestamp = num_reads_;
		mm_history[read_index].minimizers = minimizers;
		mm_history[read_index].positive_candidates = positive_candidates;
		mm_history[read_index].negative_candidates = negative_candidates;
		@@ -2079,6 +2084,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		if (num_reads_ > 2500000 && read_index >= num_loaded_reads / num_threads_) {
		break;
		}
		if (mm_history[read_index].timestamp != num_reads_)
		continue;
		mm_to_candidates_cache.Update(mm_history[read_index].minimizers, mm_history[read_index].positive_candidates, mm_history[read_index].negative_candidates, mm_history[read_index].repetitive_seed_length);
		if (mm_history[read_index].positive_candidates.size() < mm_history[read_index].positive_candidates.capacity() / 2) {
		std::vector<Candidate>().swap(mm_history[read_index].positive_candidates);

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ struct StackCell {
		};

		struct _mm_history {
		bool skip;
		unsigned int timestamp;
		std::vector<std::pair<uint64_t, uint64_t> > minimizers;
		std::vector<Candidate> positive_candidates;
		std::vector<Candidate> negative_candidates;

Admin message