Merge close candidates (66adea22) · Commits · github_fork / Chromap

src/chromap.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -429,9 +429,9 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		positive_candidates2.clear();
		negative_candidates1.clear();
		negative_candidates2.clear();
		index.GenerateCandidates(minimizers1, &positive_hits1, &negative_hits1, &positive_candidates1, &negative_candidates1);
		index.GenerateCandidates(error_threshold_, minimizers1, &positive_hits1, &negative_hits1, &positive_candidates1, &negative_candidates1);
		uint32_t current_num_candidates1 = positive_candidates1.size() + negative_candidates1.size();
		index.GenerateCandidates(minimizers2, &positive_hits2, &negative_hits2, &positive_candidates2, &negative_candidates2);
		index.GenerateCandidates(error_threshold_, minimizers2, &positive_hits2, &negative_hits2, &positive_candidates2, &negative_candidates2);
		uint32_t current_num_candidates2 = positive_candidates2.size() + negative_candidates2.size();
		if (current_num_candidates1 > 0 && current_num_candidates2 > 0) {
		positive_candidates1.swap(positive_hits1);
		@@ -949,7 +949,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		negative_hits.clear();
		positive_candidates.clear();
		negative_candidates.clear();
		index.GenerateCandidates(minimizers, &positive_hits, &negative_hits, &positive_candidates, &negative_candidates);
		index.GenerateCandidates(error_threshold_, minimizers, &positive_hits, &negative_hits, &positive_candidates, &negative_candidates);
		uint32_t current_num_candidates = positive_candidates.size() + negative_candidates.size();
		//std::cerr << "Generated candidates!\n";
		if (current_num_candidates > 0) {

src/index.cc

+7 −7

Original line number	Diff line number	Diff line
		@@ -261,7 +261,7 @@ void Index::Load() {
		std::cerr << "Loaded index successfully in "<< Chromap<>::GetRealTime() - real_start_time << "s.\n";
		}

		void Index::GenerateCandidatesOnOneDirection(std::vector<uint64_t> hits, std::vector<uint64_t> candidates) {
		void Index::GenerateCandidatesOnOneDirection(int error_threshold, std::vector<uint64_t> hits, std::vector<uint64_t> candidates) {
		hits->emplace_back(UINT64_MAX);
		if (hits->size() > 0) {
		std::sort(hits->begin(), hits->end());
		@@ -272,7 +272,7 @@ void Index::GenerateCandidatesOnOneDirection(std::vector<uint64_t> *hits, std::v
		for (uint32_t pi = 1; pi < hits->size(); ++pi) {
		uint32_t current_reference_id = (*hits)[pi] >> 32;
		uint32_t current_reference_position = (*hits)[pi];
		if (current_reference_id != previous_reference_id \|\| current_reference_position - previous_reference_position > 0) {
		if (current_reference_id != previous_reference_id \|\| current_reference_position > previous_reference_position + error_threshold) {
		if (count >= min_num_seeds_required_for_mapping_) {
		candidates->push_back(previous_hit);
		}
		@@ -338,18 +338,18 @@ void Index::CollectCandiates(int max_seed_frequency, const std::vector<std::pair
		}
		}

		void Index::GenerateCandidates(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<uint64_t> positive_candidates, std::vector<uint64_t> negative_candidates) {
		void Index::GenerateCandidates(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<uint64_t> positive_candidates, std::vector<uint64_t> negative_candidates) {
		CollectCandiates(max_seed_frequencies_[0], minimizers, positive_hits, negative_hits);
		// Now I can generate primer chain in candidates
		// Let me use sort for now, but I can use merge later.
		GenerateCandidatesOnOneDirection(positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(negative_hits, negative_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, negative_hits, negative_candidates);
		if (positive_candidates->size() + negative_candidates->size() == 0) {
		positive_hits->clear();
		negative_hits->clear();
		CollectCandiates(max_seed_frequencies_[1], minimizers, positive_hits, negative_hits);
		GenerateCandidatesOnOneDirection(positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(negative_hits, negative_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, negative_hits, negative_candidates);
		// TODO: if necessary, we can further improve the rescue. But the code below is not thread safe. We can think about this later
		// if (positive_candidates->size() + negative_candidates->size() == 0) {
		// --min_num_seeds_required_for_mapping_;

src/index.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -44,8 +44,8 @@ class Index {
		void Construct(uint32_t num_sequences, const SequenceBatch &reference);
		void Save();
		void Load();
		void GenerateCandidatesOnOneDirection(std::vector<uint64_t> hits, std::vector<uint64_t> candidates);
		void GenerateCandidates(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<uint64_t> positive_candidates, std::vector<uint64_t> negative_candidates);
		void GenerateCandidatesOnOneDirection(int error_threshold, std::vector<uint64_t> hits, std::vector<uint64_t> candidates);
		void GenerateCandidates(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<uint64_t> positive_candidates, std::vector<uint64_t> negative_candidates);
		void CollectCandiates(int max_seed_frequency, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits);
		inline static uint64_t Hash64(uint64_t key, const uint64_t mask) {
		key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;

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