Merge branch 'master' of github.com:haowenz/chromap (b49ef6c6) · Commits · github_fork / Chromap

src/index.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -287,7 +287,7 @@ void Index::GenerateCandidatesOnOneDirection(int error_threshold, std::vector<ui
		}
		}

		void Index::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) {
		void Index::CollectCandidates(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) {
		uint32_t num_minimizers = minimizers.size();
		positive_hits->reserve(max_seed_frequencies_[0]);
		negative_hits->reserve(max_seed_frequencies_[0]);
		@@ -339,7 +339,7 @@ void Index::CollectCandiates(int max_seed_frequency, const std::vector<std::pair
		}

		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);
		CollectCandidates(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(error_threshold, positive_hits, positive_candidates);
		@@ -347,7 +347,7 @@ void Index::GenerateCandidates(int error_threshold, const std::vector<std::pair<
		if (positive_candidates->size() + negative_candidates->size() == 0) {
		positive_hits->clear();
		negative_hits->clear();
		CollectCandiates(max_seed_frequencies_[1], minimizers, positive_hits, negative_hits);
		CollectCandidates(max_seed_frequencies_[1], minimizers, positive_hits, negative_hits);
		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

src/index.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -46,7 +46,7 @@ class Index {
		void Load();
		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);
		void CollectCandidates(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;
		key = key ^ key >> 24;

Admin message