Fix an issue of unsigned underflow issue in binary search. (881b28a1) · Commits · github_fork / Chromap

src/chromap.cc

+5 −6

Original line number	Diff line number	Diff line
		@@ -610,7 +610,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index) {
		read_batch1.PrepareNegativeSequenceAt(pair_index);
		read_batch2.PrepareNegativeSequenceAt(pair_index);
		//std::cerr << read_batch1.GetSequenceNameAt(pair_index);
		//std::cerr << read_batch1.GetSequenceNameAt(pair_index)<<"\n";
		if (trim_adapters_) {
		TrimAdapterForPairedEndRead(pair_index, &read_batch1, &read_batch2);
		}
		@@ -654,7 +654,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		mm_history2[pair_index].negative_candidates = negative_candidates2;
		mm_history2[pair_index].repetitive_seed_length = repetitive_seed_length2;
		}

		if (current_num_candidates1 + current_num_candidates2 == 1) {
		if (current_num_candidates1 == 1) {
		positive_hits2.clear();
		@@ -667,13 +666,13 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		repetitive_seed_length1 = 0;
		}
		if (positive_candidates1.size() == 1)
		index.GenerateCandidatesFromRepetiveReadWithMateInfo(error_threshold_, minimizers2, &repetitive_seed_length2, &negative_hits2, &negative_candidates2, &positive_candidates1, -1, 2 * max_insert_size_) ;
		index.GenerateCandidatesFromRepetitiveReadWithMateInfo(error_threshold_, minimizers2, &repetitive_seed_length2, &negative_hits2, &negative_candidates2, &positive_candidates1, -1, 2 * max_insert_size_) ;
		else if (negative_candidates1.size() == 1)
		index.GenerateCandidatesFromRepetiveReadWithMateInfo(error_threshold_, minimizers2, &repetitive_seed_length2, &positive_hits2, &positive_candidates2, &negative_candidates1, 1, 2 * max_insert_size_) ;
		index.GenerateCandidatesFromRepetitiveReadWithMateInfo(error_threshold_, minimizers2, &repetitive_seed_length2, &positive_hits2, &positive_candidates2, &negative_candidates1, 1, 2 * max_insert_size_) ;
		else if (positive_candidates2.size() == 1)
		index.GenerateCandidatesFromRepetiveReadWithMateInfo(error_threshold_, minimizers1, &repetitive_seed_length1, &negative_hits1, &negative_candidates1, &positive_candidates2, -1, 2 * max_insert_size_) ;
		index.GenerateCandidatesFromRepetitiveReadWithMateInfo(error_threshold_, minimizers1, &repetitive_seed_length1, &negative_hits1, &negative_candidates1, &positive_candidates2, -1, 2 * max_insert_size_) ;
		else if (negative_candidates2.size() == 1)
		index.GenerateCandidatesFromRepetiveReadWithMateInfo(error_threshold_, minimizers1, &repetitive_seed_length1, &positive_hits1, &positive_candidates1, &negative_candidates2, 1, 2 * max_insert_size_) ;
		index.GenerateCandidatesFromRepetitiveReadWithMateInfo(error_threshold_, minimizers1, &repetitive_seed_length1, &positive_hits1, &positive_candidates1, &negative_candidates2, 1, 2 * max_insert_size_) ;
		current_num_candidates1 = positive_candidates1.size() + negative_candidates1.size();
		current_num_candidates2 = positive_candidates2.size() + negative_candidates2.size();
		}

src/index.cc

+4 −4

Original line number	Diff line number	Diff line
		@@ -354,7 +354,7 @@ void Index::CollectCandidates(int max_seed_frequency, const std::vector<std::pai
		}
		}

		void Index::GenerateCandidatesFromRepetiveReadWithMateInfo(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> hits, std::vector<Candidate> candidates, std::vector<Candidate> mate_candidates, int direction, unsigned int range) // directoin: +1: positive; -1: negative
		void Index::GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> hits, std::vector<Candidate> candidates, std::vector<Candidate> mate_candidates, int direction, unsigned int range) // directoin: +1: positive; -1: negative
		{
		uint32_t num_minimizers = minimizers.size();
		hits->reserve(max_seed_frequencies_[0]);
		@@ -389,8 +389,8 @@ void Index::GenerateCandidatesFromRepetiveReadWithMateInfo(int error_threshold,
		uint32_t offset = value >> 32;
		uint32_t num_occurrences = value;
		// use binary search to locate the coordinate near mate position
		uint32_t l = 0, m = 0, r = num_occurrences - 1;
		uint64_t boundary = (mate_candidates->at(0).position < range) ? 0 : mate_candidates->at(0).position - range ;
		int32_t l = 0, m = 0, r = num_occurrences - 1;
		uint64_t boundary = (mate_candidates->at(0).position < range) ? 0 : (mate_candidates->at(0).position - range) ;
		while (l <= r) {
		m = (l + r) / 2;
		uint64_t value = (occurrence_table_[offset + m])>>1;

src/index.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -64,7 +64,7 @@ class Index {
		void Load();
		void GenerateCandidatesOnOneDirection(int error_threshold, std::vector<uint64_t> hits, std::vector<Candidate> candidates);
		void GenerateCandidates(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<Candidate> positive_candidates, std::vector<Candidate> *negative_candidates);
		void GenerateCandidatesFromRepetiveReadWithMateInfo(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> hits, std::vector<Candidate> candidates, std::vector<Candidate> mate_candidates, int direction, unsigned int range);
		void GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> hits, std::vector<Candidate> candidates, std::vector<Candidate> mate_candidates, int direction, unsigned int range);
		void CollectCandidates(int max_seed_frequency, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, 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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