Avoid too many supplement operations (ccd90a8d) · Commits · github_fork / Chromap

src/index.cc

+10 −3

Original line number	Diff line number	Diff line
		@@ -492,9 +492,10 @@ void Index::GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold
		++best_candidate_num;
		}
		}
		if (best_candidate_num >= 500)//\|\| max_count < min_num_seeds_required_for_mapping_)
		if (best_candidate_num >= 500
		\|\| (max_count < min_num_seeds_required_for_mapping_ && best_candidate_num >= 5)
		\|\| (max_count == min_num_seeds_required_for_mapping_ && best_candidate_num >=50))
		return;

		std::vector<std::pair<uint64_t, uint64_t> > boundaries;
		boundaries.reserve(500);
		for (uint32_t ci = 0; ci < mate_candidates_size; ++ci) {
		@@ -551,9 +552,10 @@ void Index::GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold
		} else {
		uint32_t offset = value >> 32;
		uint32_t num_occurrences = value;
		uint32_t prev_l = 0;
		for (uint32_t bi = 0; bi < boundary_size; ++bi) {
		// use binary search to locate the coordinate near mate position
		int32_t l = 0, m = 0, r = num_occurrences - 1;
		int32_t l = prev_l, m = 0, r = num_occurrences - 1;
		uint64_t boundary = boundaries[bi].first;
		while (l <= r) {
		m = (l + r) / 2;
		@@ -568,6 +570,7 @@ void Index::GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold
		break;
		}
		}
		prev_l = m;
		//printf("%s: %d %d: %d %d\n", __func__, m, num_occurrences, (int)(boundary>>32), (int)boundary) ;
		for (uint32_t oi = m; oi < num_occurrences; ++oi) {
		uint64_t value = occurrence_table_[offset + oi];
		@@ -616,12 +619,14 @@ void Index::GenerateCandidates(int error_threshold, const std::vector<std::pair<
		int repetitive_seed_count = CollectCandidates(max_seed_frequencies_[0], max_seed_frequencies_[0], minimizers, repetitive_seed_length, positive_hits, negative_hits, false);
		//std::cerr << "rep seed: " << repetitive_seed_count << "\n";
		//if ((repetitive_seed_count > (int)minimizers.size() / 2 && minimizers.size() >= 10)) {
		bool checkmore = false;
		if (positive_hits->size() + negative_hits->size() == 0) {
		positive_hits->clear();
		negative_hits->clear();
		*repetitive_seed_length = 0;
		repetitive_seed_count = CollectCandidates(max_seed_frequencies_[1], max_seed_frequencies_[0], minimizers, repetitive_seed_length, positive_hits, negative_hits, true);
		//recollect = false;
		checkmore = true;
		}
		//if ((positive_candidates->size() == 0 \|\| negative_candidates->size() == 0) && recollect) {
		////if (positive_candidates->size() + negative_candidates->size() == 0 && recollect) {
		@@ -653,6 +658,8 @@ void Index::GenerateCandidates(int error_threshold, const std::vector<std::pair<
		int num_required_seeds = minimizers.size() - repetitive_seed_count;
		num_required_seeds = num_required_seeds > 1 ? num_required_seeds : 1;
		num_required_seeds = num_required_seeds > min_num_seeds_required_for_mapping_ ? min_num_seeds_required_for_mapping_ : num_required_seeds;
		if (checkmore)
		num_required_seeds = min_num_seeds_required_for_mapping_;
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds, positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds, negative_hits, negative_candidates);
		//fprintf(stderr, "p+n: %d\n", positive_candidates->size() + negative_candidates->size()) ;

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