Supplement more (26d51a3c) · Commits · github_fork / Chromap

src/chromap.cc

+8 −8

Original line number	Diff line number	Diff line
		@@ -563,28 +563,28 @@ void Chromap<MappingRecord>::SupplementCandidates(const Index &index, uint32_t r
		uint32_t mm_count = minimizers->size();
		bool augment_flag = true;
		uint32_t candidate_num = positive_candidates->size();
		if (positive_candidates->size() >= (uint32_t)max_seed_frequencies_[0]) {
		augment_flag = false;
		} else {
		//if (positive_candidates->size() >= (uint32_t)max_seed_frequencies_[0]) {
		// augment_flag = false;
		//} else {
		for (uint32_t i = 0; i < candidate_num; ++i) {
		if (positive_candidates->at(i).count >= mm_count / 2) {
		augment_flag = false;
		break;
		}
		}
		}
		//}
		candidate_num = negative_candidates->size();
		if (augment_flag) {
		if (negative_candidates->size() >= (uint32_t)max_seed_frequencies_[0]) {
		augment_flag = false;
		} else {
		//if (negative_candidates->size() >= (uint32_t)max_seed_frequencies_[0]) {
		// augment_flag = false;
		//} else {
		for (uint32_t i = 0; i < candidate_num; ++i) {
		if (negative_candidates->at(i).count >= mm_count / 2) {
		augment_flag = false;
		break;
		}
		}
		}
		//}
		}
		if (augment_flag) {
		positive_hits->clear();

+10 −9

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_)
		return;
		std::vector<std::pair<uint64_t, uint64_t> > boundaries;
		boundaries.reserve(500);
		for (uint32_t ci = 0; ci < mate_candidates_size; ++ci) {
		if (mate_candidates->at(ci).count == max_count) {
		std::pair<uint64_t, uint64_t> r;
		@@ -649,7 +650,7 @@ void Index::GenerateCandidates(int error_threshold, const std::vector<std::pair<
		//printf("p+n: %d. %d %d\n", positive_hits->size() + negative_hits->size(), repetitive_seed_count, minimizers.size()) ;

		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 > 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;
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds, positive_hits, positive_candidates);
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds, negative_hits, negative_candidates);