Check the boundary when heuristic skipping alignment (edf24f80) · Commits · github_fork / Chromap

src/chromap.cc

+23 −6

Original line number	Diff line number	Diff line
		@@ -2024,8 +2024,24 @@ void Chromap<MappingRecord>::VerifyCandidates(const SequenceBatch &read_batch, u
		*num_best_mappings = 1 ;
		*num_second_best_mappings = 0 ;
		*min_num_errors = 0 ;
		if (candidate_direction == kPositive) {

		uint32_t rid = 0 ;
		uint32_t position = 0 ;
		uint32_t read_length = read_batch.GetSequenceLengthAt(read_index);
		if (candidate_direction == kPositive) {
		rid = positive_candidates[ci].refPos >> 32 ;
		position = positive_candidates[ci].refPos ;
		}
		else {
		rid = negative_candidates[ci].refPos >> 32 ;
		position = (uint32_t)negative_candidates[ci].refPos - read_length + 1 ;
		}
		bool flag = true ;
		if (position < (uint32_t)error_threshold_ \|\| position >= reference.GetSequenceLengthAt(rid) \|\| position + read_length + error_threshold_ >= reference.GetSequenceLengthAt(rid)) {
		flag = false ;
		}
		if (flag) {
		if (candidate_direction == kPositive) {
		positive_mappings->emplace_back(0, positive_candidates[ci].refPos + read_length - 1);
		} else {
		negative_mappings->emplace_back(0, negative_candidates[ci].refPos);
		@@ -2033,6 +2049,7 @@ void Chromap<MappingRecord>::VerifyCandidates(const SequenceBatch &read_batch, u
		//printf("Saved %d\n", positive_candidates.size() + negative_candidates.size() ) ;
		return ;
		}
		}
		//printf("Notsaved %d\n", positive_candidates.size() + negative_candidates.size()) ;

		// Use more sophicated approach to obtain the mapping