Merge branch 'master' of github.com:haowenz/chromap (560a488f) · Commits · github_fork / Chromap

src/chromap.cc

+5 −3

Original line number	Diff line number	Diff line
		@@ -1902,6 +1902,8 @@ void Chromap<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(Direction c
		} else {
		mappings->emplace_back((uint8_t)mapping_edit_distances[mi], valid_candidates[mi].position - read_length + 1 - error_threshold_ + mapping_end_positions[mi]);
		}
		} else {
		candidate_count_threshold = valid_candidates[mi].count;
		}
		}
		} else if (NUM_VPU_LANES_ == 4) {
		@@ -1942,8 +1944,8 @@ void Chromap<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(Direction c
		}
		valid_candidate_index = 0;
		// Check whether we should stop early. Assuming the candidates are sorted
		//if (GetMAPQ(num_candidates, 0, 0, 0, read_length + error_threshold_, min_num_errors, num_best_mappings, second_min_num_errors, second_min_num_errors) < mapq_threshold_)
		// break;
		if (GetMAPQForSingleEndRead(error_threshold_, num_candidates, 0, read_length + error_threshold_, min_num_errors, num_best_mappings, second_min_num_errors, second_min_num_errors) == 0)
		break;
		}
		++candidate_index;
		}
		@@ -2588,7 +2590,7 @@ uint8_t Chromap<MappingRecord>::GetMAPQForSingleEndRead(int error_threshold, int
		if (repetitive_seed_length >= alignment_length) {
		frac_rep = 0.999;
		}
		mapq = mapq * (1 - frac_rep) + 0.499;
		mapq = mapq * (1 - frac_rep / 2) + 0.499;
		}
		//mapq <<= 1;
		return (uint8_t)mapq;