Do not use mapq_pe when split alignment (e5c6c213) · Commits · github_fork / Chromap

src/chromap.cc

+4 −2

Original line number	Diff line number	Diff line
		@@ -3509,8 +3509,10 @@ uint8_t Chromap<MappingRecord>::GetMAPQForPairedEndRead(int num_positive_candida
		mapq1 = GetMAPQForSingleEndRead(error_threshold_, num_positive_candidates, repetitive_seed_length1, positive_alignment_length, min_num_errors1, num_best_mappings1, second_min_num_errors1, num_second_best_mappings1);
		mapq2 = GetMAPQForSingleEndRead(error_threshold_, num_negative_candidates, repetitive_seed_length2, negative_alignment_length, min_num_errors2, num_best_mappings2, second_min_num_errors2, num_second_best_mappings2);
		//std::cerr << " 1:" << (int)mapq1 << " 2:" << (int)mapq2 << "\n";
		if (!split_alignment_) {
		mapq1 = mapq1 > mapq_pe ? mapq1 : mapq_pe < mapq1 + 40? mapq_pe : mapq1 + 40;
		mapq2 = mapq2 > mapq_pe ? mapq2 : mapq_pe < mapq2 + 40? mapq_pe : mapq2 + 40;
		}
		//std::cerr << " 1:" << (int)mapq1 << " 2:" << (int)mapq2 << "\n";
		//if (second_min_num_errors1 > error_threshold_) {
		// second_min_num_errors1 = 2 * error_threshold_ + 1;