Add some comment for force mapq. (5afc489a) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

+4 −1

Original line number	Diff line number	Diff line
		@@ -48,6 +48,9 @@ class MappingGenerator {
		MappingMetadata &mapping_metadata,
		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);

		// When the number of supplemented candidates is greater than 0, the
		// force_mapq will be 0, and thereby setting the mapq to 0 (not mapq1 or
		// mapq2). Split alignment won't run candidate supplement.
		void GenerateBestMappingsForPairedEndRead(
		uint32_t pair_index, const SequenceBatch &read_batch1,
		const SequenceBatch &read_batch2, const SequenceBatch &barcode_batch,
		@@ -2092,7 +2095,7 @@ uint8_t MappingGenerator<MappingRecord>::GetMAPQForPairedEndRead(
		<< " #bm:" << paired_end_mapping_metadata.num_best_mappings_
		<< " sme:" << paired_end_mapping_metadata.second_min_sum_errors_
		<< " #sbm:" << paired_end_mapping_metadata.num_second_best_mappings_
		<< " ne1:" << num_errors1 << " ne2:" << num_errors2 << " me1:"
		<< " ne1:" << read1_num_errors << " ne2:" << read2_num_errors << " me1:"
		<< paired_end_mapping_metadata.mapping_metadata1_.min_num_errors_
		<< " me2:"
		<< paired_end_mapping_metadata.mapping_metadata2_.min_num_errors_