Fix an issue of MD string, where 0 is inserted between adjacent mismatches and... (9b016207) · Commits · github_fork / Chromap

src/alignment.cc

+7 −11

Original line number	Diff line number	Diff line
		@@ -110,10 +110,9 @@ void GenerateNMAndMDTag(const char pattern, const char text,
		} else {
		// a mismatch
		++mapping_in_memory.NM;
		if (num_matches != 0) {

		mapping_in_memory.MD_tag.append(std::to_string(num_matches));
		num_matches = 0;
		}
		mapping_in_memory.MD_tag.push_back(reference[reference_position]);
		}
		++reference_position;
		@@ -124,10 +123,9 @@ void GenerateNMAndMDTag(const char pattern, const char text,
		read_position += num_cigar_operations;
		} else if (cigar_operation == BAM_CDEL) {
		mapping_in_memory.NM += num_cigar_operations;
		if (num_matches != 0) {

		mapping_in_memory.MD_tag.append(std::to_string(num_matches));
		num_matches = 0;
		}
		mapping_in_memory.MD_tag.push_back('^');
		for (int opi = 0; opi < num_cigar_operations; ++opi) {
		mapping_in_memory.MD_tag.push_back(reference[reference_position]);
		@@ -137,10 +135,8 @@ void GenerateNMAndMDTag(const char pattern, const char text,
		std::cerr << "Unexpected cigar op: " << (int)cigar_operation << "\n";
		}
		}
		if (num_matches != 0) {
		mapping_in_memory.MD_tag.append(std::to_string(num_matches));
		}
		}

		int BandedAlignPatternToText(int error_threshold, const char *pattern,
		const char *text, const int read_length,

+1 −1