Fix a memory leak when outputing SAM (c5947019) · Commits · github_fork / Chromap

src/chromap.cc

+1 −1

Original line number	Diff line number	Diff line
		@@ -986,7 +986,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		uint32_t num_mappings_in_mem = 0;
		uint64_t max_num_mappings_in_mem = 1 * ((uint64_t)1 << 30) / sizeof(MappingRecord);
		if (output_mapping_in_SAM_ \|\| output_mapping_in_pairs_ \|\| output_mapping_in_PAF_) {
		max_num_mappings_in_mem = 1 * ((uint64_t)1 << 28) / sizeof(MappingRecord);
		max_num_mappings_in_mem = 1 * ((uint64_t)1 << 29) / sizeof(MappingRecord);
		}
		static uint64_t thread_num_candidates = 0;
		static uint64_t thread_num_mappings = 0;

+3 −0

Original line number	Diff line number	Diff line
		@@ -336,6 +336,7 @@ struct SAMMapping {
		bool IsPositive() const {
		return is_rev > 0 ? true : false;
		}
		// For now for convenience, we assume cigar should not be accessed after generating the cigar string for output
		std::string GenerateCigarString() const {
		if (n_cigar == 0) {
		return "*";
		@@ -349,6 +350,7 @@ struct SAMMapping {
		//cigar_string.append(std::to_string((BAM_CIGAR_STR[op])));
		cigar_string.push_back((BAM_CIGAR_STR[op]));
		}
		delete[] cigar;
		return cigar_string;
		}
		std::string GenerateIntTagString(const std::string &tag, int value) const {
		@@ -400,6 +402,7 @@ struct SAMMapping {
		num_written_bytes += fwrite(&n_cigar, sizeof(int), 1, temp_mapping_output_file);
		if (n_cigar > 0) {
		num_written_bytes += fwrite(cigar, sizeof(uint32_t), n_cigar, temp_mapping_output_file);
		delete[] cigar;
		}
		uint16_t MD_length = MD.length();
		num_written_bytes += fwrite(&MD_length, sizeof(uint16_t), 1, temp_mapping_output_file);