Fix a possible bug of using out range reference sequence (4024369b) · Commits · github_fork / Chromap

src/chromap.cc

+5 −2

Original line number	Diff line number	Diff line
		@@ -1898,9 +1898,12 @@ void Chromap<MappingRecord>::GetRefStartEndPositionForReadFromMapping(Direction
		}
		uint32_t verification_window_start_position = position + 1 > (uint32_t)(read_length + error_threshold_) ? position + 1 - read_length - error_threshold_ : 0;
		//printf("%d %d. %d\n", position, verification_window_start_position, read_length);
		if (position >= reference.GetSequenceLengthAt(rid)) {
		if (position + error_threshold_ >= reference.GetSequenceLengthAt(rid)) {
		verification_window_start_position = reference.GetSequenceLengthAt(rid) - error_threshold_ - read_length;
		}
		if (verification_window_start_position < 0) {
		verification_window_start_position = 0;
		}
		if (split_alignment_) {
		if (split_site < full_read_length) {
		split_site -= 3 * error_threshold_;
		@@ -1996,7 +1999,7 @@ void Chromap<MappingRecord>::ProcessBestMappingsForSingleEndRead(Direction mappi
		uint8_t direction = 1;

		uint32_t *cigar ;
		int n_cigar ;
		int n_cigar = 0;
		int NM = 0;
		std::string MD_tag = "" ;
		const char *effect_read = read ;