Fix a potential overflow (617ef157) · Commits · github_fork / Chromap

src/chromap.cc

+6 −6

Original line number	Diff line number	Diff line
		@@ -659,7 +659,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		bool all_merged = false;
		uint32_t last_rid = std::numeric_limits<uint32_t>::max();
		MappingRecord last_mapping;
		uint8_t dup_count = 0;
		uint32_t dup_count = 0;
		uint64_t num_uni_mappings = 0;
		uint64_t num_multi_mappings = 0;
		uint64_t num_mappings_passing_filters = 0;
		@@ -686,7 +686,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		if (dup_count > 0) {
		if (last_mapping.mapq >= mapq_threshold_) {
		//if (allocate_multi_mappings_ \|\| (only_output_unique_mappings_ && last_mapping.is_unique == 1)) {
		last_mapping.num_dups = dup_count;
		last_mapping.num_dups = std::min((uint32_t)std::numeric_limits<uint8_t>::max(), dup_count);
		if (Tn5_shift_) {
		//last_mapping.fragment_start_position += 4;
		//last_mapping.positive_alignment_length -= 4;
		@@ -720,7 +720,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		}
		if (last_mapping.mapq >= mapq_threshold_) {
		//if (allocate_multi_mappings_ \|\| (only_output_unique_mappings_ && last_mapping.is_unique == 1)) {
		last_mapping.num_dups = dup_count;
		last_mapping.num_dups = std::min((uint32_t)std::numeric_limits<uint8_t>::max(), dup_count);
		if (Tn5_shift_) {
		//last_mapping.fragment_start_position += 4;
		//last_mapping.positive_alignment_length -= 4;
		@@ -2472,12 +2472,12 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(uint32_t num_reference_sequences
		deduped_mappings_on_diff_ref_seqs_[ri].emplace_back(mappings_on_diff_ref_seqs_[ri].front()); // ideally I should output the last of the dups of first mappings.
		//std::vector<MappingRecord>::iterator last_it = mappings_on_diff_ref_seqs_[ri].begin();
		auto last_it = mappings_on_diff_ref_seqs_[ri].begin();
		uint8_t last_dup_count = 1;
		uint32_t last_dup_count = 1;
		//for (std::vector<MappingRecord>::iterator it = ++(mappings_on_diff_ref_seqs_[ri].begin()); it != mappings_on_diff_ref_seqs_[ri].end(); ++it) {
		for (auto it = ++(mappings_on_diff_ref_seqs_[ri].begin()); it != mappings_on_diff_ref_seqs_[ri].end(); ++it) {
		if (!((it) == (last_it))) {
		//last_it->num_dups = last_dup_count;
		deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = last_dup_count;
		deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = std::min((uint32_t)std::numeric_limits<uint8_t>::max(), last_dup_count);
		last_dup_count = 1;
		deduped_mappings_on_diff_ref_seqs_[ri].emplace_back((*it));
		last_it = it;
		@@ -2485,7 +2485,7 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(uint32_t num_reference_sequences
		++last_dup_count;
		}
		}
		deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = last_dup_count;
		deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = std::min((uint32_t)std::numeric_limits<uint8_t>::max(), last_dup_count);
		std::vector<MappingRecord>().swap(mappings_on_diff_ref_seqs_[ri]);
		num_mappings += deduped_mappings_on_diff_ref_seqs_[ri].size();
		}

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