Fix an issue of underflowing cause heap sort failure (ef049267) · Commits · github_fork / Chromap

src/index.cc

+12 −4

Original line number	Diff line number	Diff line
		@@ -378,6 +378,7 @@ int Index::CollectCandidates(int max_seed_frequency, int repetitive_seed_frequen
		uint32_t num_minimizers = minimizers.size();
		int repetitive_seed_count = 0 ;
		std::vector<uint64_t> mm_positive_hits = NULL, mm_negative_hits = NULL;
		bool heap_resort = false ; // need to sort the elements of heap first
		if (use_heap) {
		mm_positive_hits = new std::vector<uint64_t>[num_minimizers] ;
		mm_negative_hits = new std::vector<uint64_t>[num_minimizers] ;
		@@ -403,8 +404,9 @@ int Index::CollectCandidates(int max_seed_frequency, int repetitive_seed_frequen
		// ok, for now we can't see the reference here. So let us don't do the check.
		// Instead, we do it later some time when we check the candidates.
		uint64_t candidate = (reference_id << 32) \| candidate_position;
		if (use_heap)
		if (use_heap) {
		mm_positive_hits[mi].push_back(candidate);
		}
		else
		positive_hits->push_back(candidate);
		} else {
		@@ -427,8 +429,11 @@ int Index::CollectCandidates(int max_seed_frequency, int repetitive_seed_frequen
		if (((minimizers[mi].second & 1) ^ (value & 1)) == 0) { // same
		uint32_t candidate_position = reference_position - read_position;
		uint64_t candidate = (reference_id << 32) \| candidate_position;
		if (use_heap)
		if (use_heap) {
		if (reference_position < read_position)
		heap_resort = true ;
		mm_positive_hits[mi].push_back(candidate);
		}
		else
		positive_hits->push_back(candidate);
		} else {
		@@ -465,6 +470,9 @@ int Index::CollectCandidates(int max_seed_frequency, int repetitive_seed_frequen
		for (uint32_t mi = 0; mi < num_minimizers; ++mi) {
		if (mm_positive_hits[mi].size() == 0)
		continue;
		// only the positive part may have the underflow issue
		if (heap_resort)
		std::sort(mm_positive_hits[mi].begin(), mm_positive_hits[mi].end());
		struct mmHit nh;
		nh.mi = mi;
		nh.position = mm_positive_hits[mi][0];
		@@ -517,10 +525,10 @@ int Index::CollectCandidates(int max_seed_frequency, int repetitive_seed_frequen
		std::sort(negative_hits->begin(), negative_hits->end());
		}
		/*for (uint32_t mi = 0 ; mi < positive_hits->size() ; ++mi)
		printf("+ %llu\n", positive_hits->at(mi)) ;
		printf("+ %llu %d %d\n", positive_hits->at(mi), (int)(positive_hits->at(mi)>>32), (int)(positive_hits->at(mi))) ;

		for (uint32_t mi = 0 ; mi < negative_hits->size() ; ++mi)
		printf("- %llu\n", negative_hits->at(mi)) ;*/
		printf("- %llu %d %d\n", negative_hits->at(mi), (int)(negative_hits->at(mi)>>32), (int)(negative_hits->at(mi))) ;*/
		return repetitive_seed_count ;
		}

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