Handle the case in cache that may underflow when shifting at beginning of ref 0. (0ccd2c7a) · Commits · github_fork / Chromap

src/mmcache.hpp

+14 −9

Original line number	Diff line number	Diff line
		@@ -133,7 +133,11 @@ class mm_cache {
		repetitive_seed_length = cache[hidx].repetitive_seed_length;
		int size = pos_candidates.size();
		int shift = (int)minimizers[0].second >> 1;
		for (i = 0; i < size; ++i) pos_candidates[i].position -= shift;
		for (i = 0; i < size; ++i) {
		uint64_t rid = pos_candidates[i].position >> 32;
		int rpos = (int)pos_candidates[i].position;
		pos_candidates[i].position = (rid << 32) + (uint32_t)(rpos - shift);
		}
		size = neg_candidates.size();
		for (i = 0; i < size; ++i) neg_candidates[i].position += shift;
		return hidx;
		@@ -146,9 +150,11 @@ class mm_cache {
		kmer_length - 1;

		pos_candidates = cache[hidx].negative_candidates;
		for (i = 0; i < size; ++i)
		pos_candidates[i].position =
		cache[hidx].negative_candidates[i].position + shift - read_len + 1;
		for (i = 0; i < size; ++i) {
		uint64_t rid = cache[hidx].negative_candidates[i].position >> 32;
		int rpos = (int)cache[hidx].negative_candidates[i].position;
		pos_candidates[i].position = (rid << 32) + (uint32_t)(rpos + shift - read_len + 1);
		}
		size = cache[hidx].positive_candidates.size();
		neg_candidates = cache[hidx].positive_candidates;
		for (i = 0; i < size; ++i)
		@@ -250,11 +256,10 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
		// adjust the candidate position.
		int size = cache[hidx].positive_candidates.size();
		int shift = (int)minimizers[0].second >> 1;
		for (i = 0; i < size; ++i)
		{
		int rid = (int)(cache[hidx].positive_candidates[i].position >> 32);
		for (i = 0; i < size; ++i) {
		uint64_t rid = (int)(cache[hidx].positive_candidates[i].position >> 32);
		int rpos = (int)cache[hidx].positive_candidates[i].position;
		cache[hidx].positive_candidates[i].position = ((uint64_t)rid << 32) + rpos + shift;
		cache[hidx].positive_candidates[i].position = (rid << 32) + (uint32_t)(rpos + shift);
		}
		size = cache[hidx].negative_candidates.size();
		for (i = 0; i < size; ++i)

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