Allowing shifted read with same minimizers in cache. Handle paired-end case (9ecc860e) · Commits · github_fork / Chromap

src/mmcache.hpp

+40 −12

Original line number	Diff line number	Diff line
		@@ -21,6 +21,7 @@ class mm_cache
		private:
		int cache_size ;
		struct _mm_cache_entry *cache ;
		int kmer_length ;

		// 0: not match. -1: opposite order. 1: same order
		int IsMinimizersMatchCache(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, const struct _mm_cache_entry &cache)
		@@ -39,7 +40,7 @@ private:
		{
		for (i = 0 ; i < size - 1 ; ++i)
		{
		if (cache.offsets[i] != ((int)(minimizers[i + 1].second)>>1) - ((int)(minimizers[i].second)>>1))
		if (cache.offsets[i] != ((int)minimizers[i + 1].second>>1) - ((int)minimizers[i].second>>1))
		break ;
		}
		if (i >= size - 1)
		@@ -58,7 +59,7 @@ private:
		{
		for (i = 0, j = size - 1; i < size - 1; ++i, --j)
		{
		if (cache.offsets[i] != ((int)(minimizers[j].second)>>1) - ((int)(minimizers[j - 1].second)>>1))
		if (cache.offsets[i] != ((int)minimizers[j].second>>1) - ((int)minimizers[j - 1].second>>1))
		break ;
		}

		@@ -82,6 +83,11 @@ public:
		delete[] cache ;
		}

		void SetKmerLength(int kl)
		{
		kmer_length = kl ;
		}

		// Return the hash entry index. -1 if failed.
		int Query(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers,
		std::vector<struct _candidate> &pos_candidates, std::vector<struct _candidate> &neg_candidates,
		@@ -98,19 +104,29 @@ public:
		{
		pos_candidates = cache[hidx].positive_candidates ;
		neg_candidates = cache[hidx].negative_candidates ;
		int size = pos_candidates.size() ;
		int shift = (int)minimizers[0].second>>1 ;
		for (i = 0 ; i < size ; ++i)
		pos_candidates[i].refPos -= shift ;
		size = neg_candidates.size() ;
		for (i = 0 ; i < size ; ++i)
		neg_candidates[i].refPos += shift ;
		return hidx ;
		}
		else if (direction == -1)
		else if (direction == -1) // The "read" is on the other direction of the cached "read"
		{
		int size = cache[hidx].negative_candidates.size() ;
		// Start position of the last minimizer shoud equal the first minimizer's end position in rc "read".
		int shift = read_len - ((int)minimizers[msize - 1].second>>1) - 1 + kmer_length - 1 ;

		pos_candidates = cache[hidx].negative_candidates ;
		for (i = 0 ; i < size ; ++i)
		pos_candidates[i].refPos = cache[hidx].negative_candidates[i].refPos - read_len + 1 ;
		pos_candidates[i].refPos = cache[hidx].negative_candidates[i].refPos + shift - read_len + 1 ;

		size = cache[hidx].positive_candidates.size() ;
		neg_candidates = cache[hidx].positive_candidates ;
		for (i = 0 ; i < size ; ++i)
		neg_candidates[i].refPos = cache[hidx].positive_candidates[i].refPos + read_len - 1 ;
		neg_candidates[i].refPos = cache[hidx].positive_candidates[i].refPos - shift + read_len - 1 ;
		return hidx ;
		}
		else
		@@ -139,17 +155,29 @@ public:
		if (cache[hidx].weight <= 0)
		{
		cache[hidx].weight = 1 ;
		int size = minimizers.size() ;
		cache[hidx].minimizers.resize(size) ;
		cache[hidx].offsets.resize(size - 1) ;
		for (i = 0 ; i < size ; ++i)
		cache[hidx].minimizers.resize(msize) ;
		if (msize == 0)
		return ;

		cache[hidx].offsets.resize(msize - 1) ;
		for (i = 0 ; i < msize ; ++i)
		cache[hidx].minimizers[i] = minimizers[i].first ;
		for (i = 0 ; i < size - 1; ++i)
		for (i = 0 ; i < msize - 1; ++i)
		{
		cache[hidx].offsets[i] = ((int)(minimizers[i + 1].second)>>1) - ((int)(minimizers[i].second)>>1) ;
		cache[hidx].offsets[i] = ((int)minimizers[i + 1].second>>1) - ((int)minimizers[i].second>>1) ;
		}
		cache[hidx].positive_candidates = pos_candidates ;
		cache[hidx].negative_candidates = neg_candidates ;

		// adjust the candidate position.
		int size = cache[hidx].positive_candidates.size() ;
		int shift = (int)minimizers[0].second>>1;
		for (i = 0 ; i < size ; ++i)
		cache[hidx].positive_candidates[i].refPos += shift ;
		size = cache[hidx].negative_candidates.size() ;
		for (i = 0 ; i < size ; ++i)
		cache[hidx].negative_candidates[i].refPos -= shift ;

		}
		}

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