Commit 6e7e1b38 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 2.2.1

parent 11cdcb81

Bloom/HashAgnosticCascadingBloom.h

+5 −4
Original line number Diff line number Diff line
@@ -26,6 +26,7 @@ 
class HashAgnosticCascadingBloom

{

  public:

	typedef uint64_t hash_t;

	/** Default constructor */

	HashAgnosticCascadingBloom()

	  : m_k(0)
@@ -91,7 +92,7 @@ class HashAgnosticCascadingBloom 
	 * Return true if the element with the given hash values

	 * has count >= levels.

	 */

	bool contains(const std::vector<size_t>& hashes) const

	bool contains(const std::vector<hash_t>& hashes) const

	{

		assert(m_data.back() != NULL);

		return m_data.back()->contains(hashes);
@@ -101,14 +102,14 @@ class HashAgnosticCascadingBloom 
	 * Return true if the element with the given hash values

	 * has count >= levels.

	 */

	bool contains(const size_t hashes[]) const

	bool contains(const hash_t hashes[]) const

	{

		assert(m_data.back() != NULL);

		return m_data.back()->contains(hashes);

	}



	/** Add the object with the specified index to this multiset. */

	void insert(const std::vector<size_t>& hashes)

	void insert(const std::vector<hash_t>& hashes)

	{

		for (unsigned i = 0; i < m_data.size(); ++i) {

			assert(m_data.at(i) != NULL);
@@ -120,7 +121,7 @@ class HashAgnosticCascadingBloom 
	}



	/** Add the object with the specified index to this multiset. */

	void insert(const size_t hashes[])

	void insert(const hash_t hashes[])

	{

		for (unsigned i = 0; i < m_data.size(); ++i) {

			assert(m_data.at(i) != NULL);

Bloom/RollingBloomDBGVisitor.h

+2 −1
Original line number Diff line number Diff line
@@ -29,6 +29,7 @@ class RollingBloomDBGVisitor : public DefaultBFSVisitor<GraphT> 


	typedef std::vector<std::pair<std::string, BloomFilter*>> BloomProperties;

	typedef typename BloomProperties::const_iterator BloomPropertiesIt;

	typedef uint64_t hash_t;



	/** Constructor */

	template<typename VertexSetT>
@@ -110,7 +111,7 @@ class RollingBloomDBGVisitor : public DefaultBFSVisitor<GraphT> 
				m_out << "," << it->first;

		}



		size_t hashes[MAX_HASHES];

		hash_t hashes[MAX_HASHES];

		v.rollingHash().getHashes(hashes);



		for (BloomPropertiesIt it = m_bloomProperties.begin(); it != m_bloomProperties.end();

BloomDBG/RollingBloomDBG.h

+6 −4
Original line number Diff line number Diff line
@@ -205,9 +205,10 @@ struct graph_traits< RollingBloomDBG<BF> > { 


	/**

	 * Identifier for accessing a vertex in the graph.

	 * The second member of the pair (std::vector<size_t>) is

	 * The second member of the pair (std::vector<hash_t>) is

	 * a set of hash values associated with the k-mer.

	 */

	typedef uint64_t hash_t;

	typedef RollingBloomDBGVertex vertex_descriptor;

	typedef boost::directed_tag directed_category;

	struct traversal_category
@@ -223,11 +224,11 @@ struct graph_traits< RollingBloomDBG<BF> > { 
	typedef unsigned degree_size_type;



	// VertexListGraph

	typedef size_t vertices_size_type;

	typedef uint64_t vertices_size_type;

	typedef void vertex_iterator;



	// EdgeListGraph

	typedef size_t edges_size_type;

	typedef uint64_t edges_size_type;

	typedef void edge_iterator;



// AdjacencyGraph
@@ -438,7 +439,8 @@ vertex_exists( 
	const typename graph_traits<RollingBloomDBG<BloomT> >::vertex_descriptor& u,

	const RollingBloomDBG<BloomT>& g)

{

	size_t hashes[MAX_HASHES];

	typedef uint64_t hash_t;

	hash_t hashes[MAX_HASHES];

	u.rollingHash().getHashes(hashes);

	return g.m_bloom.contains(hashes);

}

BloomDBG/RollingHash.h

+7 −5
Original line number Diff line number Diff line
@@ -19,11 +19,13 @@ class RollingHash 
{

private:



	typedef uint64_t hash_t;



	/**

	 * Determine the canonical hash value, given hash values for

	 * forward and reverse-complement of the same k-mer.

	 */

	uint64_t canonicalHash(uint64_t hash, uint64_t rcHash) const

	hash_t canonicalHash(hash_t hash, hash_t rcHash) const

	{

		return (rcHash < hash) ? rcHash : hash;

	}
@@ -136,7 +138,7 @@ public: 
	 *

	 * @param hashes array for returned hash values

	 */

	void getHashes(size_t hashes[]) const

	void getHashes(hash_t hashes[]) const

	{

		for (unsigned i = 0; i < m_numHashes; ++i)

			hashes[i] = NTE64(m_hash, m_k, i);
@@ -208,12 +210,12 @@ private: 
	/** k-mer length */

	unsigned m_k;

	/** value of first hash function for current k-mer */

	uint64_t m_hash1;

	hash_t m_hash1;

	/** value of first hash function for current k-mer, after

	 * reverse-complementing */

	uint64_t m_rcHash1;

	hash_t m_rcHash1;

	/** current canonical hash value */

	uint64_t m_hash;

	hash_t m_hash;

};



#endif

BloomDBG/RollingHashIterator.h

+3 −2
Original line number Diff line number Diff line
@@ -98,6 +98,7 @@ private: 


public:



	typedef uint64_t hash_t;

	/**

	 * Default constructor. Creates an iterator pointing to

	 * the end of the iterator range.
@@ -142,7 +143,7 @@ public: 
	}



	/** get reference to hash values for current k-mer */

	const size_t* operator*() const

	const hash_t* operator*() const

	{

		assert(m_pos + m_k <= m_seq.length());

		return m_hashes;
@@ -216,7 +217,7 @@ private: 
	/** number of hash functions */

	unsigned m_numHashes;

	/** hash values */

	size_t m_hashes[MAX_HASHES];

	hash_t m_hashes[MAX_HASHES];

	/** k-mer size */

	unsigned m_k;

	/** internal state for rolling hash */