Commit 2fd2fcae authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 2.2.3

parent 6ab3b099

BloomDBG/bloom-dbg.cc

+6 −3
Original line number Diff line number Diff line
@@ -357,11 +357,14 @@ countingBloomAssembly(int argc, char** argv, const BloomDBG::AssemblyParams& par 
		cerr << params;



	/* Initialize a counting Bloom filter:

	   Divide the requested memory in bytes by the byte-size of each counter to determine the number

	   of counters, and then round up that count to the next multiple of 64.*/

	   Divide the requested memory in bytes by 1.125 to account for the memory used

	   in building the visitedKmer BloomFilter. Then further divide the byte-size

	   of each counter to determine the number of counters, and then round up that

	   count to the next multiple of 64.*/



	double countingBloomFilterSize = params.bloomSize / 1.125 / sizeof(BloomCounterType);

	size_t counters =

	    BloomDBG::roundUpToMultiple(params.bloomSize / sizeof(BloomCounterType), (size_t)64);

	    BloomDBG::roundUpToMultiple((size_t) round(countingBloomFilterSize), (size_t)64);



	CountingBloomFilterType bloom(counters, params.numHashes, params.k, params.minCov);

ChangeLog

+9 −1
Original line number Diff line number Diff line 
2019-09-20  Johnathan Wong <jowong@bcgsc.ca>



	* Release version 2.2.3

	* Revert memory consumption of Bloom filters to pre 2.2.0 behaviour

	ABySS will now share the specified memory among all Bloom filters

	instead of just the counting Bloom filter.

	* Fix gcc-9 compilation warnings



2019-08-16  Johnathan Wong <jowong@bcgsc.ca>



	* Release version 2.2.2
@@ -11,7 +19,7 @@ 
2019-08-01  Johnathan Wong <jowong@bcgsc.ca>



	* Release version 2.2.0

	* Construct a counting bloom filter instead of a cascading bloom filter.

	* Construct a counting Bloom filter instead of a cascading Bloom filter.



	abyss-bloom:

	* Add 'counting' as valid argument to '-t' option to build a counting

Common/ContigNode.h

+5 −0
Original line number Diff line number Diff line
@@ -69,6 +69,11 @@ ContigNode operator^(bool sense) const 
	return ContigNode(m_index ^ sense);

}



/** Copy constructors */

ContigNode(ContigNode&&) = default;

ContigNode& operator=(const ContigNode&) = default;

ContigNode& operator=(ContigNode&&) = default;



/** Return whether this ContigNode is ambiguous. */

bool ambiguous() const

{

Graph/ContigGraph.h

+7 −0
Original line number Diff line number Diff line
@@ -15,6 +15,13 @@ using boost::graph_traits; 
template <typename G>

class ContigGraph : public G {

  public:



	/** Copy constructors */

	ContigGraph(const ContigGraph&) = default;

	ContigGraph(ContigGraph&&) = default;

	ContigGraph& operator=(const ContigGraph&) = default;

	ContigGraph& operator=(ContigGraph&&) = default;



	typedef G base_type;



	// Graph

Graph/DirectedGraph.h

+8 −1
Original line number Diff line number Diff line
@@ -545,8 +545,15 @@ class Edge 
		return ui < m_removed.size() ? m_removed[ui] : false;

	}



  protected:



	/** Copy constructors */

	DirectedGraph(const DirectedGraph& d) = default;

	DirectedGraph(DirectedGraph&&) = default;

	DirectedGraph& operator=(const DirectedGraph&) = default;

	DirectedGraph& operator=(DirectedGraph&&) = default;



  private:

	DirectedGraph& operator =(const DirectedGraph& x);



	/** The set of vertices. */

	Vertices m_vertices;