Merge branch 'develop'

Bloom/HashAgnosticCascadingBloom.h

@@ -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

@@ -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

@@ -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

@@ -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 @@ class RollingHash
 	 *
 	 * @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 @@ class RollingHash
 	/** 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

@@ -98,6 +98,7 @@ class RollingHashIterator
 
 public:
 
+	typedef uint64_t hash_t;
 	/**
 	 * Default constructor. Creates an iterator pointing to
 	 * the end of the iterator range.
@@ -142,7 +143,7 @@ class RollingHashIterator
 	}
 
 	/** 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 @@ class RollingHashIterator
 	/** 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 */

ChangeLog

@@ -1,3 +1,8 @@
+2019-08-12  Johnathan Wong <[email protected]>
+
+	* Release version 2.2.1
+	* Fix abyss-bloom for macOS
+
 2019-08-01  Johnathan Wong <[email protected]>
 
 	* Release version 2.2.0

Misc/samtobreak.hs

@@ -279,7 +279,7 @@ parseArgs = do
   where
   help = putStr (usageInfo usage options) >> exitSuccess
   tryHelp = "Try 'abyss-samtobreak --help' for more information."
-  version = "abyss-samtobreak (ABySS) 2.2.0\n"
+  version = "abyss-samtobreak (ABySS) 2.2.1\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp

@@ -25,7 +25,7 @@ TEST(HashAgnosticCascadingBloom, base)
 	RollingHashIterator itB(b, numHashes, k);
 	RollingHashIterator itC(c, numHashes, k);
 	RollingHashIterator itD(d, numHashes, k);
-	size_t hash;
+	hash_t hash;
 
 	x.insert(*itA);
 	EXPECT_EQ(x.popcount(), 0U);

Unittest/BloomDBG/RollingBloomDBGTest.cpp

@@ -11,6 +11,7 @@ using namespace boost;
 typedef RollingBloomDBG<BloomFilter> Graph;
 typedef graph_traits<Graph> GraphTraits;
 typedef graph_traits<Graph>::vertex_descriptor V;
+typedef uint64_t hash_t;
 
 /** Test fixture for RollingBloomDBG tests. */
 class RollingBloomDBGTest : public ::testing::Test
@@ -42,7 +43,7 @@ class RollingBloomDBGTest : public ::testing::Test
 		 * complements of these k-mers.
 		 */
 
-		size_t hashes[MAX_HASHES];
+		hash_t hashes[MAX_HASHES];
 		RollingHash("CGACT", m_numHashes, m_k).getHashes(hashes);
 		m_bloom.insert(hashes);
 		RollingHash("TGACT", m_numHashes, m_k).getHashes(hashes);
@@ -156,7 +157,7 @@ TEST_F(RollingBloomDBGTest, pathTraversal)
 	const V GACTC("GACTC", RollingHash("GACTC", m_numHashes, m_k));
 	const V ACTCG("ACTCG", RollingHash("ACTCG", m_numHashes, m_k));
 
-	size_t hashes[MAX_HASHES];
+	hash_t hashes[MAX_HASHES];
 	CGACT.rollingHash().getHashes(hashes);
 	bloom.insert(hashes);
 	GACTC.rollingHash().getHashes(hashes);
@@ -268,7 +269,7 @@ class RollingBloomDBGSpacedSeedTest : public ::testing::Test
 		 * any additional edges in the graph.
 		 */
 
-		size_t hashes[MAX_HASHES];
+		hash_t hashes[MAX_HASHES];
 		RollingHash("CGACT", m_numHashes, m_k).getHashes(hashes);
 		m_bloom.insert(hashes);
 		RollingHash("TGACT", m_numHashes, m_k).getHashes(hashes);

azure-pipelines.yml

@@ -1,4 +1,25 @@
 jobs:
+- job: linux_gcc8_32bit
+  pool:
+    vmImage: Ubuntu 16.04
+  steps:
+  - script: |
+      sudo apt-get update -qq
+      sudo apt-get install -qq software-properties-common
+      sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+      sudo apt-get update -qq
+      sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
+    displayName: Install common
+  - script: sudo apt-get install -qq gcc-8 g++-8
+    displayName: Install gcc-8
+  - script: sudo apt-get install gcc-8-multilib g++-8-multilib
+    displayName: Install 32-bit compilation support
+  - script: |
+      ./autogen.sh
+      ./configure CC=gcc-8 CXX=g++-8 --build=i686-linux-gnu "CFLAGS=-m32" "CXXFLAGS=-m32" "LDFLAGS=-m32" --with-mpi=/usr/lib/openmpi
+      make -j12 distcheck
+    displayName: Compiling ABySS with gcc-8
+
 - job: linux_clang6
   pool:
     vmImage: Ubuntu 16.04
@@ -118,3 +139,19 @@ jobs:
     displayName: Install clang-format
   - script: make clang-format
     displayName: Run clang-format
+
+- job: macOS_gcc8
+  pool:
+    vmImage: macOS-10.14
+  steps:
+  - script: |
+      brew update
+      brew install automake [email protected] openmpi google-sparsehash make pandoc ghc
+    displayName: Install common
+  - script: brew install gcc@8
+    displayName: Install gcc
+  - script: |
+      ./autogen.sh
+      ./configure CC=gcc-8 CXX=g++-8 --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/
+      make -j12 distcheck
+    displayName: Compiling ABySS with gcc 8

bin/abyss-pe

@@ -398,7 +398,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or [email protected].'
 
 version:
-	@echo "abyss-pe (ABySS) 2.2.0"
+	@echo "abyss-pe (ABySS) 2.2.1"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.0, [email protected], abyss,
+AC_INIT(ABySS, 2.2.1, [email protected], abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.0" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.1" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.0" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.1" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.0" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.1" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br

vendor/btl_bloomfilter/.clang-format

@@ -0,0 +1,9 @@
+BasedOnStyle: Mozilla
+AlignAfterOpenBracket: AlwaysBreak
+AlignOperands: true
+ColumnLimit: 100
+ContinuationIndentWidth: 4
+IndentCaseLabels: false
+IndentWidth: 4
+TabWidth: 4
+UseTab: ForIndentation

vendor/btl_bloomfilter/.gitignore

@@ -0,0 +1,29 @@
+INSTALL
+Makefile
+Makefile.in
+Tests/AdHoc/BloomFilterTests
+Tests/AdHoc/ParallelFilter
+Tests/Unit/BloomFilterTests
+aclocal.m4
+autom4te.cache
+autoscan-*.log
+autoscan.log
+compile
+config.guess
+config.h
+config.h.in
+config.status
+config.sub
+configure
+configure.scan
+depcomp
+install-sh
+missing
+stamp-h1
+test-driver
+
+*.Po
+*.Tpo
+*.log
+*.o
+*.trs