Merge branch 'develop'

.circleci/config.yml

@@ -21,6 +21,7 @@ jobs:
       - checkout
       - run: |
           ./autogen.sh
+          export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"
           ./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi
       - run: make -j12 distcheck
 
@@ -34,6 +35,7 @@ jobs:
       - checkout
       - run: |
           ./autogen.sh
+          export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"
           ./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi
       - run: make -j12 distcheck
 
@@ -47,6 +49,7 @@ jobs:
       - checkout
       - run: |
           ./autogen.sh
+          export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"
           ./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi
       - run: make -j12 distcheck
 
@@ -60,6 +63,7 @@ jobs:
       - checkout
       - run: |
           ./autogen.sh
+          export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"
           ./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi
       - run: make -j12 distcheck
 
@@ -73,6 +77,7 @@ jobs:
       - checkout
       - run: |
           ./autogen.sh
+          export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"
           ./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi
       - run: make -j12 distcheck
 

ChangeLog

@@ -1,3 +1,8 @@
+2019-08-16  Johnathan Wong <[email protected]>
+
+	* Release version 2.2.2
+	* Fix abyss-overlap for 32-bit systems
+
 2019-08-12  Johnathan Wong <[email protected]>
 
 	* Release version 2.2.1

Map/index.cc

@@ -146,7 +146,7 @@ static void buildFMIndex(FMIndex& fm, const string& path)
 	std::vector<FMIndex::value_type> s;
 	readFile(path.c_str(), s);
 
-	size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+	uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
 	if (s.size() > MAX_SIZE) {
 		std::cerr << PROGRAM << ": `" << path << "', "
 			<< toSI(s.size())

Map/map.cc

@@ -505,7 +505,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)
 	std::vector<FMIndex::value_type> s;
 	readFile(path, s);
 
-	size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+	uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
 	if (s.size() > MAX_SIZE) {
 		std::cerr << PROGRAM << ": `" << path << "', "
 			<< toSI(s.size())

Map/overlap.cc

@@ -293,7 +293,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)
 	std::vector<FMIndex::value_type> s;
 	readFile(path, s);
 
-	size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+	uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
 	if (s.size() > MAX_SIZE) {
 		std::cerr << PROGRAM << ": `" << path << "', "
 			<< toSI(s.size())

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) 2.2.1\n"
+  version = "abyss-samtobreak (ABySS) 2.2.2\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

azure-pipelines.yml

@@ -16,6 +16,7 @@ jobs:
     displayName: Install 32-bit compilation support
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=\"gcc-8 -m32\" CXX=\"g++-8 -m32\" --build=i386-linux-gnu"
       ./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
@@ -35,6 +36,7 @@ jobs:
     displayName: Install clang-6.0
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"
       ./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi
       make -j12 distcheck
     displayName: Compiling ABySS with clang 6.0
@@ -54,6 +56,7 @@ jobs:
     displayName: Install gcc-5
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"
       ./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-5
@@ -73,6 +76,7 @@ jobs:
     displayName: Install gcc-6
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"
       ./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-6
@@ -92,6 +96,7 @@ jobs:
     displayName: Install gcc-7
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"
       ./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-7
@@ -111,6 +116,7 @@ jobs:
     displayName: Install gcc-8
   - script: |
       ./autogen.sh
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"
       ./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-8
@@ -140,18 +146,16 @@ jobs:
   - script: make clang-format
     displayName: Run clang-format
 
-- job: macOS_gcc8
+- job: macOS_default_gcc
   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/
+      ./configure --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
+    displayName: Compiling ABySS with default gcc

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) 2.2.1"
+	@echo "abyss-pe (ABySS) 2.2.2"
 	@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, 2.2.1, [email protected], abyss,
+AC_INIT(ABySS, 2.2.2, [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) 2.2.1" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.2" "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) 2.2.1" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.2" "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 2.2.1" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.2" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br