.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

+2019-08-16  Johnathan Wong <jowong@bcgsc.ca>
+
+	* Release version 2.2.2
+	* Fix abyss-overlap for 32-bit systems
+
 2019-08-12  Johnathan Wong <jowong@bcgsc.ca>
 
 	* 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
@@ -140,7 +146,7 @@ jobs:
   - script: make clang-format
     displayName: Run clang-format
 
-- job: macOS_gcc8
+- job: macOS_default_gcc
   pool:
     vmImage: macOS-10.14
   steps:
@@ -148,10 +154,8 @@ jobs:
       brew update
       brew install automake boost@1.70 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 abyss-users@bcgsc.ca.'
 
 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

 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.1, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.2.2, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

debian/changelog

+abyss (2.2.2-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 17 Aug 2019 08:53:07 +0200
+
 abyss (2.2.1-1) unstable; urgency=medium
 
   * New upstream release, should fix failing builds on 32-bit architectures.

debian/clean

+Sealer/abyss-sealer.1

debian/patches/series

@@ -2,3 +2,4 @@ abyss-pe.patch
 # gtest.patch
 abyss-32-bit.patch
 strict_alignment.patch
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: typo fixes, courtesy lintian
+--- abyss.orig/Sealer/README.md
++++ abyss/Sealer/README.md
+@@ -24,7 +24,7 @@
+ Description
+ ===========
+ 
+-Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, succesfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
++Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, successfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
+ 
+ Installation
+ ============
+@@ -159,6 +159,6 @@
+ * `--help`: display this help and exit
+ * `--version`: output version information and exit
+ 
+-*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the nubmer of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
++*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the number of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
+ 
+ *P* is the threshold for number of paths allowed to be traversed. When set to 10, Konnector will attempt to close gaps even when there are 10 different paths found. It would attempt to create a consensus sequence between these paths. The default setting is 2.
+--- abyss.orig/doc/abyss-pe.1
++++ abyss/doc/abyss-pe.1
+@@ -113,7 +113,7 @@
+ SS=--SS to assemble in strand-specific mode
+ .br
+ Requires that all libraries are strand-specific RNA-Seq libraries.
+-Assumes that the first read in a read pair is reveresed WRT the
++Assumes that the first read in a read pair is reversed WRT the
+ transcripts sequenced.
+ .TP
+ .B t
+@@ -242,7 +242,7 @@
+ 
+ .SS "MPI COMPATIBILITY"
+ Due to its use of multi-threading, DIDA has known deadlocking issues
+-with OpenMPI.  Using the MPICH MPI library is strongly recommmended
++with OpenMPI.  Using the MPICH MPI library is strongly recommended
+ when running assemblies with DIDA. Testing was done with MPICH 3.1.3,
+ compiled with --enable-threads=funneled.
+ 

debian/rules

 #!/usr/bin/make -f
 
-export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0
+export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 

doc/ABYSS.1

-.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

-.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

-.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