[med-svn] [Git][med-team/abyss][upstream] New upstream version 2.2.2
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Aug 17 08:29:57 BST 2019
Michael R. Crusoe pushed to branch upstream at Debian Med / abyss
Commits:
6ab3b099 by Michael R. Crusoe at 2019-08-17T06:53:02Z
New upstream version 2.2.2
- - - - -
12 changed files:
- .circleci/config.yml
- ChangeLog
- Map/index.cc
- Map/map.cc
- Map/overlap.cc
- Misc/samtobreak.hs
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1
Changes:
=====================================
.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 <jowong at bcgsc.ca>
+
+ * Release version 2.2.2
+ * Fix abyss-overlap for 32-bit systems
+
2019-08-12 Johnathan Wong <jowong at 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 at 1.70 openmpi google-sparsehash make pandoc ghc
displayName: Install common
- - script: brew install gcc at 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 at 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
=====================================
@@ -1,5 +1,5 @@
AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.1, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.2.2, abyss-users at bcgsc.ca, 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
View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/6ab3b0995a34b1a177a00f5d944c326400a0b576
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