Update version and drop gcc5 support

Author: vlad0x00

ChangeLog

@@ -1,3 +1,15 @@
+2021-12-20 Vladimir Nikolic <[email protected]>
+
+  * Release version 2.3.4
+
+    General:
+	* Dropped support for gcc5 due to lack of support for more recent C++ features.
+
+	abyss-rresolver-short:
+	* Reduced memory consumption.
+	* Better calculation of read size proportions in the input dataset.
+	* Increased max read read size allowed.
+
 2021-11-10 Vladimir Nikolic <[email protected]>
 
   * Release version 2.3.3
@@ -7,7 +19,7 @@
 
 	abyss-rresolver-short:
 	* Multiple read sizes are better handled. E.g. 150 and 151 are processed as one read size.
-  * Updated default parameters.
+    * Updated default parameters.
 
 2021-10-13 Vladimir Nikolic <[email protected]>
 

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) 2.3.3\n"
+  version = "abyss-samtobreak (ABySS) 2.3.4\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

README.md

@@ -156,10 +156,10 @@ This installs ABySS at the provided path, in this case `/path/to/abyss`.
 Not specifying `--prefix` would install in `/usr/local`, which requires
 sudo privileges when running `make install`.
 
-ABySS requires a modern compiler such as GCC 4.2 or greater. If you have multiple
+ABySS requires a modern compiler such as GCC 6 or greater. If you have multiple
 versions of GCC installed, you can specify a different compiler:
 
-	../configure CC=gcc-4.6 CXX=g++-4.6
+	../configure CC=gcc-10 CXX=g++-10
 
 If Boost is installed at a non-standard location, you can specify the path to it:
 

azure-pipelines.yml

@@ -131,27 +131,6 @@ jobs:
       make -j12 distcheck
     displayName: Compiling ABySS with clang 10
 
-- job: linux_gcc5
-  pool:
-    vmImage: ubuntu-latest
-  steps:
-  - script: |
-      sudo apt-get update -qq
-      sudo apt-get install -qq software-properties-common
-      sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
-      sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
-      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-5 g++-5
-    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
-
 - job: linux_gcc6
   pool:
     vmImage: ubuntu-latest

bin/abyss-pe

@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or [email protected].'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.3"
+	@echo "abyss-pe (ABySS) 2.3.4"
 	@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, 2.3.3, [email protected], abyss,
+AC_INIT(ABySS, 2.3.4, [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) 2.3.3" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.4" "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) 2.3.3" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.4" "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 2.3.3" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.4" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br