[med-svn] [Git][med-team/abyss][upstream] New upstream version 2.3.9

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / abyss


Commits:
94b91747 by Étienne Mollier at 2024-09-12T22:40:58+02:00
New upstream version 2.3.9
- - - - -


11 changed files:

- Align/Makefile.am
- ChangeLog
- Misc/samtobreak.hs
- README.md
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- dialign/museq.c
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1


Changes:

=====================================
Align/Makefile.am
=====================================
@@ -34,3 +34,4 @@ abyss_mergepairs_LDADD = $(builddir)/libalign.a \
 	$(top_builddir)/Common/libcommon.a
 
 abyss_mergepairs_SOURCES = mergepairs.cc
+


=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+2024-09-11 Johnathan Wong <jowong at bcgsc.ca>
+
+  * Release version 2.3.9
+
+      General:
+                * Deallocate memory used by alignment data structure in dialign
+
 2024-07-18 Lauren Coombe <lcoombe at bcgsc.ca>
 
   * Release version 2.3.8


=====================================
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) 2.3.8\n"
+  version = "abyss-samtobreak (ABySS) 2.3.9\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 


=====================================
README.md
=====================================
@@ -1,5 +1,5 @@
 [![Release](https://img.shields.io/github/release/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/releases)
-[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.8/abyss-2.3.8.tar.gz)
+[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.9/abyss-2.3.9.tar.gz)
 [![Conda](https://img.shields.io/conda/dn/bioconda/abyss?label=Conda)](https://anaconda.org/bioconda/abyss)
 [![Issues](https://img.shields.io/github/issues/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/issues)
 


=====================================
azure-pipelines.yml
=====================================
@@ -21,11 +21,8 @@ jobs:
     displayName: Install btllib
   - script: |
       ./autogen.sh
-      export CXXFLAGS="$CXXFLAGS -fuse-ld=lld"
-      echo $CXXFLAGS
-      export CFLAGS="$CFLAGS -fuse-ld=lld"
-      export OBJCFLAGS="$OBJCFLAGS -fuse-ld=lld"
-      export OBJCXXFLAGS="$OBJCXXFLAGS -fuse-ld=lld"
+      export CC=gcc-14
+      export CXX=g++-14
       export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install"
       ./configure CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install
       make -j12 distcheck AM_CXXFLAGS=-Wno-error=dangling-reference


=====================================
bin/abyss-pe
=====================================
@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.8"
+	@echo "abyss-pe (ABySS) 2.3.9"
 	@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, 2.3.8, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.9, abyss-users at bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])


=====================================
dialign/museq.c
=====================================
@@ -310,6 +310,8 @@ int main(int argc, char **argv)
   duration = (clock()-tim)/CLOCKS_PER_SEC;
   printf("Total time:   %f secs\n", duration);
   printf("Total weight: %f \n", algn->total_weight);
+  free_alignment(algn);
+  free_alignment(salgn);
   exit(EXIT_SUCCESS);
 }
 


=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.8" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.9" "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) 2.3.8" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.9" "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 2.3.8" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.9" "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/94b917476372f6116d67baef5d32a9a3062753e8

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