release 2.1.2

bcgsc · Oct 24, 2018 · a30c4bc · a30c4bc
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commit a30c4bc
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,30 @@
+2018-10-24  Ben Vandervalk <benv@bcgsc.ca>
+
+	* Release version 2.1.2
+	* Improved scaffold N50 on human by ~10% by
+	implementing a new `DistanceEst --median`
+	option (thanks to @lcoombe!)
+	* Added a `--max-cost` option to `konnector` and
+	`abyss-sealer`. This address a long-standing issue
+	with indeterminately long running times, particularly
+	for low values of `k`.
+
+	abyss-pe:
+	* Use the new `DistanceEst --median` option as the
+	default for the scaffolding stage
+
+	Dockerfile:
+	* Fix OpenMPI setup
+
+	DistanceEst:
+	* Added `--median` option
+
+	konnector:
+	* Added `--max-cost` option to bound running time
+
+	sealer:
+	* Added `--max-cost` option to bound running time
+
 2018-09-11  Ben Vandervalk <benv@bcgsc.ca>
 
 	* Release version 2.1.1

diff --git a/Misc/samtobreak.hs b/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) 2.1.1\n"
+  version = "abyss-samtobreak (ABySS) 2.1.2\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

diff --git a/bin/abyss-pe b/bin/abyss-pe
@@ -395,7 +395,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.1.1"
+	@echo "abyss-pe (ABySS) 2.1.2"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

diff --git a/configure.ac b/configure.ac
@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.1.1, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.1.2, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 m4_include(m4/m4_ax_pthread.m4)
 AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)
@@ -263,7 +263,7 @@ elif test x"$enable_werror" = x"yes"; then
 	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
 else
 	# default
-	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
+	AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
 fi
 
 # Build abyss-paired-dbg and abyss-paired-dbg-mpi

diff --git a/doc/ABYSS.1 b/doc/ABYSS.1
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.1" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.2" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.1" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.2" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.1" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.2" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br
@@ -13,7 +13,7 @@ or
 Convert the input files to FASTA or FASTQ format. FILE may be in
 FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and may be
 compressed with gz, bz2 or xz and may be tarred.
-.SH AUTHOR
+jSH AUTHOR
 Written by Shaun Jackman.
 .SH "REPORTING BUGS"
 Report bugs to <abyss-users@bcgsc.ca>.