release 2.1.2

ChangeLog

@@ -1,3 +1,30 @@
+2018-10-24  Ben Vandervalk <[email protected]>
+
+	* 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 <[email protected]>
 
 	* Release version 2.1.1

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"
 

bin/abyss-pe

@@ -395,7 +395,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or [email protected].'
 
 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"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.1.1, [email protected], abyss,
+AC_INIT(ABySS, 2.1.2, [email protected], 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

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

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

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 <[email protected]>.