release 2.1.1

BloomDBG/Makefile.am

@@ -26,4 +26,4 @@ abyss_bloom_dbg_SOURCES = \
 	RollingHashIterator.h \
 	SpacedSeed.h \
 	$(top_srcdir)/lib/bloomfilter/BloomFilter.hpp \
-	$(top_srcdir)/lib/rolling-hash/rolling.h
+	$(top_srcdir)/lib/nthash/nthash.hpp

ChangeLog

@@ -1,3 +1,34 @@
+2018-09-11  Ben Vandervalk <[email protected]>
+
+	* Release version 2.1.1
+
+	abyss-bloom-dbg:
+	* upgrade to most recent version of ntHash to reduce
+	some assembly/hashing artifacts. On a human assembly, this
+	reduced QUAST major misassemblies by 5% and increased
+	scaffold contiguity by 10%
+	* `kc` parameter now also applies to MPI assemblies (see below)
+
+	abyss-fac:
+	* change N20 and N80 to N25 and N75, respectively
+
+	ABYSS-P:
+	* add `--kc` option, with implements a hard minimum k-mer
+	multiplicity cutoff
+
+	abyss-pe:
+	* fix `zsh: no such option: pipefail` error with
+	old versions of `zsh` (fallback to `bash` instead)
+	* adding `time=1` now times *all* assembly commands
+
+	abyss-sealer:
+	* parallelize gap sealing with OpenMP (thanks to
+	@schutzekatze!)
+	* add `--gap-file` option (thanks to @schutzekatze!)
+
+	DistanceEst:
+	* add support for GFA output
+
 2018-04-13  Ben Vandervalk <[email protected]>
 
 	* Release version 2.1.0

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) 2.1.0\n"
+  version = "abyss-samtobreak (ABySS) 2.1.1\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) 2.1.0"
+	@echo "abyss-pe (ABySS) 2.1.1"
 	@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, 2.1.0, [email protected], abyss,
+AC_INIT(ABySS, 2.1.1, [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) 2.1.0" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.1" "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) 2.1.0" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.1" "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 2.1.0" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.1" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br