From aafcb4c7053d21964dfb822c7e7b01cd97812e4b Mon Sep 17 00:00:00 2001
From: Ben Vandervalk <benv@bcgsc.ca>
Date: Tue, 11 Sep 2018 12:20:23 -0700
Subject: [PATCH] release 2.1.1

---
 BloomDBG/Makefile.am |  2 +-
 ChangeLog            | 31 +++++++++++++++++++++++++++++++
 Misc/samtobreak.hs   |  2 +-
 bin/abyss-pe         |  2 +-
 configure.ac         |  4 ++--
 doc/ABYSS.1          |  2 +-
 doc/abyss-pe.1       |  2 +-
 doc/abyss-tofastq.1  |  2 +-
 8 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/BloomDBG/Makefile.am b/BloomDBG/Makefile.am
index 3c05820b8..fdbc15f0d 100644
--- a/BloomDBG/Makefile.am
+++ b/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
diff --git a/ChangeLog b/ChangeLog
index 95eb3f886..4ca167183 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,34 @@
+2018-09-11  Ben Vandervalk <benv@bcgsc.ca>
+
+	* 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 <benv@bcgsc.ca>
 
 	* Release version 2.1.0
diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs
index 08e30c814..50b8cce54 100644
--- 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) 2.1.0\n"
+  version = "abyss-samtobreak (ABySS) 2.1.1\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 
diff --git a/bin/abyss-pe b/bin/abyss-pe
index 2441ad364..88d3f5a04 100755
--- 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) 2.1.0"
+	@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"
diff --git a/configure.ac b/configure.ac
index 956747492..34274f04b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.1.0, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.1.1, 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
index 5828b04f7..1fba94edd 100644
--- a/doc/ABYSS.1
+++ b/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
diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1
index 76dd80c7c..e77e347a3 100644
--- a/doc/abyss-pe.1
+++ b/doc/abyss-pe.1
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.0" "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
diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1
index f4c457c56..3f7662284 100644
--- a/doc/abyss-tofastq.1
+++ b/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