Release 1.9.0

ChangeLog

@@ -1,3 +1,45 @@
+2015-05-28  Ben Vandervalk <benv@bcgsc.ca>
+
+	* Release version 1.9.0
+	* New paired de Bruijn graph mode for assembly.
+	* First official release of Sealer, a tool for closing
+	scaffold gaps by navigating a Bloom filter de Bruijn graph.
+	* New outward extension feature for Konnector to generate
+	long pseudo-reads.
+	* Support for the DIDA (Distributed Indexing Dispatched
+	Alignment) framework, for computing sequence alignments
+	in parallel across multiple machines.
+	* Unit tests can now be run easily with 'make check', without
+	external dependencies.
+
+	abyss-bloom:
+	* abyss-bloom 'build' command now supports -j option for
+	multi-threaded Bloom filter construction.
+
+	abyss-map:
+	* New --protein option for mapping protein sequences.
+
+	abyss-pe:
+	* New paired de Bruijn graph mode for assembly. Enable by
+	setting `k` to the k-mer pair span and `K` to size of an
+	individual k-mer in a k-mer pair. See README.md for further
+	details.
+	* New `aligner=dida` option for using the DIDA parallel alignment
+	framework. See the DIDA section of the abyss-pe man page
+	for usage details.
+	* New `graph=gfa` option to use the GFA (Graphical
+	Fragment Assembly) format for intermediate graph files.
+
+	abyss-sealer:
+	* New tool for closing scaffold gaps by navigating a Bloom
+	filter de Bruijn graph
+	* See Sealer/README.md or abyss-sealer man page for details
+	and examples.
+
+	konnector:
+	* New --extend option for extending merged and unmerged
+	reads outwards in the de Bruijn graph.
+
 2014-07-09  Anthony Raymond  <traymond@bcgsc.ca>
 
 	* Release version 1.5.2

bin/abyss-pe

@@ -318,7 +318,7 @@ Report bugs to <abyss-users@bcgsc.ca>.\n'
 
 version:
 	@printf '\
-abyss-pe (ABySS) 1.5.2\n\
+abyss-pe (ABySS) 1.9.0\n\
 Written by Shaun Jackman and Anthony Raymond.\n\
 \n\
 Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n'

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 1.5.2, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 1.9.0, 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)

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.2" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 1.9.0" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS
@@ -94,4 +94,4 @@ Written by Jared Simpson and Shaun Jackman.
 .SH "REPORTING BUGS"
 Report bugs to <abyss-users@bcgsc.ca>.
 .SH COPYRIGHT
-Copyright 2014 Canada's Michael Smith Genome Sciences Centre
+Copyright 2015 Canada's Michael Smith Genome Sciences Centre

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.2" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 1.9.0" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS
@@ -311,4 +311,4 @@ Written by Shaun Jackman.
 .SH "REPORTING BUGS"
 Report bugs to <abyss-users@googlegroups.com>.
 .SH COPYRIGHT
-Copyright 2014 Canada's Michael Smith Genome Sciences Centre
+Copyright 2015 Canada's Michael Smith Genome Sciences Centre

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.2" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 1.9.0" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br
@@ -18,4 +18,4 @@ Written by Shaun Jackman.
 .SH "REPORTING BUGS"
 Report bugs to <abyss-users@bcgsc.ca>.
 .SH COPYRIGHT
-Copyright 2014 Canada's Michael Smith Genome Sciences Centre
+Copyright 2015 Canada's Michael Smith Genome Sciences Centre

doc/flowchart.graffle

@@ -5198,7 +5198,7 @@
 {\colortbl;\red255\green255\blue255;}
 \pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural\qc
 
-\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.5.2}</string>
+\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.9.0}</string>
 				<key>VerticalPad</key>
 				<integer>0</integer>
 			</dict>