Release 1.3.6

bcgsc · Jul 31, 2013 · c1c45b5 · c1c45b5
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,40 @@
+2013-07-15  Anthony Raymond  <traymond@bcgsc.ca>
+
+	* Release version 1.3.6
+	* Improved documentation for GitHub devs.
+	* ABYSS-P performance improvement.
+	* Various portability and bug fixes.
+
+	abyss-mergepairs:
+	* Fix program name.
+
+	abyss-fac:
+	* New option --exp-size to give the expected genome size needed
+	for NG50 calculation.
+	* New option --count-ambig include ambiguities in calculations.
+
+	ABYSS/ABYSS-P:
+	* Performance improvement. Runtime reduced by ~20%.
+	* Fix support for MPICH.
+
+	abyss-map:
+	* No longer require POPCNT instruction.
+	* New option --order to force output order the same as input.
+
+	abyss-filtergraph:
+	* New option --remove to remove specified contigs from graph.
+
+	PopBubbles:
+	* Bug fix. Setting branches > 2 will now work.
+
+	abyss-fixmate:
+	* Improved error when first and second read IDs do not match.
+	* New option --cov to compute and store the physical coverage in
+	a Wiggle file.
+
+	AdjIO:
+	* Bug fix for non-GCC compilers.
+
 2013-03-04  Anthony Raymond  <traymond@bcgsc.ca>
 
 	* Release version 1.3.5

diff --git a/bin/abyss-pe b/bin/abyss-pe
@@ -234,7 +234,7 @@ Report bugs to <abyss-users@bcgsc.ca>.\n'
 
 version:
 	@printf '\
-abyss-pe (ABySS) 1.3.5\n\
+abyss-pe (ABySS) 1.3.6\n\
 Written by Shaun Jackman.\n\
 \n\
 Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n'

diff --git a/configure.ac b/configure.ac
@@ -1,5 +1,5 @@
 AC_PREREQ(2.59)
-AC_INIT(ABySS, 1.3.5, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 1.3.6, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 AM_INIT_AUTOMAKE(foreign)
 AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])

diff --git a/doc/ABYSS.1 b/doc/ABYSS.1
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2013-Mar" "ABYSS (ABySS) 1.3.5" "User Commands"
+.TH ABYSS "1" "2013-Jul" "ABYSS (ABySS) 1.3.6" "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" "2013-Mar" "abyss-pe (ABySS) 1.3.5" "User Commands"
+.TH abyss-pe "1" "2013-Jul" "abyss-pe (ABySS) 1.3.6" "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" "2013-Mar" "ABySS 1.3.5" "User Commands"
+.TH abyss-tofastq "1" "2013-Jul" "ABySS 1.3.6" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br