Release 1.3.7

Author: traymond

ChangeLog

@@ -1,3 +1,51 @@
+2013-11-20  Anthony Raymond  <traymond@bcgsc.ca>
+
+	* Release version 1.3.7
+	* Use long sequences to rescaffold scaffolds. May be run by
+	adding libraries to the `long’ parameter. When Scaffolding
+	with RNA-Seq contigs from a Trans-ABySS assembly, the genic
+	contiguity is greatly improved.
+	* Added support gcc 4.8+, and Mac OS X 10.9 Mavericks with clang.
+	* Licensed as GPL for non-commercial purposes.
+
+	abyss-fac:
+	* Added e-size to contiguity statistics as described in the GAGE
+	paper.
+
+	abyss-filtergraph:
+	* Bug fix. `--assemble’ will not fail an assertion.
+	* New option, --max-length, used to remove contigs over the
+	specified threshold.
+	* Trim 2-in 0-out tips when removing tips.
+
+	abyss-map:
+	* Bug fix. Correctly set mapq=0 for reads that multi map.
+
+	abyss-longseqdist:
+	* New program. Generate distance estimates between all contigs a
+	single read maps to.
+
+	abyss-mergepairs:
+	* Report number of reads chastity filtered.
+
+	abyss-overlap:
+	* Bug fix. Handle ambiguity codes.
+
+	abyss-pe:
+	* Support BWA-MEM with assembly. Run using parameter
+	`aligner=bwamem’.
+	* Added another scaffolding stage using long sequences. May be
+	run by adding libraries to the `long’ parameter.
+
+	ABYSS-P:
+	* Bug fix. Do not use awk to merge fasta files.
+
+	abyss-samtobreak:
+	* Building bug fix. Check that ghc modules are installed.
+
+	UnitTest:
+	* The Google C++ testing framework has been added to ABySS.
+
 2013-07-15  Anthony Raymond  <traymond@bcgsc.ca>
 
 	* Release version 1.3.6

bin/abyss-pe

@@ -237,7 +237,7 @@ Report bugs to <abyss-users@bcgsc.ca>.\n'
 
 version:
 	@printf '\
-abyss-pe (ABySS) 1.3.6\n\
+abyss-pe (ABySS) 1.3.7\n\
 Written by Shaun Jackman.\n\
 \n\
 Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n'

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.59)
-AC_INIT(ABySS, 1.3.6, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 1.3.7, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 AM_INIT_AUTOMAKE(foreign subdir-objects)
 AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2013-Jul" "ABYSS (ABySS) 1.3.6" "User Commands"
+.TH ABYSS "1" "2013-Nov" "ABYSS (ABySS) 1.3.7" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2013-Jul" "abyss-pe (ABySS) 1.3.6" "User Commands"
+.TH abyss-pe "1" "2013-Nov" "abyss-pe (ABySS) 1.3.7" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2013-Jul" "ABySS 1.3.6" "User Commands"
+.TH abyss-tofastq "1" "2013-Nov" "ABySS 1.3.7" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br