Release 1.5.0

ChangeLog

@@ -1,3 +1,60 @@
+2014-05-01  Anthony Raymond  <[email protected]>
+
+	* Release version 1.5.0
+	* Assemble strand-specific RNA-Seq libraries into strand-specific
+	contigs.
+	* New parameters, Q and xtip. Improves assembly in high-coverage
+	regions by removing recurrent read errors.
+	* Portability fixes for Fujitsu C Compiler.
+
+	abyss-pe:
+	* New parameter, `Q`, to mask low quality bases to N. 
+	* New parameter, `xtip=1`, to remove 2-in 0-out tips.
+	* New parameter, `ss=1`, to perform strand-specific assembly
+	using ssRNA-Seq libraries.
+	* New command, `scaftigs`. Breaks scaffold sequences at 'N's and
+	produce a scaftigs.fa file.
+	* Include long-scaffs.fa in FAC statistics if `long` parameter
+	used.
+
+	abyss-fixmate:
+	* Performance improvement for GCC-4.6 and older.
+
+	DistanceEst:
+	* Report an estimation of duplicate fragments from read pairs
+	mapping to different contigs.
+
+	abyss-fixmate:
+	* Report number of fragments removed as noise and outliers.
+
+	ABYSS/ABYSS-P:
+	* New option, --SS, to support strand-specific assembly.
+
+	abyss-layout:
+	* New option, --SS, to support strand-specific assembly.
+
+	abyss-map:
+	* New option, --SS, to support strand-specific assembly.
+
+	abyss-overlap:
+	* New option, --SS, to support strand-specific assembly.
+
+	abyss-PathOverlap:
+	* New option, --SS, to support strand-specific assembly.
+
+	abyss-scaffold:
+	* New option, --SS, to support strand-specific assembly.
+	* Don't prune xtips when scaffolding.
+
+	AdjList:
+	* New option, --SS, to support strand-specific assembly.
+
+	Overlap:
+	* New option, --SS, to support strand-specific assembly.
+
+	PopBubbles:
+	* New option, --SS, to support strand-specific assembly.
+
 2013-11-20  Anthony Raymond  <[email protected]>
 
 	* Release version 1.3.7

bin/abyss-pe

@@ -1,6 +1,7 @@
 #!/usr/bin/make -rRf
 # Run the ABySS assembler.
-# Written by Shaun Jackman <[email protected]>.
+# Written by Shaun Jackman <[email protected]> and
+# Anthony Raymond <[email protected]>.
 
 # Set pipefail to require that all commands of a pipe must succeed.
 SHELL=/bin/bash -o pipefail
@@ -263,8 +264,8 @@ Report bugs to <[email protected]>.\n'
 
 version:
 	@printf '\
-abyss-pe (ABySS) 1.3.7\n\
-Written by Shaun Jackman.\n\
+abyss-pe (ABySS) 1.5.0\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, 1.3.7, [email protected], abyss,
+AC_INIT(ABySS, 1.5.0, [email protected], abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)
 AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2013-Nov" "ABYSS (ABySS) 1.3.7" "User Commands"
+.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.0" "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-Nov" "abyss-pe (ABySS) 1.3.7" "User Commands"
+.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.0" "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-Nov" "ABySS 1.3.7" "User Commands"
+.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.0" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br

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 1.3.6}</string>
+\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.5.0}</string>
 				<key>VerticalPad</key>
 				<integer>0</integer>
 			</dict>
@@ -8382,7 +8382,7 @@
 	<key>MasterSheets</key>
 	<array/>
 	<key>ModificationDate</key>
-	<string>2013-09-19 18:10:26 +0000</string>
+	<string>2014-05-01 22:25:41 +0000</string>
 	<key>Modifier</key>
 	<string>Tony Raymond</string>
 	<key>NotesVisible</key>
@@ -8413,7 +8413,7 @@
 		<key>NSPaperName</key>
 		<array>
 			<string>string</string>
-			<string>B75A40CE-5BEE-4C78-A6CE-A00AA144D84B</string>
+			<string>69FD0149-2077-40BA-84CF-28739E407FEB</string>
 		</array>
 		<key>NSPaperSize</key>
 		<array>
@@ -8482,7 +8482,7 @@
 		<key>SidebarWidth</key>
 		<integer>120</integer>
 		<key>VisibleRegion</key>
-		<string>{{-12, 0}, {1121, 778}}</string>
+		<string>{{-4, 0}, {1107, 794}}</string>
 		<key>Zoom</key>
 		<real>1</real>
 		<key>ZoomValues</key>