Release 2.2.5 (#348)

* release 2.2.5

* ChangeLog: add poster link to RResolver

* ChangeLog: improve RResolver description

* ChangeLog: improve RResolver description

Author: jwong-1

ChangeLog

@@ -1,3 +1,20 @@
+2020-09-17  Johnathan Wong <jowong@bcgsc.ca>
+
+	* Release version 2.2.5
+
+	General:
+	* Resolve various compilation errors in newer versions of clang
+	* Use ntHash's 0th hash as the default hash instead of the 1st hash
+	* Added optional RResolver module, not currently part of the ABySS assembly pipeline
+
+	abyss-rresolver-short:
+	* Improves genome assemblies at unitig stage by using a sliding window at read size level
+	across repeats to determine which paths are correct
+	* For further information: consult http://www.birollab.ca/assets/posts/195_Nikolic_Vladimir_HiTSeq_ISMB2020.pdf
+	
+	misc:
+	* Extract all tags in a SAM file
+
 2020-01-30  Johnathan Wong <jowong@bcgsc.ca>
 
 	* Release version 2.2.4
@@ -14,7 +31,6 @@
 	abyss-bloom-dbg:
 	* Report coverage information of unitigs
 
-
 2019-09-20  Johnathan Wong <jowong@bcgsc.ca>
 
 	* Release version 2.2.3

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) 2.2.4\n"
+  version = "abyss-samtobreak (ABySS) 2.2.5\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 

bin/abyss-pe

@@ -398,7 +398,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.2.4"
+	@echo "abyss-pe (ABySS) 2.2.5"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"

configure.ac

@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.4, abyss-users@bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.2.5, abyss-users@bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])

doc/ABYSS.1

@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.4" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.5" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS

doc/abyss-pe.1

@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.4" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.5" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS

doc/abyss-tofastq.1

@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.4" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.5" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br