diff --git a/ChangeLog b/ChangeLog index 450d5c0f0..a0231bca5 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,20 @@ +2020-09-17 Johnathan Wong + + * 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 * Release version 2.2.4 @@ -14,7 +31,6 @@ abyss-bloom-dbg: * Report coverage information of unitigs - 2019-09-20 Johnathan Wong * Release version 2.2.3 diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index fd70deff9..7ca68d6d2 100644 --- a/Misc/samtobreak.hs +++ b/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" diff --git a/bin/abyss-pe b/bin/abyss-pe index 99176300a..b9fcdfea1 100755 --- a/bin/abyss-pe +++ b/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" diff --git a/configure.ac b/configure.ac index b2fd90930..849cbf277 100644 --- a/configure.ac +++ b/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]) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index b39841adf..895067bfe 100644 --- a/doc/ABYSS.1 +++ b/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 diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index ea7652852..ab2db3c71 100644 --- a/doc/abyss-pe.1 +++ b/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 diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index 97e005f24..d88d49e77 100644 --- a/doc/abyss-tofastq.1 +++ b/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