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Release 2.2.5 #348

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Sep 18, 2020
Merged

Release 2.2.5 #348

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545e309
release 2.2.5
jwcodee Sep 17, 2020
19614ba
ChangeLog: add poster link to RResolver
jwcodee Sep 17, 2020
b146b6d
ChangeLog: improve RResolver description
jwcodee Sep 17, 2020
41fce93
ChangeLog: improve RResolver description
jwcodee Sep 17, 2020
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18 changes: 17 additions & 1 deletion ChangeLog
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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 RResolver

abyss-rresolver-short:
* Improves genome assemblies at unitig stage by using a sliding window at read size level
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Do we want to say this? Just thinking that someone might infer that their assemblies will be improved but it isn't actually in the pipeline?
Not sure what @schutzekatze thinks

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I agree with @lcoombe. I would just rephrase it to "Added optional RResolver code" or something like that, to indicate it's not a regularly executed algorithm.

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better?

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I guess we can also explicitly just say "currently not part of the main pipeline".

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Yeah I agree with @schutzekatze - I think good to be clear that it isn't currently part of the main abyss-pe driver

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is the newest update clear enough?

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Yeah that looks good to me -- what do you think @schutzekatze ?

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A p p r o v e d

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
Expand All @@ -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
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2 changes: 1 addition & 1 deletion Misc/samtobreak.hs
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Expand Up @@ -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"

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2 changes: 1 addition & 1 deletion bin/abyss-pe
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion configure.ac
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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])
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2 changes: 1 addition & 1 deletion doc/ABYSS.1
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.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
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2 changes: 1 addition & 1 deletion doc/abyss-pe.1
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.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
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2 changes: 1 addition & 1 deletion doc/abyss-tofastq.1
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.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
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