diff --git a/ChangeLog b/ChangeLog index 4ca167183..deba1c6ec 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,30 @@ +2018-10-24 Ben Vandervalk + + * Release version 2.1.2 + * Improved scaffold N50 on human by ~10% by + implementing a new `DistanceEst --median` + option (thanks to @lcoombe!) + * Added a `--max-cost` option to `konnector` and + `abyss-sealer`. This address a long-standing issue + with indeterminately long running times, particularly + for low values of `k`. + + abyss-pe: + * Use the new `DistanceEst --median` option as the + default for the scaffolding stage + + Dockerfile: + * Fix OpenMPI setup + + DistanceEst: + * Added `--median` option + + konnector: + * Added `--max-cost` option to bound running time + + sealer: + * Added `--max-cost` option to bound running time + 2018-09-11 Ben Vandervalk * Release version 2.1.1 diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index 50b8cce54..f3881069d 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) 2.1.1\n" + version = "abyss-samtobreak (ABySS) 2.1.2\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 d8e3ee758..561e5f26c 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -395,7 +395,7 @@ help: @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.' version: - @echo "abyss-pe (ABySS) 2.1.1" + @echo "abyss-pe (ABySS) 2.1.2" @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 bb87350b6..7e62d805f 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.1.1, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.1.2, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) m4_include(m4/m4_ax_pthread.m4) AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects) @@ -263,7 +263,7 @@ elif test x"$enable_werror" = x"yes"; then AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror') else # default - AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror') + AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra') fi # Build abyss-paired-dbg and abyss-paired-dbg-mpi diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index 1fba94edd..faca2e3ab 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.1" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.1.2" "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 e77e347a3..1cadab6c5 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.1" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.1.2" "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 3f7662284..96cdfbc0a 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.1" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.1.2" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br @@ -13,7 +13,7 @@ or Convert the input files to FASTA or FASTQ format. FILE may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and may be compressed with gz, bz2 or xz and may be tarred. -.SH AUTHOR +jSH AUTHOR Written by Shaun Jackman. .SH "REPORTING BUGS" Report bugs to .