From cfde2ec3a9201606a33d0bb8b83aa4753ca5a8bc Mon Sep 17 00:00:00 2001 From: Ben Vandervalk Date: Wed, 14 Mar 2018 14:55:45 -0700 Subject: [PATCH] Release 2.0.3 --- ChangeLog | 60 +++++++++++++++++++++++++++++++++++++++++++ bin/abyss-pe | 2 +- configure.ac | 4 +-- doc/ABYSS.1 | 2 +- doc/abyss-pe.1 | 2 +- doc/abyss-tofastq.1 | 2 +- doc/flowchart.graffle | 2 +- 7 files changed, 67 insertions(+), 7 deletions(-) diff --git a/ChangeLog b/ChangeLog index f07eadead..74a6131d9 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,63 @@ +2017-12-19 Ben Vandervalk + + * Release version 2.0.3 + * Many compiler fixes for GCC >= 6, Boost >= 1.64 + * Read and write GFA 2 assembly graphs with abyss-pe graph=gfa2 + * Support reading CRAM via samtools + + abyss-bloom: + * New `abyss-bloom build -t rolling-hash` option, to + pre-build input Bloom filters for `abyss-bloom-dbg` + * Fix incorrect output of `abyss-bloom kmers -r` + (thanks to @notestaff!) + + abyss-bloom-dbg: + * New `-i` option to read Bloom filter files built by + `abyss-bloom build -t rolling-hash` + * Improved error branch trimming (reduces number of + small output sequences) + * Fix intermittent segfaults caused by non-null-terminated + strings + + abyss-map: + * Append BX tag to SAM output (Chromium 10x Genomics data) + + ABYSS-P: + * Increase default number of sparsehash buckets from + 200,000,000 => 1,000,000,000 + * Benefit: Allows larger datasets to be assembled without + time-consuming sparsehash resize operations (e.g. H. sapiens) + * Caveat: Increases minimum memory requirement per + CPU core from 89 MB to 358 MB + + abyss-pe: + * Parallelize `gzip` with `pigz`, if available + * Report time/memory for each program with `zsh`, if available + * Fix: use `N` instead of `n` for scaffold stage, + when set by user + + abyss-samtobreak: + * New `--alignment-length` (`-a`) option to exclude alignments + shorter than a given length + * New `--contig-length` (`-l`) option to exclude contigs + shorter than a given length + * New `--genome-size` (`-G`) option, for contiguity metrics + that depend on the reference genome size + * New `--mapq` (`-q`) option for minimum MAPQ score + * New `--patch-gaps` (`-g`) option to join alignments + separated by small gaps + * New TSV output format with additional contiguity + stats (e.g. L50, NG50) + * Fix handling of hard-clipped alignments + + abyss-todot: + * New `--add-complements` option + + abyss-tofastq: + * New `--bx` option to copy BX tag from from SAM/BAM + to FASTQ header comment (Chromium 10x Genomics + data) + 2016-10-21 Ben Vandervalk * Release version 2.0.2 diff --git a/bin/abyss-pe b/bin/abyss-pe index 87463e6ee..8cdeaf247 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -371,7 +371,7 @@ help: @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.' version: - @echo "abyss-pe (ABySS) 2.0.2" + @echo "abyss-pe (ABySS) 2.0.3" @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 be1792922..3a904fb3a 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.0.2, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.0.3, 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 8f3a30a2b..f824b88ff 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.0.2" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.0.3" "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 e6af3d795..b53364d7c 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.0.2" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.0.3" "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 d8fd0eac3..82784adec 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.0.2" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.0.3" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br diff --git a/doc/flowchart.graffle b/doc/flowchart.graffle index 73a03b0d4..5ce48271d 100644 --- a/doc/flowchart.graffle +++ b/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 2.0.2} +\f0\b\fs28 \cf0 ABySS paired-end pipeline version 2.0.3} VerticalPad 0