Release 2.0.3

bcgsc · Mar 14, 2018 · cfde2ec · cfde2ec
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,63 @@
+2017-12-19  Ben Vandervalk <benv@bcgsc.ca>
+
+	* 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 <benv@bcgsc.ca>
 
 	* Release version 2.0.2

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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}</string>
+\f0\b\fs28 \cf0 ABySS paired-end pipeline version 2.0.3}</string>
 				<key>VerticalPad</key>
 				<integer>0</integer>
 			</dict>