Skip to content

Commit

Permalink
Release 1.5.2
Browse files Browse the repository at this point in the history
  • Loading branch information
traymond committed Jul 9, 2014
1 parent c063910 commit e58e5a6
Show file tree
Hide file tree
Showing 8 changed files with 45 additions and 10 deletions.
41 changes: 38 additions & 3 deletions ChangeLog
Original file line number Diff line number Diff line change
@@ -1,3 +1,38 @@
2014-07-09 Anthony Raymond <[email protected]>

* Release version 1.5.2
* First official release of Konnector and abyss-bloom.
* More GCC 4.8+ fixes! Modified Boost install instructions.
* Fixed rare bug when parsing output of BWA.

ABYSS:
* New option, --mask-cov, use kmers with lowercased bases, but
don't count them towards multiplicity.

abyss-bloom:
* Construct reusable Bloom filter files for use with Konnector.
* Perform boolean operations on two or more bloom filters.
Currently supports union and intersection operations.

abyss-fixmate:
* Check for boost 1.43+ when using `unordered_map::quick_erase`.
* New option, --all, to report all alignments.
* Set mate unmapped flag for mateless reads.

abyss-longseqdist:
* Fixed `error: invalid CIGAR` when reading BWA output.

configure:
* Include mpi and boost libraries as system libraries. Silences
warnings (treated as errors) when compiling with GCC 4.8+.

konnector:
* Merge read pairs into a single sequence (pseudoread) by
building a Bloom filter de Bruijn graph and searching for paths
between the paired end reads. Input reads may be
FASTA/FASTQ/SAM/BAM. The input files must be sorted by read name
and may not contain orphan reads.

2014-05-07 Anthony Raymond <[email protected]>

* Release version 1.5.1
Expand All @@ -24,7 +59,7 @@
* Portability fixes for Fujitsu C Compiler.

abyss-pe:
* New parameter, `Q`, to mask low quality bases to N.
* New parameter, `Q`, to mask low quality bases to N.
* New parameter, `xtip=1`, to remove 2-in 0-out tips.
* New parameter, `ss=1`, to perform strand-specific assembly
using ssRNA-Seq libraries.
Expand Down Expand Up @@ -125,7 +160,7 @@
* Improved documentation for GitHub devs.
* ABYSS-P performance improvement.
* Various portability and bug fixes.

abyss-mergepairs:
* Fix program name.

Expand Down Expand Up @@ -168,7 +203,7 @@

abyss-pe:
* Attempt to fill scaffold gap with consensus of all paths between
contigs.
contigs.

AdjList:
* Increase the default value of m from 30 to 50.
Expand Down
2 changes: 1 addition & 1 deletion bin/abyss-pe
Original file line number Diff line number Diff line change
Expand Up @@ -263,7 +263,7 @@ Report bugs to <[email protected]>.\n'

version:
@printf '\
abyss-pe (ABySS) 1.5.1\n\
abyss-pe (ABySS) 1.5.2\n\
Written by Shaun Jackman and Anthony Raymond.\n\
\n\
Copyright 2012 Canada'\''s Michael Smith Genome Science Centre\n'
Expand Down
2 changes: 1 addition & 1 deletion configure.ac
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
AC_PREREQ(2.62)
AC_INIT(ABySS, 1.5.1, [email protected], abyss,
AC_INIT(ABySS, 1.5.2, [email protected], abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AM_INIT_AUTOMAKE(1.9.6 foreign subdir-objects)
AC_CONFIG_SRCDIR([ABYSS/Abyss.cpp])
Expand Down
2 changes: 1 addition & 1 deletion doc/ABYSS.1
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.1" "User Commands"
.TH ABYSS "1" "2014-May" "ABYSS (ABySS) 1.5.2" "User Commands"
.SH NAME
ABYSS \- assemble short reads into contigs
.SH SYNOPSIS
Expand Down
2 changes: 1 addition & 1 deletion doc/abyss-pe.1
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.1" "User Commands"
.TH abyss-pe "1" "2014-May" "abyss-pe (ABySS) 1.5.2" "User Commands"
.SH NAME
abyss-pe - assemble reads into contigs
.SH SYNOPSIS
Expand Down
2 changes: 1 addition & 1 deletion doc/abyss-tofastq.1
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.1" "User Commands"
.TH abyss-tofastq "1" "2014-May" "ABySS 1.5.2" "User Commands"
.SH NAME
abyss-tofastq \- convert various file formats to FASTQ format
.br
Expand Down
4 changes: 2 additions & 2 deletions doc/flowchart.graffle
Original file line number Diff line number Diff line change
Expand Up @@ -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 1.5.1}</string>
\f0\b\fs28 \cf0 ABySS paired-end pipeline version 1.5.2}</string>
<key>VerticalPad</key>
<integer>0</integer>
</dict>
Expand Down Expand Up @@ -8413,7 +8413,7 @@
<key>NSPaperName</key>
<array>
<string>string</string>
<string>3F3966D3-439E-49FE-9DBC-7CBF4BBA8A92</string>
<string>E409205B-47EF-41DB-B00B-53E0115DBFAE</string>
</array>
<key>NSPaperSize</key>
<array>
Expand Down
Binary file modified doc/flowchart.pdf
Binary file not shown.

0 comments on commit e58e5a6

Please sign in to comment.