Staden Package / News: Recent posts

We have moved io_lib from SourceForge SVN to GitHub:

https://github.com/jkbonfield/io_lib

This should make it easier for people to supply patches and to track issues. The SVN repository here will remain for posterity and as a backup incase the svn to git conversion made any errors, but will not be receiving updates. The main Staden Package is staying where it is as active development has stalled.

We haven't looked at package releases yet and will make that decision at the time, but likely github will be the primary download potentially with a copy here for ease.... read more

The asymptoptic approach of version 2.0 is now one step closer. Alas we still haven't had time to give the documentation a work over, hence still labelling this release as Beta.

The primary changes are to Gap5, mainly involving stability and bug fixing although several new features have arrived too. Release notes follow.

April 2016 - 2.0.0b11

Gap5 Updates

• Find Haplotypes function for use within the contig editor. This
  replaces the old Sort By Sequence mode as well as generating lists
  of read IDs per haplotype. It also creates a master "haplotypes"
  list of lists.... read more

Primarily a bug fix release and minor updates to conform to the recent 2.1 CRAM specification update. From the CHANGES file:

Version 1.13.4 (17th February 2014)

• BAM: Fixed some buffer overruns in BAM decoding.

• CRAM: Added support for CRAM EOF blocks (new in CRAM v2.1
  specification). Also improved BAM EOF block checking. v2.1 is now
  the default output version.

• CRAM: Fixed an error causing multi-threading to take longer for the
  first additional thread.... read more

Staden io_lib (aka libstaden-read) version 1.13.0 has been released.

The main addition is the inclusion of SAM, BAM and CRAM (both 1.0 and 2.0 specification) support along with a tool called "scramble" to convert between them. For the rest of the package the changes are minimal.

The sam/bam/cram code should be considered as beta quality and subject to changes, both in the code and APIs themselves but also potentially to the cram 2.0 specification which is still in "release candidate" form. The other tools are as stable as before and can be considered production quality.... read more

An installer for Microsoft Windows is now available.

Like the Mac binaries, this installer is somewhat experimental due to the limited nature of our Windows build environment. Any feedback is welcome.

Andrew

Binaries are now available for Mac OS X, both 32-bit and 64-bit intel machines. They're available in .dmg format.

Note this is experimental work as I'm not primarily a Mac user, so please do provide feedback on where this can be improved. I'm also open to suggestions (or better still files) on improving the icons for applications.

James

It's been a long time since the last release, but finally a new gap5 release is available. (There have only been very minor tweaks to other programs.)

Although I had hoped to have gap5 out of beta by now, our internal users are still finding several problems so it's justified to make another beta release. The full release notes can be found on the download page:

https://sourceforge.net/projects/staden/files/staden/2.0.0b9/... read more

The latest release of the main Staden Package (comprising gap4, gap5, spin, trev and ancillary tools) has just been uploaded.

This is the first release since 1.7 to run on Microsoft Windows again (tested on Vista and XP) and we've also added imroved support for MacOS X thanks to the wonderful open-source community. In addition to that most of the documentation is complete for Gap5. These factors combined means that 2.0 is close to non-beta at long last - probably the next release.... read more

I've made a new release to Io_lib (aka staden-io_lib), as a minor bug fix was required for the new main Staden Package release. Practically speaking it likely only impacts MacOS X 10.6 users (I think).

Version 1.12.5 (3rd Feb 2011)
--------------

* Fixed detection of requirement for va_copy(); affecting some Mac
builds.

* Added hash_exp. I'm not sure this is of pratical use, but it was in
the source tree and in theory at least still works.... read more

(Yes still beta! It'll move out of it when I eventually write some Gap5 documentation.)

The latest Staden Package release, currently in source tar-ball only, is now available. Windows users will still unfortunately need to stick with the 1.7.0 download, but I plan on trying to port back to windows again soon.

The main changes since 2.0.0b6 are:

Gap5/tg_index v1.2.9.

Gap5 changes
------------

* Added an Import GFF Annotations option to Gap5. This deals
with padded and unpadded data, although for now the GFF types
are not used, instead using the "type=<tag_type>;" attribute
in the last GFF column to select a gap5 tag type. GFF Export
has been improved too.... read more

Io_lib 1.12.4 has been released, rapidly following 1.12.3 (now removed) due to a last-minute change introducing a bug. My apologies for insufficient testing.

The changes since 1.12.2 are minor, mainly focusing around a few tweaks to srf tools and improvements to the .hash interface to allow hash_tar to build a single index from multiple .tar files.

Full details follow.

James

Version 1.12.4 (7th July 2010)
--------------... read more

Please accept my apologies for another release so soon after the last, but I found (and fixed) a bug which had been lurking for a few months a matter of hours after releasing b5. Such things happen! It only mattered though if you use sam/bam files with multiple read-groups.

As before x86_64 and i686 linux binaries have been provided in addition to the normal source tarball. Please submit any problems you have here. Thanks.... read more

Also note that this is the first recent release to contain prebuilt binaries. Currently these are linux only, both i686 and x86_64 based platforms.

I have tried to include enough libraries to make these reasonably robust with respect to running on different distributions, but this is non-trivial to do and even trickier to fully test. If you have problems running the binaries, then please let me know via a forum post. Also feel free to try compiling from source which should be getting easier with each release too.... read more

Still beta as still lacking gap5 documentation. However this release contains numerous bug fixes, especially in the gap5 contig editor.

A summary of changes follows. Full release notes can be found in the Files download area.

Staden 2.0.0b5, March 22nd 2010

Gap5 1.2.7
Gap4 4.11.2

This release requires io_lib 1.12.2 or newer.

Gap5 changes since 1.2.6
------------------------... read more

The latest beta-release of 2.0.0 has been bundled. Once again it's a source release only. Primarily the changes since 2.0.0b2 are in Gap5. A summary follows.

Staden 2.0.0b4, January 15th 2010

(Gap5 1.2.6)

Gap5 Changes since 1.2.4
------------------------

* Added support for lzma (via XZ Utils' liblzma library)
compression in addition to the existing zlib code. This is
about 14% smaller than zlib, although at a cost of 2-3x
slower. Use "tg_index -c lzma" to enable this.... read more

The latest 2.0 beta release source tarball has been uploaded to:
https://sourceforge.net/projects/staden/files/staden/2.0.0b2/staden-2.0.0b2-src.tar.gz/download

This is primarily a set of Gap5 changes, with a few improvements to aid compilation on some systems too (especially 64-bit systems). More details will be posted to the forum thread reached by clicking on this news header.

I'm pleased to announce the first beta-test release of what will become version 2.0 of the Staden Package.

In the last few releases Gap5 has been releases as a separate package with it's own directory layout. In version 2.0 I plan for the Staden Package to be integrated as a whole again, with a single package containing gap4, gap5, spin, etc.

The other major change in 2.0 vs 1.x releases is the directory layout and source building has had a large overhaul. The code should be vastly easier to build than the old crufty release, and to encourage testing for the first beta test I'm only releasing source. ... read more

A new release of Gap5 has been made - version 1.2.0.

*NOTE* this is binary incompatible with the gap5 databases produced in 1.1.3 and earlier, but this break was made in order to produce a substantially (sometimes 10 fold) reduction in database size. The new format allows room for tweaking too without invalidating old gap5 databases, so hopefully file formats changing shoudn't be a problem in the future.... read more

I've uploaded some more Gap5 binaries (linux on x86_64 only currently). This is compatible with the previous release, but also now supports an export function to a variety of file formats.

This will allow migration of gap5 1.1.x database format to 1.2.x (being worked on now and is substantially smaller).

James

I finally gave in sitting on the Gap5 tree for so long and built some binaries for public release; 32-bit and 64-bit binaries for linux only. See the download section.

Please note this is very much a test release showing how development is coming along. It lacks all sorts of things needed for use as a production system including docuementation, robustness (there are lots of bugs I know of but haven't yet fixed), missing features and even stability of the file format. Don't expect gap5 databases produced by this code to necessarily work with subsequent gap5 releases (although I'm working on ways to stop this from becoming an issue long-term).... read more

Due to a bug in illumina2srf I made a new release of io_lib.

Specifically if you use BOTH -qf and -qr parameters, or you use -qc (qcal format) parameter then please upgrade. The confidence values in the SRF file were incorrect when using the above parameters.

Due to a bug in illumina2srf I made a new release of io_lib.

Specifically if you use BOTH -qf and -qr parameters, or you use -qc (qcal format) parameter then please upgrade. The confidence values in the SRF file were incorrect when using the above parameters.

The latest incremental updates to io_lib has now been released. This fixes a major bug on Intel Macs in addition to a few minor bug fixes elsewhere and some new SRF related tools.

There are no major changes outside of SRF though.

James

A major bug was discovered in illumina2srf when using the "-r" option to output raw trace data.

Please upgrade ASAP if using this program and see the discussion on the bug at here too:

http://www.bcgsc.ca/pipermail/ssrformat/2008-July/000531.html

James

The latest source tarball of "tgap" (text-mode gap) has been released.

WARNING: The database files are binary incompatible with previous releases.

Practically speaking this is still very much "alpha" quality work and is here simply for people to experiment with. See the ChangeLog in the package for details on progress.