Staden Package / News: Recent posts

io_lib-1.11.0b8 released

Yet another new io_lib beta release made, but I think this should be the last beta release before a real non-beta 1.11.0 is released. I'll do this in a couple weeks unless I receive bug reports or SRF changes.

See for a list of changes since 1.11.0b7.


Posted by James Bonfield 2008-01-25

Staden binaries for x86_64 linux systems

My apologies for doing this so late, but it seems given the number of people still having issues getting either the 32-bit binaries to work on 64-bit systems or compiling from scratch that I really should have done this a year ago.

I've put our current Gap4 build for AMD 64 systems in the 1.7.0 staden file-release area. Technically this build is much newer, but the changes aren't significant given very little time has been spent on Gap4 recently.... read more

Posted by James Bonfield 2008-01-15

io_lib-1.11.0b7 released

The latest 1.11 beta release of io_lib is available. Note that this has a major bug fix over 1.11.0b6 in that the SRF files produced now correctly adhere to v1.3 specification. (A bug in b6 produced corrupted files, albeit ones that the code could still read due to the buf existing in both writer and reader.)

I do not anticipate SRF format changes now, but until the code moves out of beta I will not be providing backwards compatibility if the format did change.... read more

Posted by James Bonfield 2008-01-11

Tgap 0.6 available (text-mode gap)

(NB: A previous release of this code is available at Li Heng's MAQ site;

"tgap" is an experimental curses based (Unix) sequence viewer. It's a completely new program designed to explore new algorithms for handling the huge scale of data from modern sequencing instruments (Illumina/Solexa, ABI SOLiD, etc).

It's not a robust and finished product, and nor is it likely to remain stable in terms of file formats. For now though it'll probably remain text based as this happens to be fast and easy for development/debugging. My advise would be if you want to experiment with it keep a copy of the source and binary along side your databases you produce. I'm not likely to be keeping binary compatibility between releases until much further down the development process.... read more

Posted by James Bonfield 2008-01-03

io_lib-1.11.0b5 released

Anoter incremental update to the io_lib package; still in beta. See the ChangeLog for information.

Posted by James Bonfield 2007-11-12

io_lib-1.11.0b4 released

Io_lib 1.11 have been undergoing beta releases for a while now, but hopefully it is approaching maturity. (This release mainly sees further speed improvements for SRF I/O.)

The main improvements with 1.11 over 1.10 are related to the new short-read format (SRF) archives and a corresponding upgrade to the ZTR specification. If you're at all interested in ZTR or SRF please do check it out and email me (as time constraints mean I don't get to read the forums here particularly often still).... read more

Posted by James Bonfield 2007-10-26

Ongoing work

I'm aware that several people are asking about Gap4's suitability for the newer sequencing technologies. Currently gap4 gets pretty memory hungry and slow when dealing with millions of small fragments, but intrinsically it doesn't have any soon-to-be-reached hard limitations. Also the current (or maybe CVS tree version? Sorry for being vague!) gap4 release does support viewing of 454 and solexa trace data too.... read more

Posted by James Bonfield 2007-02-20

Staden Package version 1.7.0 available

The latest Staden Package release has finally been built. Sorry it's taken so long this time.

For now I have just built the source release (which is basically a CVS checkout) and x86 binaries for Linux and Windows. If there's no major problems I'll build releases for other architectures soon.


Posted by James Bonfield 2006-07-06

io_lib-1.10.1 released

Various bug fixes to 1.9 and support for 454 SFF archives.

See the release notes ( for full information.

Posted by Andrew Whitwham 2006-06-20

io_lib-1.9.2 released

Mainly a bug fix update and improved support for SFF files. See the release notes for more information.

Posted by James Bonfield 2005-12-14

Release 1.6.0 available

Binaries and source for Staden Package 1.6.0 are now available.

I have built binaries for Linux (x86), Linux (IA64), Tru64 (Alpha), Solaris (Sparc), MacOSX (PPC) and Windows (x86).

I'll update the web site with release notes etc soon, but for now they can also be read from the files section:

Sorry it's been so long!


Posted by James Bonfield 2005-10-07

Staden Package beta release (1.6.0b4)

I've built the latest Staden Package code under MS Windows once more and made a new test release for the forthcoming 1.6.0. Experience shows that the windows version has been the hardest to get bug free, mainly due to all development (and hence testing) being done under Linux. Therefore I've put this release out first.

I'll work on the others soon and after some feedback I hope to make an official tested 1.6.0 release. For now I'll work on updating the documentation as I know this is out of date.... read more

Posted by James Bonfield 2005-07-14

io_lib-1.9.0 released

The 1.9.0 release of io_lib has finally been uploaded. Please see the release notes and changelog in the files section to view the full list of changes.

Posted by James Bonfield 2005-07-07

io_lib updates

It's getting to that stage where io_lib is well overdue for a major overhaul. Not least is the point that the ZTR format can cope with much more than the core Read structure allows, so I propose that the new format has a totally different Read structure (with backwards compatibility mode perhaps).

It is also very inefficient when reading lots of formats due to the insistance on reading from disk. In-memory decoders would streamline the process immensly.... read more

Posted by James Bonfield 2005-05-09

New gcphrap patch

The gcphrap 'patch' (phrap_extras tar, containing additional files for phrap) has been updated. The only change is that sequences longer than 50Kb are now supported when writing out experiment files.

Posted by James Bonfield 2005-04-18

1.5.3 binaries for MacOSX and Solaris 9

I've now uploaded prebuilt binaries for MacOS X and Solaris 9 for the Staden Package.


Posted by James Bonfield 2004-11-11

New package release: 1.5.3

I've finished working on the current release of the Staden Package and have uploaded a source tarball for version 1.5.3. Please use the files section to read the release notes.

Over the next few days I will upload more binary distributions. Currently available are ix86-linux, alpha-tru64 and (finally) an updated Microsoft Windows version.

Posted by James Bonfield 2004-11-09


I've packaged up a new version of io_lib, as a separate easy to compile and install (hopefully) version. This is the same as is currently in use in the Staden Package, but it came to my attention that the standalone version was out of date.

The most significant changes are the ability to read confidence values in AB1 files and the addition of a trace_dump (instead of scf_dump) program.

Posted by James Bonfield 2004-05-28

Rel-1.4 Solaris binaries uploaded

The Sparc Solaris binaries for 1.4 have been added to the file release area. Many thanks to the staff at the Bioinformatics Centre in Imperial College for making these available.

I appreciate that this isn't the latest official release, but it's pretty close and the only major change with 1.4.1 was improved documentation. (If you are interested, you could copy this from another 1.4.1 unix release as the documentation is not platform specific except for unix vs windows.)

Posted by James Bonfield 2004-04-21

1.4.1 release

I've updated the 1.4.0 release to 1.4.1. The key change is the addition of the documentation and some source changes to make it work (with luck!).


Posted by James Bonfield 2004-03-22

SGI Irix binaries uploaded

I've added the SGI (Irix 6.5) binaries to the 1.4 Staden Package release.

Posted by James Bonfield 2004-02-24

Source tarball and binaries for V1.4

The source .tar.gz for V1.4 has been made available along with binaries for Alpha-Tru64, i386-linux and PPC-MacOSX. I may be able to build sparc-solaris and mips-irix/sgi soon, but currently I am unable to build a MS Windows release due to lack of suitable software and hardware.

Volunteers would be most welcome!

Posted by James Bonfield 2004-02-16

Change in version numbering

In order to keep easier track of versions between the CVS tree and released tars of source and binaries, I have decided to move away from the date version numbering.

From now on, versions are numbered according to the CVS branch. Eg the new 1.4 would have been known as 2004.0. The next release will be either 1.4.1 or 1.5, regardless of the year it is released in.

Posted by James Bonfield 2004-02-16

CVS tree uploaded

Thanks to the SF staff, the latest CVS tree has been uploaded. I will make a source tarball soon and in the coming week I plan to upload binary distributions of the latest version for several (but almost certainly not all) systems.


Posted by James Bonfield 2004-02-13

An OpenSource release of the Staden Package

On Friday 23rd January MRC sent me a new BSD-style licence for the Staden Package giving me the right to redistribute the package in source and binary form.

Hence my first redistribution will be to here, SourceForge.

The initial MRC source and binaries should appear over the next few days. After that I plan to migrate my local CVS tree (populated originally from the last MRC sources) to SourceForge.... read more

Posted by James Bonfield 2004-01-26

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