Staden 2.0.0b5 release

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
------------------------

* Numerous contig editor bug fixes:
- Major undo overhaul. It should work far better now.
- Moving sequences moves tags with them
- Issues with saving giving "error -1" resolved.
- We can now adjust the read clip points using < and > keys.
- Fixed an editing-cache problem where cancelling a join and
reopening the join editor sometimes had the old edits
retained in memory (but not saved on disk).

* Joining and complementing contigs is now handled better by
various plots. For example joining two contigs no longer
clears the contig selector window and plots, but updates them
correctly instead.

* Fixed some compilation issues.
- libpng problems resolved.
- helped compilation when linking against io_lib releases that
aren't yet in your LD_LIBRARY_PATH.
- LARGEFILE_SOURCE64 definitions removed, which caused
problems on Ubuntu 9 (and others?).

* Opening a database we do not have write access to (but read
access) now works. Read-only mode is more obvious in the title
bar too.

* BAF export now includes consensus tags. We can also export in
CAF too (although it's not a recommended output format).

* The consensus can now be saved in fastq format.

* Tg_index gained the option to store SAM/BAM auxillary records
with "-x". This is experimental at the moment.

* Tg_index can now stored unmapped data with the "-u" option,
although it is still visible within the contig editor. This is
experimental and a work in progress.

* Improved SAM output - the data is now written in the same
order it was read (assuming no edits). There is also an option
to try and fix the flags and mate-pair data when writing out
SAM, but be warned this is information substantially slower to
compute and output.

* Put back the old staden.profile script, but it's now in
$STADENROOT/share/staden instead of the main root. Also added
a stash binary to wrap up tclsh so old stash scripts should
work again.

* Various speed ups to the template display.

* The editor control-a and control-e keys (beginning and end of
sequence) now take heed of whether cutoff data is shown.

* Export Contigs now picks sensible filenames when changing
format.

Other Gap5 Bug fixes
--------------------

* Very long sequences (>64kb) could sometimes cause the cached
consensus to omit some regions, giving problems for find
internal joins and save consensus.

* Block attempts to join a contig to itself.

* Removed various minor memory leaks.

* Inserting bases to sequences could previously rarely cause memory
corruptions.

* Complement contig no longer moves the used (unclipped)
start/end positions of a contig.

* Exporting complementing contigs in ace/sam/baf fixes.

* Using tg_index -a to add data to an existing database now
works when the existing contigs have been complemented.

* Reenabled the Results Manager window in normal mode, rather
than hiding it for experts only.

* Gap5's File->New menu item has been removed, use tg_index to
create databases.

* Creating a 1bp long annotation in the editor no longer crashes
if you haven't dragged a selection to cover 1bp.

Gap4
----

* Alignments in find internal joins fast-mode should have their
5' end aligned better. (Also true for gap5)