Staden Package 2.0.0b8 released

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.

The source is already available. I'll be uploading precompiled binary distributions for various platforms over the remainder of the week, so if they're not available yet, please check in a few days.

Details of changes follow.

Staden 2.0.0b8, 8th Feb 2011

Gap5/tg_index 1.2.11

General changes
---------------

* Microsoft Windows version. The code should now compile and run
under MinGW/Msys on windows.

* MacOS X updates: improved compilation and fixed a few Mac
specific display glitches.

* Various code tidyups - less compiler warnings, more portable
for linux variants (eg Centos).

* Removed dependency on samtools. (This also avoids a few
samtools related bugs, but hopefully not creating new ones to
replace them.)

* Removed dependency on IncrTcl, IncrTk, IncrWidgets. These can
still be used for one part of Gap4 (prefinish GUI) but the
code will build and execute without these now.

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

* In-program help should now be working.

* A Disassemble Readings option has been added to the main Edit
menu. (This performs the same task as in Gap4.)

* Tg_index now supports the CAF, fasta and fastq
formats. When importing fasta/fastq we just create single-read
contigs, so it's simply an easy way of importing consensus
sequences or a *few* finishing reads. CAF support will import
entire assemblies though. Also improved the CAF exporting code.

* First draft of a Find Read Pairs function (as in Gap4). At
present read-pair orientation needs some work still, but the
basic plot and searching is working.

* Internal record numbers are now 64-bit instead of 32-bit,
removing the need for reserving sequence record IDs in
tg_index (-r option) and allowing for more than 2 billion
sequences in a gap5 db.

* Contig editor "tag macros" (from gap4) have been added. Use
Shift + function key to define a tag macro and then that
function key to apply it.

* A "readings" list now exists (as in Gap4) which is displayed
and can be populated using the contig editor "names"
panel. The copying (cut/paste) of read names binding has also
changed from left-click+drag to middle-click, now matching
Gap4.

* Quality value 100 now has a special meaning for the consensus
algorithm, as in Gap4. It forces the base to be considered as
true (as it's only possible via a manual edit).

* More contig editor key bindings: Page up/down (already existed
for scrolling in 1Kb) can be modified by Shift, Control or
Shift+Control to scroll in 10, 100 and 1000Kb steps; [,] keys
for setting base quality to 0 or 100; Shift Up/Down arrow and
Control Up/Down arrow for incrementing/decrementing base
qualities by 1 or 10.

* Editor Delete now only works on pad characters unless Control
Delete is used, in order to prevent accidental removal of real
data.

* Added contig editor "Save Settings" command.

* Internal changes to the template display and Tk canvas.

* Sped up contig editor when dealing with excessively deep
alignments.

* Reading names in the contig editor are now be selected for
copy and pasting using the left mouse button.

* Tg_index now has a -q option to limit the number of unpaired
reads held in memory (for the "-p" option). This significantly
reduces the memory usage on large data sets, at the expense of
longer running times.

Bug fixes
---------

* Various fixes to compilation: parallel makes, improved DESTDIR
support.

* Big tidy up on the cache refence counting system, fixing
multiple sporadic crashes and rarely even data corruptions.

* Fixes to consensus caching sometimes storing corrupted data.

* More robust when we run out of disc space.

* Import GFF should be more robust. This now also supports
"colour=<0-17>" tags to match those used in Artemis.

* The insert size in the Libraries panel is now displayed
correctly (when filled out) instead of at 1/100th of the size.

* Reduced excessive memory usage of tg_index -t on large data
sets. Also fixed a few memory leaks and reference count leaks
(appear like memory leaks).

* SAM export now works correctly when auxillary fields or
read-group data is present.

* Removed a small memory corruption when shutting down
plots. This sometimes caused crashes when quitting the contig
editor.

* Fixed occasional crash when joining contigs.

* Editor searching crash fixes.