Staden 2.0.0b4 release

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.

Also reordered data somewhat for both lzma and libz
compression, reducing file size by another ~7% when dealing
data mixed from multiple read-groups.

* Added an Export Tags function to write GFF data. (Largely
untested and experimental.)

* Improved BAF output so it now contains tags.

* Tg_index now has the ability to select the types of data to
store using -d. These can one or more from seq, qual, anno or
name (or "all" - the default). This allows for more compact
databases at the cost of missing some data.

* Substantially rduced the amount of I/O operations needed when
reading the aux file.

* Sam/Bam @RG records and the RG:Z:* auxillary tags are now
parsed. These are used to place sequences into libraries,
although we may wish to rename these as read-groups in gap5
too.

* Added some simple search tools within the contig editor: by
sequence, name (if indexed), consensus quality.

* The template display should now be substantially faster at
drawing large numbers of sequences.

* Gap5 has a simple mapped assembly menu, currently using bwa
(which must be installed). Behind the scenes this uses the
new tg_index -g option to append to the existing assembly.

* Tg_index -a -g (gapped) mode; this assumes that the sam/bam file
being added has been aligned against a ungapped copy of the
consensus from the gap5 database we are appending
too. Tg_index will add gaps to either the existing consensus
or the newly input data as appropriate, to merge the two
assemblies together.

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

* Various cached consensus fixes.

* Removed occasional memory corruptions while editing sequences.

* Fixes to the "align" button in the join editor.

* Improved saving the consensus, involving contig clip point
changes and pad stripping.

* Fixed cases of inserting to contigs formed by joining
complemented contigs together.

* Fixed several sam parsing bugs.

* Break contig should produce fewer (hopefully no) inconsistent
contigs.

* Export Sequences in SAM format no longer shifts the
coordinates by 1.

* Improved maq long/short format autodetection.

Gap4
----

* Fixed an issue with turning off undo in the "remove pad
columns" editor function.

* Fixed an ancient bug involving the C to Fortran interface.

* Fixed a problem with incorrectly sized trace windows.