Staden 2.0.0b7 release

(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.

* Tg_index now has support for spliced alignments in SAM/BAM,
using the CIGAR "N" character. This isn't fully implemented
yet as the read-pairing breaks in this case, but the data at
least can be imported now.

* Gap5 should now compile under MacOS X, provided the X11
version of Tcl/Tk is used rather than native aqua.

* Extra contig-editor search methods - by annotation, by tag

* Selecting large regions is easier in the contig editor now. It
either auto-scrolls at the window edge or we can use
shift+click to extend.

* Gap5 now has basic primer-walking oligo picking support. (PCR
to come later.)

* Improvements to SAM support: fixed flags when exporting; tags
are supported (via user-defined key=value auxillary data - Zs
and Zc record types) in both import/export; faster export;
output is now sorted; protection against quality values higher
than ASCII ~; now parse the PL field in read-group lines in

* The Join Editor now displays overlap length and match score,
confirming whether we still wish to make a join. Also
bug-fixed the align button when one or both contigs didn't
start at base position 1.

* Two new scripts: gap5_consensus, gap5_export. These wrap up
gap5 menu items as non-interactive command line tools.

* The contig editor has a Goto... menu to jump to other
sequences on this template.

* It should be easier to keep track of sequences when scrolling
in the editor as it attempts to adjust the Y scrollbar to keep
data on screen. Additionally the Y-layout doesn't change so
much when scrolling rightwards (although left scrolling still
changes Y layout). Improved efficiency by caching some more

* The contig editor now sorts by sequence technology first and
then X coordinate, meaning that ABI capillary sequences are
always at the top of the display. NOTE: This requires the
platform tag (PL) in SAM/BAM @RG read-group header lines.

* Bug fix writing reading names when importing a mixture of data
with and without read-groups.

* Fixed the Map Reads interface, when adding to contigs that do
not start at base 1. Also fixed some memory free issues here.

* The Show Diagonal and Clear All commands of the contig
selector window now work. The results menu (and Results
Manager window) now update too.

* Disable a few more options and buttons when in read-only
mode. Previously it wouldn't actually have written data, but
tried and aborted.

* Fixed a rare bug with single base-pair tags vanishing under
certainc onditions.

Other changes

* [Gap4/Gap5] Updated the primer melting temperature code to use
the latest published formulae.

* Various compilation improvements: better detection of Large
File Support under some linux systems; control over the
location of curses/ncurses libraries (and which to use); fixed
"make depend" when running from a subdirectory instead of the
top src root; forced use of the staden os.h instead of
sometimes picking up a copy in io_lib.

The release notes file contains a more complete ChangeLog.


Posted by James Bonfield 2010-07-15

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