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Version-1.4 (aka 2004.0) Release Notes, February 2003

This release marks the first Staden Package release made available since Rodger Staden's group disbanded at MRC (due to funding issues). Since then MRC released the package under an Open Source licence and the package has migrated to SourceForge.net.

One important change is the focus of development. The main body of changes here have been implemented by myself (James Bonfield) at the Wellcome Trust Sanger Institute, with the exception of the Contig Navigation function (by Mark Griffiths, also of WTSI). It is clear that ALL changes apply to Gap4 and Prefinish. This is as a direct consequence of the group disbanding and my new position at WTSI. If there are areas of the package that you feel are now being neglected (which there certainly are!) and you are in a position to help, please email me using 'jkbonfield at users.sourceforge.net'.

One other important change is the level of support available. Basically no support is guaranteed, and no support should be expected. However PLEASE do submit any bugs you find (even if it's in part of the package no longer being actively worked on) to the SourceForge bug tracking system. It may be found at: https://sourceforge.net/tracker/?group_id=100316&atid=627058

Currently the package has been built for most Unix systems we previously supported (possibly all - check the SourceForge downloads links to check), however MS Windows support is likely to be lagging behind. This is primarily because I do not yet have the resources available to maintain a set of MS Windows binaries. Again, if you can assist in this area please contact me.

Now, on to the changes themselves. The full list is rather long and only included below incase you are a glutton for punishment. A summaried version follows.

Gap4 Tag Editing

This has had quite a major overhaul. The most obvious change is that the Edit Tag and Delete Tag functions have now become cascading menus showing all the tags under the current editing cursor position. This solves the problem of how to manipulate tags that are not the top-most displayed ones, but it does mean editing is slower.

Therefore to speed up editing the F11 and F12 keys are bound to edit (F11) and delete (F12) the top-most visible tag. Note that you will need to enable F12 in the Edit Modes menu as by default it is disabled.

Tag Macros are another new feature. Using Shift-F1 to Shift-F10 a tag editor window will appear. From here you can set the tag type, strand and comment and then use "Save Macro" to remember those settings. They are remembered for this session only, so use the editor Settings -> Save Macros to store these to disk. Once defined, a tag macro may be applied by underlining the region you wish to tag and then pressing the appropriate function key, F1 to F10.

By positioning the editor cursor above a tag and using Control-F1 to Control-F10 you can take a copy of the tag underneath the cursor and store it in the appropriate tag macro (without bringing up the macro editor). Combined with F1 to F10 this then provides an equivalent to tag cut-and-paste.

The Tag Editor window itself has also undergone some changes. The existing Save command works just as before, but there are now two new ways to Save; Move and Copy. To use these firstly underline a new region that you wish to tag. Move then moves the tag to that region while Copy creates a duplicate at that region. The underlined region does not need to be within the same sequence, or even the same contig editor. (Although it does need to be an editor within the same Gap4!)

Contig Navigation

At the editor level right clicking on a sequence name now shows a submenu "goto...". This contains a list of the readings sharing that template. The sub-menu can be torn off if you wish.

Hyperlinks have also been added to the reading list produced in the editor using Settings -> Set Active Readings. Just double click on a name in the list to goto that reading in the contig editor. Similarly hyperlinks are now on lists loaded in via the main Lists menu.


However by far the most flexible way of navigating through contigs using an external file is the Contig Navigation function (in main gap4 View menu). This needs a filename, which should contain a series of lines containing the reading name, position, and then an arbitrary text comment. Once loaded a new dialogue allows stepping forwards and backwards along the list. This is a replacement for the original contig editor Search By File method.

Reading selection and Disassemble Readings

The Disassemble Readings function has been completely rewritten (along with Break Contig too). It is now much much faster, but the key change for functionality is the "Move readings to new contigs" and "Split into single-read contigs" options. Moving readings to new contigs will try to keep the assembly together as far as is possible. So for example it is now possible to select all members of a repeat falsely assembled and to disassemble the repeat to form one new contig (rather than one per reading as in the previous Gap4, and as per the "split into single-read contigs" option).

From this it follows that disassembling a reading and all readings to its right is directly equivalent to the old break contig function. Indeed Break Contig has now been written to do just this, but it is still available as before.

This means that production of the lists of readings to pass into disassemble readings has undergone a much needed improvement.

Manual generation of lists of readings from within the editor has been simplified. There is no longer a difference between clicking using the left mouse button and the middle mouse button. Additionally the popup menu (via the right mouse button) on the reading names panel contains options to "Select this reading and all to right" and "Deselect this reading and all to right". (It is recommended that you use these while in the editor "sort by positions" mode so that the consequences will be obvious.)

Together these functions serve an easy way of selecting all readings within designated regions. Furthermore, once selected the list can be manually adjusted in the usual way by clicking on/off the highlight for individual sequences.


Template information in the editor

The Contig Editor name panel has a coloured character (between the reading number and name) to encode the consistency of the template. It is white when consistent, so only inconsistent templates will have a colour associated with them. The template consistency is also shown in the status line of the editor when hovering the mouse over a reading name.

The meanings are:

D / Light Grey
Length of template ("D"istance). The size is computed either from using the position of forward and reverse readings or from the SVEC vector tags on a single reading.

S / Red
Strand. Either two forward (or two reverse) sequences are on opposing strands, or a forward and reverse read pair are on the same strand.

P / Blue
Primer position. If the start or end of the template is computed using multiple sequences (eg via two forward readings) and the start or end is not consistently determined within 100bp then this is flagged.

? / Dark Grey
More than one of the above inconsistencies.

When making a join in the join editor, using quit/join to make the join will now inform you how many read-pairs span this contig, and how many of those are consistent or inconsistent. (This information is shown before you accept the join.)

- - -

And finally... the bionet/usenet newsgroup (bionet.software.staden) seems very underutilised, but it can also be hard to post there sometimes. The SourceForge forums are available at: https://sourceforge.net/forum/?group_id=100316

If you wish to be kept up to date with new package releases and any announcements, please either subscribe to the staden-package mailing list held at sourceforge here: https://sourceforge.net/mail/?group_id=100316

or create a SourceForge account and add a monitor to the 'staden' package. ~ James Bonfield

Full Change List


New features

Bug fixes


Changes/New features

Bug fixes


Changes/New features

Bug fixes



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