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Release 1996.2 Bug Fixes

We recently released a new version of the Staden Package (1996.2). Since then we've discovered a few bugs in gap4 for which fixes are now available.

New tapes sent out will have these bugs fixed and the release number changed slightly to 1996.2.1.


Note that all three bugs listed below are also present in the earlier releases of gap4. However do not apply these fixes to any release other than 1996.2. Doing so will most certainly cause problems.

  1. Shuffle pads had a memory overflow that could occasionally corrupt the data within the editor. This does not directly corrupt the database permanently, but will do so if the data in the editor is then saved.

  2. Tags added to experiments files prior to assembly could be placed in the wrong location (by a few bases, depending on the number of pads to the reading). This only affects the normal shotgun assembly mode.

  3. The default font for the tk dialogue boxes does not exist on Solaris systems without the optional SUNWxwoft package installed. Changing the font from -Adobe-Times-... to -*-Times-... has hopefully fixed the problem.


New gap4sh binaries are available from our ftp site. See one of:


Where 'sun' is short for SunOS 4.x/Solaris 1.x and solaris is short for SunOS 5.x/Solaris 2.x.

This binary (when uncompressed) should be placed in the $STADENROOT/bin directory (backup your old one first) and will fix bugs 1 and 2 listed above.

Bug number 3 above is fixed by getting a new dialog.tcl file from


This should be placed in the $STADENROOT/lib/tk/ directory. As mention above this is only necessary for users of Solaris without the SUNWxwoft package installed. ("pkginfo SUNWxwoft" will claim that information was not found if the package is not installed.)


Due to a compilation error on SunOs 4.x and DEC Alpha systems the fixes introduced other problems. Apologies for this. Corrected binaries are now in place.

The $STADENROOT/tables/BAP.MRG file was missing from 1996.2 and 1996.2.1 distributions. The implications are that the graphical plots (excluding the contig editor) of gap and xgap do not work. Gap4, which is the latest assembly program, is unaffected. The BAP.MRG file should contain the following.

PLOT POSITIONS FOR SAP. DRAWING BOARD SIZE, X0 XLENGTH, OPT Y0 YLEN 10000 10000 1100 8500 12 5000 5000 13 1 100 15 1 10000 16 20 20 29 4000 1000 33 5000 4000 34 9000 1000 39 2000 2000
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