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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.

Bugs

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.

Availability

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

ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/alpha/gap4sh.gz
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/sgi/gap4sh.gz
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/solaris/gap4sh.gz
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/sun/gap4sh.gz

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

ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/common/dialog.tcl

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.)

Update

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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