IMPORTANT: Bug fix to 1997.0

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue Jul 8 12:18:25 EST 1997

Bug fixes are now available to the 1997.0 release. It is important
that these are applied as a serious bug was introduced in the 1997.0
release that could corrupt the tag information in databases. This
would cause crashes, and in the worst case, could prevent access to
the database. The patch also includes a modified copy_db program to
correct these corruptions. PLEASE DO read the patch release notes,
which are included at the end of this article.

To obtain the patch, use anonymous ftp to list the following directory:


This contains a variety of patch files for each system. Download the
appropriate patch file, uncompress it if needed, untar it, and then
read the instructions contained in the README file.

We apologise for any inconvenience caused by this fix. Please do mail
us back if you have any problems with the patch.

	James Bonfield

---- patch release notes follow ----
				1997.0 patch 1

This tar file contains a patch for the 1997.0, 1997.0.1 and 1997.0.2 releases
of the Staden Package. It MUST NOT be applied to any other version. Note that
the most serious bug fixed is a database corruption caused by using the "Save
Contig" option of the contig editor. The complete list of bugs fixed is listed
in Appendix A. Please read this carefully.

To apply the patch, make sure that the STADENROOT environment variable is set,
and run the apply_patch command contained within this directory. This will
stores the old files in a tar file named "$STADENROOT/unpatch1.tar" and will
update the distribution to be the new version. Please do not run the
apply_patch command several times, as this will overwrite the
unpatch1.tar file. If you plan to do this, take a copy of unpatch1.tar

If the patched version should fail for any reason, the original distribution
can be restored by changing directory to $STADENROOT and typing "tar xvf
unpatch1.tar". PLEASE MAIL US (staden-package at mrc-lmb.cam.ac.uk) if you have

Note that the patch overwrites several files. The list is in Appendix B. If
local modifications have been made for any of these files, the modifications
will be lost. In this case, you'll need to extract the backups from
unpatch1.tar to a temporary directory and merge manually.


Appendix A

-- Fix 1 --

Gap4 tag corruption and copy_db

Fixed a database corruption caused by the Save Contig option of the contig
editor. This would reveal itself as fatal crashes. It is important to realise
that unlike the other bugs fixed, this one changes your data. Typically, the
only change is to remove one of the "comments" sections of an annotation

The copy_db program has been updated to attempt to fix these problems. For any
databases where Save Contig from 1997.0 has been used, there is a chance that
the annotation data has been corrupted. Note that it is not possible to tell
this simply by using the "check database command". It is advisable to use
copy_db to produce a new copy of your database. For example, version 0 of
database FRED can be copied to version 1 using:

	copy_db -f -v FRED.0 FRED.1

If this produces no error reports then your version 0 was fine. If errors are
reported, but copy_db finishes, then version 1 should be an error free copy of
the database. If for any reason copy_db fails to copy the database, or the
newly created copy fails the "check database" function, please email
staden-package at mrc-lmb.cam.ac.uk explaining the problem.

-- Fix 2 --

Gap4 on SunOS 4.x

Gap4 failed on many SunOS 4.x systems with complaints about unable to find
the memmove function. This occurs when using several of the graphical plots in
Gap4. The problem did not affect any other system type.

-- Fix 3 --

Gap4 with large numbers of contigs

A Gap4 database with many contigs (approx 400 or more, depending on the
reading name length) could crash when using the find internal joins, find read
pairs, find repeats, and possibly other functions. This has now been fixed.

-- Fix 4 --

Gap4, Find Internal Joins

The "Probe against single segment" search of Find Internal Joins errornously
had a large allowable maximum probe length. The maximum probe length is now
correctly set to 4096. Attempting to use longer probes would crash Gap4.

-- Fix 5 --

Trev sequence vector clips

Trev now saves the sequencing vector clip points to the experiment file (SL
and SR line types). The previous version allowed editing of these positions,
but did not save them.

-- Fix 6 --

Trev when called from pregap

The interaction between trev and pregap had the "Reject" and "Exit" meanings
switched. They have now been corrected so that "Exit" will accept this reading
and "Reject" will tell pregap to skip this reading.

-- Fix 7 --

Trev right quality clipping

When Trev edits an experiment file containing no right quality clip point,
saving this experiment file (without changing the clip point) would sometimes
set the clip point to be INT_MAX (approx 2 billion). This did now always
happen, and should not cause problems for other applications. However it has
been fixed.

-- Fix 8 --


The convert program (for convering dap or bap databases to gap4 databases)
failed in the 1997.0.x release. It now works again.

-- Fix 9 --

Pregap and SCF files

Pregap was incorrect in its extraction of reading names from SCF files that
contained a 'NAME=' comment.

-- Fix 10 --


Trace_diff now writes out mutation tags when ran on experiment files.


Appendix B

The following files are replaced by this patch. (This list is also available
by typing "tar tvf patch1.tar".)

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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