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Version-1997.0 Release Notes

Some of the changes in this release will not be obvious to the user. Many changes were required to improve the Gap4 scripting language. We consider this important as it puts us in a better position for future development and allows other people to easily extend gap4 themselves. The first draft of the documentation on this scripting system is now available and can be dound in the scripting_manual/scripting_toc.html file.

The most noticable changes are within gap4, however two new programs have also been added. Vector_clip is is a replacement for vepe, which is still distributed at present. Trace_diff is a tool for comparing pairs of trace files to produce a "difference" trace file and to automatically find and mark mutations.

Gap4 has a much improved Template Display that can now display more than one contig. This provides a much easier way of investigating the relationships between contigs.

Gap4 editing has had several improvements too: it redisplays faster; superedit now provides a larger diversity of editing abilities; a vertical scrollbar, trace differencing, and showing disagreements by colour aid using the editor for mutation studies; and the disassemble readings and break contig functions now have interfaces available directly from within the editor.

Trev has had a few updates to allow repositioning of the vector clips. We've also fixed a couple of bugs to do with saving the accuracy values after editing.

Pregap is now more robust and has an extra question to control whether it should derive reading names from ABI samplenames (held within the files themselves) or the ABI filenames.

Dynamic linking is now used for many programs. This should be transparent to the user, but should use fewer system resources on crowded machines and allows for greater flexibility. The programs using tcl and tk have been updated to use tcl version 7.6 and tk version 4.2 to allow for on-the-fly loading of dynamic libraries, which translate to "packages" to extend gap4, sip4 or trev. See the scripting documentation for details.

Finally, trace file compression is better supported. Gap4 and trev can compress and uncompress trace files (whatever format) on the fly, thus allowing for significant reductions in disk space. The "gzip_trace" and "bzip_trace" scripts can be used to compress your SCF files, saving around 70% of your disk space, which is equivalent to at least a 10 to 1 compression of ABI files.

A more verbose list of changes follows. Note though that only the more important bug fixes are listed, and we consider those marked with asterisks to be most important.

New Programs







For bug fixes to this release please see the news.230497a.html and news.070597a.html news pages.

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