Pregap4 Change Log

21st December 1998 - 1.0b4

This will probably be the last Pregap4 distribution before the real thing, which will be part of the 1998.1 (or more releastically now 1999.0) Staden Package distribution. Please note though that the documentation is still for the beta3 distribution. Sorry, but if I'm to get it out now then something has to give way.

• Added bzip2 support. Since then I've noticed that szip gives even better compression ratios - oh well! Not done that yet.

• Better error handling in many modules. Some modules (eg screen_seq) were considered to fail if they produce any messages on stderr. We now check the Tcl errorCode variable.

• Better handing of spaces in directory names. When generating new filenames we only strip spaces from the filename component and not the pathname component.

• Rerun init_modules at each GUI "run" command. Changed the init_modules to also reset the report variable. This fixes a problem where some modules just append to report each time, and so running several times gives duplicate reports.

• Added recognition code for the naming scheme configuration system. Basically if the [naming_scheme] section sets the "ns_regexp" variable then we parse it to generate the naming scheme procedures.

• Changed xentry and xyn widgets to use Jeffrey Hobb's megawidget package. Added an xcheck megawidget too. This provides a cleaner interface than our old widget code, although it requires a somewhat odd definition style. This fixes some of the colour changing problems we see with Tix.

• Allow for more than one instance of a module. The first module still has a namespace named "module_name". Subsequent ones are "module_name#2", "module_name#3" etc. This also required updates to the module selection code.

• Fixed bug with the "variable" syntax used in the process_dialogue for enter_assembly.p4m.

• Added a RepeatMasker module, but it's not got all of the options for the very latest Dec 1998 version (it should still work though). NB: There is no documentation for this yet.

• Fixed the evaluation of "global_conf". This fixes a problem with saving changes using the edit exp line types dialogue.

• Use the BINARIES config definition from fak2rc. This tells us where to pick up the fakii binaries. This is required to avoid name clashes on Irix 6, where Irix has an "assemble" command (which then promptly core dumps).

• Added code to set the FAKII environment variable (to an assumed location within the main STADENROOT directory) if it's not already set.

• Removed the *_use_sample_names settings from the main pregap4 script. These incorrectly overrode any specified in the users own config files.

• Fixed use of screen_seq. We passed the wrong arguments to the program when screening against a single file.

• Allow conversion of SCF to SCF format. It sounds daft, but is necessary if we wish to enable compression. To not do SCF to SCF conversion, just disable the module. Perhaps we should have a separate compression module to allow compression of ABI files if one desired this.

• The `edit experiment file line types' dialogue now has the scrollbar on the right, for consistencies sake.

• Fixed a problem with the 'select files' window. We can now cut-n-paste (or edit by other means) the file list to use. This was a bug in the earlier version.

• Added PLN_filename_to_exp_name function. This prevented use of plain format files.

12th August 1998 - 1.0b3

• Changed the default list of modules to include pretty much everything, but with most things disabled.

• Hooked up help buttons to the online help.

• Improved handling of file of filenames. When the fofn is local we don't add the directory component to the front of each file (this breaks phrap, cap2 and fakii). The output prefix name now also is the basename of the fofn, not the full fofn name.

• Allow an error of 5 bases in computing the SL and SR values in cross_match_svec, instead of only accepting a match extending right to the start or end of the sequence. The optimal alignment is sometimes from (eg) 3 to 34 instead of 1 to 34, but we still want to write "SL 34". The default tag types for other matches is now SVEC, but it's also now adjustable (tag_type local variable).

• Use init::*_use_sample_name instead of *use_sample_name in the file conversion steps. This is because I moved these variables from global space into 'init' space - possibly not wise! This now allows for the "Use ABI sample names?" questions to work properly, again.

• Added a create_dialogue proc to the augment modules to point users in the direction of Simple Text Database and Experiment File Line Types windows.

• Added a version number to the config file. It's not used at present, but may be useful in future for updating anything which could break the config file format, allowing us to autodetect and autoconvert the config file.

• Renamed the modules to .p4m and the templates to .p4t. This avoids possible confusion with perl modules (.pm).

• Tidied up pregap4 -nowin output by adding some textual headers.

• Renamed "Select Modules" to "Add/Remove Modules" and removed it from the tabbed note book (it's still in the menu).

• The 'cancel' command from file browsers now works correctly. Previously it was clearing the currently specified filename.

• Make sure the filename component of a full pathname is always visible at startup in the entry boxes.

• Don't supply blank sequences to blast as this crashes it. It's still possible to crash blast with many other cases (all Ns, all ambig. codes, sequences (length >= 7) entirely the same letter), but that's blast bugs and not our fault.

• Fixed file descriptor leak in read_exp_file (used in cross_match_svec).

• Removed the vector file name query from the screen vector module. It was misleading - it always uses the same vector that sequence vector clip uses.

• Added a "Experiment File Line Types" configuration section to specify things like "SI" (insert size).

• The default window style is now compact.

• Don't check error codes returned from cap2 and cap3 as they do not return sensible values from main (no return at all).

• Check tcl errorCode to distinguish between stderr output and real errors. Important when dealing with "sequence too short" messages, which are just diagnostics rather than complete program failure. This effects the screen_vector, cloning_vector_clip and sequence_vector_clip modules.

• The "simple text database" config file generation now does "string match" on the lines when no exact match is found. This allows for db files like: # ID SF SC SP 6abz91* m13mp18.vec 6249 41/-24 6aca68* puc18.vec 248 40/-28

• Added "global modules" lines to the cloning vector clip, screen vector and trace_diff modules prevent Tk errors.

• Updated Cap3 module (and cap3_s source) to use "fofn" instead of "outfile" as the file of filenames.

• The trev next/prev/reject/accept file buttons now check when cancel is pressed on the save dialogue and do not move onto the next/prev file.

• The trev "-pregap_mode" mode now correctly turns off trace sequence editing as the default mode.

22nd July 1998 - 1.0b2

• SP value (sequencing vector primer site) can now be entered as two numbers separated by a /. Eg 41/-24. This specifies both forward and reverse primer site values. Requires PR (primer type) to be known.

• Improved error messages, report generation, and filename usage.

• The config file is now easier to read. The "module" command is no longer needed (manual configuration) as the namespace is taken from the config section.

• The *_use_sample_name configurations are now part of the init.pm module instead of global variables.

• File of filenames from remote directories now works better - we assume that all filenames listed within it are pathnames relative to the directory containing the fofn.

• Loading a new config file with the configure dialogue not displayed (in separate window mode) was producing a tk error.

• Editing the "files" list box now actually updates the list of files to process.

• Added a Cap3 module.

• The report mechanism was displaying reports for modules no longer enabled.

• The .log file now includes 'file history'. Eg: 02ap1a.exp (EXP) <- 02ap1a.scf (SCF) <- Sample01.abi (ABI)

• Greatly improved error detection and recovery for all modules.

9th July 1998 - 1.0b1

(Initial release.)