Ignoring terms referenced in intersection_of lines, until we redesign the db/ parsing script to be able to store them.

any whitespace.


Some reformatting.

-force command line option added to remove user interaction so that the farm can be utilised. if -force is used then user will not be asked if they want to update or delete data it will just be done

dependencys added so that for a source to be loaded then all of its dependecies must be loaded before it. Stored in a table dependent_source.

new print_stats method created from code already there, which has been tidied up. -force checked before user requests and if set default actions are taken (for use with farm). Removed old subs that are never called. Plus general tidying :-)

The display Xref for Gene should come from FlyBase and not choosen from
the transcript display xrefs sources.
Moreover, since we run the pipeline in fullmode, the method called is
from the drosophila module and not the generic method from the DisplayXrefs
module.

mode (like FlyBase ftp server).

DirectXrefs code moved to DirectXref.pm module and this module now only loads data form the core database into the xref one

For release 64 we've found that features on human HSCHR5_1_CTG1 would
not get fetched since its seq_region_id is an internal_seq_region_id
with a corresponding, but non-existent, external_seq_region_id in the
seq_region_mapping table.

Check that the Master xref id is present if xref for a source are extracted from different databases (like EMBL for FlyBase)

in the patch (patch_63_64_d.sql).

Also delete spaces at end of lines.

This module is basically code removed from BasicMapper.pm but is to do with the official naming code only. Lots of subs added to try and reduce the complexity and ease of reading. More docs needed still though. Saving now, just incase.

This has been created from bits removed from CoreInfo.pm. Removed all the bits wrt direct xrefs from CoreInfo.pm for easier maintainance and put this in the new module. Still needs better docs but more modular

Bringing in assertions for strand as well as for boolean types. Extending the test cases accordingly

Add new "lsf_opt_exonerate" parameter.

Add running time estimates (not hard limits) for the various jobs.

"lsf_opt_exonerate" in the configuration file.