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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.

for 1.35 and above use OBO::Core::Ontology->subset_def_map()

if you first check if the transcript exists, you won't get any warnings about undefined values anymore

to difference in seq_region names.

Previous change backed out, as not in all cases 1bp slice start = seq_region_start or slice end = seq_region_end.