allows testing on patches and similar

using current_schema_no_cvs everywhere now

The big post-merge alt allele commit. Changes to alt_allele table, new tests, and a couple of new objects.

currently not compatible with most existing tests

An option from the command-line (-current-schema-no-cvs) allows to load the
schema from the file system instead of fetching it from the CVS repository.

was not tested by PAR, as patches are stored on scaffolds, ie a different coord system

[ENSCORESW-499]. schemaPatches.t checks that the table.sql patch set matches what is in the patched database

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

[ENSCORESW-479]. Making this module better at handling homologue Compara errors and also get it to die when you try to get homologues without a compara adaptor configured

Added a method that lists the species in available databases. Ancestral_ are ignored, and the list is filtered to a group type, defaulting to core dbs. Testcase is less than perfect, because the test db has so few species in it.

[ENSCORESW-448]. new overlap algorithm and better test cases. supports overlaps when you do not want to normalise WRT the backing slice

[ENSCORESW-445]. Fixes an issue with transformed and transfered transcripts. Attribute arrays are shallowed copied so attributes meant for the transformed object go back into the parent object. This causes more issues when you start to do multiple transformations from the same transcript. Regression test case added

[ENSCORESW-438]. Fixed API when someone can specify a _rna_edit where the substring length was not equal to the substituting string length

better testing of meta_coord and the container object. Now testing if updates work to existing data sets