GitLab

ensemblgenomes-20-73'.

Sprout from master 2013-08-22 09:32:14 UTC Magali Ruffier <mr6@sanger.ac.uk> 'added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively'
Cherrypick from master 2013-09-06 15:16:53 UTC Alessandro Vullo <avullo@ebi.ac.uk> 'Tests for subroutines in the Bio::EnsEMBL::Utils::IO module.':
    modules/t/io.t
    modules/t/test-genome-DBs/ontology/ontology/table.sql
    sql/patch_73_74_a.sql
    sql/patch_73_74_b.sql
    sql/patch_73_74_c.sql
    sql/patch_73_74_d.sql
    sql/patch_73_74_e.sql
    sql/patch_73_74_f.sql
Cherrypick from branch-ensembl-73 2013-08-30 09:06:03 UTC Magali Ruffier <mr6@sanger.ac.uk> 'revert changes for metacontainer support':
    misc-scripts/ontology/sql/patch_72_73_b.sql
    misc-scripts/ontology/sql/tables.sql
    modules/Bio/EnsEMBL/DBSQL/AssemblyAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
    modules/Bio/EnsEMBL/RepeatFeature.pm
    modules/Bio/EnsEMBL/Slice.pm
    modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

we have too many reg starting variables to use shortened names

The code previously allowed bogus numbers through into the final slice which
caused errors in later methods. The website crashed because of this. We will
reject anything that was not an integer if the start or end was defined.

[ENSCORESW-377]. Fixing the seq region synonym as mentioned by Steve S. Also added a test case which looks for synonyms with a coordinate system not as before which only worked when we had no coordinate system)

moving logic for slice projection filtering into sliceadaptor so compara have an easier time using it and getting better patch support in

will return a list of slices which are part of the karyotype
solves issues with genomes where slices are called chromosomes when they should not be

[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad

Enforced strict matching in fetch_by_region synonym lookup. Returns undef, rather than giving the user what might be the correct answer, and emits a warning. Only allowed to auto-select coordinate system when it is not known.

Fixed regression problem in fetch_by_region, where a valid synonym with an invalid coordinate system caused a never-ending loop. Added a coordinate system check to ensure the synonym query is on the correct coordinate system.

[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these

Assignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.

Made the circular slice code compartmentalised to just SliceAdaptor (making cache initalisation code easier) and we now only build circular slices when the seqregion it is based off is flagged as circular

toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.

not needed and move declaration of a statment handle to aviod having to
declare another one.

Slice::dbID().

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Added new option to method fetch_all which is include_lrg. By defualt lrg slices willl NOT be returned if this is not set (default is off) also since at present all lrg regions are non reference this flag must be set too to get the lrg regions.

added new method fetch_by_region_unique which returns the non duplicate regions. This is mainly for getting non duplicated regions like assembly patches or haplotype regions