This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git.
Pull mirroring updated .
- 06 Sep, 2013 1 commit
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cvs2git authored
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
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- 12 Aug, 2013 1 commit
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Magali Ruffier authored
we have too many reg starting variables to use shortened names
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- 06 Aug, 2013 1 commit
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Andy Yates authored
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.
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- 25 Mar, 2013 1 commit
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Andy Yates authored
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- 22 Mar, 2013 1 commit
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Andy Yates authored
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- 12 Mar, 2013 1 commit
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Andy Yates authored
[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)
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- 06 Mar, 2013 1 commit
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Andy Yates authored
moving logic for slice projection filtering into sliceadaptor so compara have an easier time using it and getting better patch support in
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- 20 Feb, 2013 1 commit
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Magali Ruffier authored
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
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- 04 Dec, 2012 1 commit
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Andy Yates authored
[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad
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- 26 Oct, 2012 1 commit
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Andy Yates authored
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- 01 Oct, 2012 2 commits
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Kieron Taylor authored
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.
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Kieron Taylor authored
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.
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- 28 Sep, 2012 1 commit
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Andy Yates authored
[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these
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- 16 Aug, 2012 1 commit
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Andy Yates authored
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- 13 Aug, 2012 1 commit
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Magali Ruffier authored
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- 10 Aug, 2012 1 commit
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Magali Ruffier authored
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- 06 Aug, 2012 1 commit
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Magali Ruffier authored
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- 19 Jun, 2012 1 commit
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Andy Yates authored
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.
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- 23 Mar, 2012 1 commit
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Andy Yates authored
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- 20 Mar, 2012 2 commits
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Andy Yates authored
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Andy Yates authored
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- 15 Mar, 2012 2 commits
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Andy Yates authored
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Andy Yates authored
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- 27 Feb, 2012 1 commit
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Andy Yates authored
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- 23 Feb, 2012 1 commit
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Andy Yates authored
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
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- 10 Jan, 2012 1 commit
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Andy Yates authored
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- 24 Nov, 2011 1 commit
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Andy Yates authored
toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.
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- 21 Sep, 2011 1 commit
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Andy Yates authored
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- 15 Sep, 2011 1 commit
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Andy Yates authored
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- 18 Apr, 2011 1 commit
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Monika Komorowska authored
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- 05 Jan, 2011 1 commit
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Andreas Kusalananda Kähäri authored
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- 30 Nov, 2010 1 commit
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Ian Longden authored
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- 12 Nov, 2010 1 commit
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Ian Longden authored
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- 16 Sep, 2010 2 commits
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Andreas Kusalananda Kähäri authored
not needed and move declaration of a statment handle to aviod having to declare another one.
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Andreas Kusalananda Kähäri authored
Slice::dbID().
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- 16 Aug, 2010 1 commit
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Andreas Kusalananda Kähäri authored
<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.
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- 13 Aug, 2010 1 commit
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Andreas Kusalananda Kähäri authored
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- 15 Jun, 2010 1 commit
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Ian Longden authored
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- 08 Jun, 2010 1 commit
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Ian Longden authored
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.
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- 04 Jun, 2010 1 commit
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Ian Longden authored
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
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