Commits · 43554d01f88c33332ecddf9f6d8bd152989c6002 · ensembl-gh-mirror / ensembl

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Jun 23, 2011
- Changes for submit_density_features.pl script · 43554d01
  Monika Komorowska authored 13 years ago
  
  43554d01
- Changed parameter names in density feature scripts · a60cc9ea
  Monika Komorowska authored 13 years ago
  
  a60cc9ea
- added POD for fetch_Iterator_by_Slice · 26ace380
  Nathan Johnson authored 13 years ago
  
  26ace380
Jun 22, 2011
- Test for dependencies on Variation, Funcgen or Compara modules in Core modules. · 5c965f5e
  Monika Komorowska authored 13 years ago
  
  5c965f5e
- Updated to load GL accession as a synonym of the patch scaffold/supercontig. · 54a327d0
  Susan Fairley authored 13 years ago
  
  54a327d0
- Added 1000genomes populations, minimumnumber of observations and also includes LRG transcripts · 35e9f364
  Pontus Larsson authored 13 years ago
  
  35e9f364
- look for assembled and component overlaps · 14066c44
  Ian Longden authored 13 years ago
  
  14066c44
- Updated store method to set stable id version to 1 if it's undefined. · 75297b92
  Monika Komorowska authored 13 years ago
  
  75297b92
- Updated store method to set stable id version to 1 if it's undefined. · 17d6bdfb
  Monika Komorowska authored 13 years ago
  
  17d6bdfb
- Fixed a HTML tag error · 86f724fb
  Laurent Gil authored 13 years ago
  
  86f724fb
- Updated store method to set stable id version to 1 if it's undefined. · 2f22d315
  Monika Komorowska authored 13 years ago
  
  2f22d315
Jun 21, 2011
- Add a link to the colour legend · c9e637c2
  Laurent Gil authored 13 years ago
  
  c9e637c2
- Remove the Variation Bio::EnsEMBL::Variation::Utils::Constants import · 60a277ec
  Laurent Gil authored 13 years ago
  
  60a277ec
- - Add a new optional @colour tag, to colour the tables (if you want to be... · dc04b7bc
  Laurent Gil authored 13 years ago
```
- Add a new optional @colour tag, to colour the tables (if you want to be consistent with colours used in your database schema).
- Add a colour legend at the bottom of the HTML page, if colours are found.
- You can disable this feature using the option '-c 0'
```
  dc04b7bc
Jun 20, 2011

Updated code to get the list of taxIds from xref_config.ini and check the... · dd6e4d73

Arnaud Kerhornou authored 13 years ago

Updated code to get the list of taxIds from xref_config.ini and check the PHIbase mapping based on all returned taxIds rather then just the spiecies_id

dd6e4d73

Jun 17, 2011
- Update the 'get_all_StructuralVariations' method · 8577e57b
  Laurent Gil authored 13 years ago
  
  8577e57b
Jun 16, 2011
- Added new sources, ncRNA::EG and PHIbase, added new species Nectria · 33196725
  Arnaud Kerhornou authored 13 years ago
  
  33196725
- PHIbase parser · 95c6c885
  Arnaud Kerhornou authored 13 years ago
  
  95c6c885
- Added specific display_xrefs behaviour for species nectria · 1c0f0439
  Arnaud Kerhornou authored 13 years ago
  
  1c0f0439
Jun 14, 2011
- now actually uses Iterator · 3148cd29
  Nathan Johnson authored 13 years ago
  
  3148cd29
Jun 13, 2011
- fixed NR issue with fetch_all_by_dbID_list · ad0538cf
  Nathan Johnson authored 13 years ago
  
  ad0538cf
Jun 10, 2011
- tweaks to automatic logging · de639b78
  Steve Trevanion authored 13 years ago
  
  de639b78
Jun 09, 2011
- Remain Pod tweaks. Majority of errors removed ready for Doxygen · 9dacbe88
  Kieron Taylor authored 13 years ago
  
  9dacbe88
- Guess what? Pod messed up · 2c9685da
  Kieron Taylor authored 13 years ago
  
  2c9685da
- Pod corrections. Sometimes I even surprise myself · 24e56a8b
  Kieron Taylor authored 13 years ago
  
  24e56a8b
- pod me do · 029ef7b2
  Kieron Taylor authored 13 years ago
  
  029ef7b2
- Pod section moved closer to method it refers to · 1944f890
  Kieron Taylor authored 13 years ago
  
  1944f890
- Wish I knew who had combined method documentation for so many methods. Very inconvenient. · 7d6992d3
  Kieron Taylor authored 13 years ago
  
  7d6992d3
- Guess what? Pod split to cover methods independently · 42e27976
  Kieron Taylor authored 13 years ago
  
  42e27976
- Pod fix. Sloppy update of Pod after renaming of get_all_DAS_Features? · 1d7ea1b1
  Kieron Taylor authored 13 years ago
  
  1d7ea1b1
- Pod fix. Method documentation was nowhere near the method · 872dbad5
  Kieron Taylor authored 13 years ago
  
  872dbad5
Jun 08, 2011
- Major POD update, removal of reference to Ensembl::Lite · 474eb0d1
  Kieron Taylor authored 13 years ago
  
  474eb0d1
- Added new method: cds2genomic. · c996feea
  Monika Komorowska authored 13 years ago
  
  c996feea
- POD fix for method get_all_DAS_Features · 5f0644b0
  Kieron Taylor authored 13 years ago
  
  5f0644b0
- Updated descriptions for pep2genomic · d87acfea
  Monika Komorowska authored 13 years ago
  
  d87acfea
- Amended description for method pep2genomic · 4c98cd1f
  Monika Komorowska authored 13 years ago
  
  4c98cd1f
Jun 06, 2011
- Updated comments. · d3c979f5
  Monika Komorowska authored 13 years ago
  
  d3c979f5
- Updated methods store_on_ and remove_from_ to undefine Slice->{'circular'}... · 56342d8f
  Monika Komorowska authored 13 years ago
```
Updated methods store_on_ and remove_from_ to undefine Slice->{'circular'} SliceAdaptor->{'is_circular'} and SliceAdaptor->{'circular_sr_id_cache'} when the attribute code is 'circular_seq' and object is a slice
```
  56342d8f
- removed some comments · c0513e94
  Nathan Johnson authored 13 years ago
  
  c0513e94
- corrected local vs sr check for overlap splice on fetch_Iterator_by_Slice · 5da89472
  Nathan Johnson authored 13 years ago
  
  5da89472