Commits · b6e8d70b89d51e46dfe7b5f1d21d6c7634f9fd3e · ensembl-gh-mirror / ensembl

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Aug 13, 2010
- set up regexp filters for gene descriptions do not allow undefined or UNKNOWN · b6e8d70b
  Ian Longden authored 14 years ago
  
  b6e8d70b
- If the translations do not have stable IDs, use their dbIDs to compare · 81f06bd0
  Andreas Kusalananda Kähäri authored 14 years ago
```
them instead.  Bug fix for Amy.
```
  81f06bd0
- Fix for splice sites being called at transcript ends · a2c01565
  William McLaren authored 14 years ago
  
  a2c01565
- Added new direct Jamboree mappings · af19e37c
  Ian Longden authored 14 years ago
  
  af19e37c
Aug 12, 2010
- Modify comment that wasn't right anymore. · 63bbcd60
  Andreas Kusalananda Kähäri authored 14 years ago
  
  63bbcd60
- Handle cicular chromosomes in _objs_from_sth(). Patch from EG. · eacfb265
  Andreas Kusalananda Kähäri authored 14 years ago
  
  eacfb265
- Minor cleanup of package head. · 8e2369a8
  Andreas Kusalananda Kähäri authored 14 years ago
  
  8e2369a8
- Always display API version with exceptions, warnings, and deprecation · 554b6817
  Andreas Kusalananda Kähäri authored 14 years ago
```
messages.  Makes it easier to debug reported errors...
```
  554b6817
- Make the registry use the new ApiVersion module. · 79fb61a9
  Andreas Kusalananda Kähäri authored 14 years ago
  
  79fb61a9
- Put the API version into its own module: · 995e9733
  Andreas Kusalananda Kähäri authored 14 years ago
```
  DESCRIPTION
    The module exports the software_version() subroutine which
    returns the release version of the Ensembl Core API.
```
  995e9733
- Detect duplicated source sections in the configuration file. · 6affe06e
  Andreas Kusalananda Kähäri authored 14 years ago
  
  6affe06e
- Get rid of old commented-out code in _objs_from_sth(). · ff99106b
  Andreas Kusalananda Kähäri authored 14 years ago
  
  ff99106b
- In fetch_all_by_Transcript(): Handle cicular genomes. Patch from EG. · 35ecf251
  Andreas Kusalananda Kähäri authored 14 years ago
  
  35ecf251
- added dog_ensembl_proteins · 4c3fd99c
  Magali Ruffier authored 14 years ago
  
  4c3fd99c
Aug 11, 2010
- Add VB_Community_Annotation + change status for Aedes/Ixodes ManualAnnotation · 819bef51
  Karyn Megy authored 14 years ago
  
  819bef51
- In _type_by_external_id(): Take species_id into account. Patch from EG. · 823d0a1d
  Andreas Kusalananda Kähäri authored 14 years ago
  
  823d0a1d
- In _slice_fetch(), deal with circular genomes. Patch from EG. · 7c4c5913
  Andreas Kusalananda Kähäri authored 14 years ago
  
  7c4c5913
- Updated usage docs, added --views and standardised innodb opt · fcbcc3b9
  Nathan Johnson authored 14 years ago
  
  fcbcc3b9
Aug 09, 2010
- Bug fix from user Alison on dev@ensembl.org · 3fb171c2
  Andreas Kusalananda Kähäri authored 14 years ago
  
  3fb171c2
Aug 05, 2010
- Anopheles & Aedes - Remove the ARRAY related sources (in funcgene now) · c2711000
  Karyn Megy authored 14 years ago
  
  c2711000
- added panda config · 5f3efb64
  Magali Ruffier authored 14 years ago
  
  5f3efb64
Aug 04, 2010
- alternative options dbhost / dbuser /dbpass / dbport added · 8cca1139
  Jan-hinnerk Vogel authored 14 years ago
  
  8cca1139
- Modify Culex and Ixodes xref info. · 3b3df3ca
  Karyn Megy authored 14 years ago
  
  3b3df3ca
Jul 29, 2010
- Get rid of double 'my'. · ef1438d8
  Andreas Kusalananda Kähäri authored 14 years ago
  
  ef1438d8
- Make get_all_alternative_translations() call the renamed · 6fea2f7b
  Andreas Kusalananda Kähäri authored 14 years ago
```
fetch_all_alternative_by_Transcript() method in TranslationAdaptor.
```
  6fea2f7b
- Rename method fetch_all_by_Transcript() to · fba60baa
  Andreas Kusalananda Kähäri authored 14 years ago
```
fetch_all_alternative_by_Transcipt() and let it only fetch alternative
translations.
```
  fba60baa
Jul 27, 2010
- Add ancestral_sequences (production-like name) as an alias for Ancestral sequences · 45a6bc95
  Javier Herrero authored 14 years ago
  
  45a6bc95
- Merge back revision 1.15 which got lost in last commit. · 5e2ba19e
  Andreas Kusalananda Kähäri authored 14 years ago
  
  5e2ba19e
- Backing out patches from Dan S. for release 59. · 825b182f
  Andreas Kusalananda Kähäri authored 14 years ago
  
  825b182f
- Backing out Dan's patches for release 59. · a7c35a55
  Andreas Kusalananda Kähäri authored 14 years ago
  
  a7c35a55
Jul 26, 2010

Adding a new method as a result of benchmarking to keep developers using... · 590b6d63

Andy Yates authored 14 years ago

Adding a new method as a result of benchmarking to keep developers using SqlHelper with very large data sets. We now can allow the developer to define how they wish to iterate through a result set

590b6d63

Jul 23, 2010
- _merge_ajoining_coords added to make sure that having more than one coord is... · 1f714d13
  Ian Longden authored 14 years ago
```
_merge_ajoining_coords added to make sure that having more than one coord is wrong. Andy Yates wrote the code i just checked it and added it.
```
  1f714d13
- Only submit sequence dumping jobs if there are jobs to submit. · c25b660f
  Andreas Kusalananda Kähäri authored 14 years ago
  
  c25b660f
Jul 22, 2010
- Add some more command line options for EG. · 76bfdd44
  Andreas Kusalananda Kähäri authored 14 years ago
  
  76bfdd44
- Dan S's patch. · a15638f9
  Andreas Kusalananda Kähäri authored 14 years ago
  
  a15638f9
- Remove hard-coded paths. · d83c83b6
  Andreas Kusalananda Kähäri authored 14 years ago
  
  d83c83b6
Jul 21, 2010
- Get rid of nested loop. · b47cc039
  Andreas Kusalananda Kähäri authored 14 years ago
  
  b47cc039
- Formatting changes. · 0d64fcd5
  Andreas Kusalananda Kähäri authored 14 years ago
  
  0d64fcd5
Jul 20, 2010
- Forgot patching this with Dan's patch... · be71ab17
  Andreas Kusalananda Kähäri authored 14 years ago
  
  be71ab17
- Change meta key name 'species.db_name' to 'species.production_name'. · f4be3985
  Andreas Kusalananda Kähäri authored 14 years ago
  
  f4be3985