Commits · eccc46f6114d1eb08717bd42cd2413abfe54b579 · ensembl-gh-mirror / ensembl

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Oct 13, 2015
- test dbs patched for release 83 · eccc46f6
  Magali Ruffier authored 9 years ago
  
  eccc46f6
- schema update for release 83 · c6681fb1
  Magali Ruffier authored 9 years ago
  
  c6681fb1
Oct 08, 2015
- [ENSCORESW-1521 ]. Specifying the most appropriate for the extra_data attribute. · d437054f
  Alessandro Vullo authored 9 years ago
  
  d437054f
Oct 06, 2015
- Provide some accessors for people that don't have Ensembl objects but still... · 7ee48bbd
  Kieron Taylor authored 9 years ago
```
Provide some accessors for people that don't have Ensembl objects but still require the SO term mappings for things.
```
  7ee48bbd
Sep 24, 2015
- ENSCORESW-1483 : include predicted RefSeq in overlap · 6b64e2e6
  Magali Ruffier authored 9 years ago
  
  6b64e2e6
Sep 23, 2015
- ENSCORESW-1478 : use direct file access if history not available · 29cc8895
  Magali Ruffier authored 9 years ago
  
  29cc8895
Sep 22, 2015
- added missing join for multispecies dbs · 6ca36cf1
  Dan Staines authored 9 years ago
  
  6ca36cf1
- Merge branch 'master' of https://github.com/danstaines/ensembl · cd64f99b
  Dan Staines authored 9 years ago
  
  cd64f99b
Sep 21, 2015
- Merge branch 'master' of https://github.com/Ensembl/ensembl · 794e0ee4
  Magali Ruffier authored 9 years ago
  
  794e0ee4
Sep 17, 2015
- Merge pull request #84 from muffato/registry_failures · 033bcb73
  Alessandro Vullo authored 9 years ago
```
Die if there is no available config file in Registry::load_all()
```
  033bcb73
Sep 16, 2015
- Merge pull request #88 from james-monkeyshines/master · b9ffab64
  Alessandro Vullo authored 9 years ago
```
Master
```
  b9ffab64
Sep 15, 2015
- Merge branch 'master' of https://github.com/Ensembl/ensembl · a79d021c
  Magali Ruffier authored 9 years ago
  
  a79d021c
- Merge pull request #86 from Ensembl/experimental/merged_alternative_sequence_store · 27719a31
  Magali Ruffier authored 9 years ago
```
Experimental/merged alternative sequence store
```
  27719a31
- branches are only available if already checked out, use origin instead · 14a1b1f3
  Magali Ruffier authored 9 years ago
  
  14a1b1f3
Sep 14, 2015
- test on single object rather than element of an array · f5c014c8
  Magali Ruffier authored 9 years ago
  
  f5c014c8
- objects might be returned in different order · ac06f7f6
  Magali Ruffier authored 9 years ago
  
  ac06f7f6
- check frame, peptide and flush_sf methods · 38a26dbe
  Magali Ruffier authored 9 years ago
  
  38a26dbe
- check archive string · 5e6001cb
  Magali Ruffier authored 9 years ago
  
  5e6001cb
- more methods for GenomeContainer · 31709a72
  Magali Ruffier authored 9 years ago
  
  31709a72
- added test for UTR features · b3273403
  Magali Ruffier authored 9 years ago
  
  b3273403
- comparing fetch_by_child and get_all_parents · 27ff6746
  Magali Ruffier authored 9 years ago
  
  27ff6746
- exons in PredictionTranscript are PredictionExons · c86d6b5f
  Magali Ruffier authored 9 years ago
  
  c86d6b5f
- some tests on Genome object · be1ca0dd
  Magali Ruffier authored 9 years ago
  
  be1ca0dd
- added tests for untested methods · 2c6c30db
  Magali Ruffier authored 9 years ago
  
  2c6c30db
- testing old methods · af0df2ae
  Magali Ruffier authored 9 years ago
  
  af0df2ae
- fixed sql typos · a44a90f2
  Magali Ruffier authored 9 years ago
  
  a44a90f2
Sep 11, 2015
- remove unused code · 6c5ba3d2
  Magali Ruffier authored 9 years ago
  
  6c5ba3d2
- test lists of features · 6620c8ea
  Magali Ruffier authored 9 years ago
  
  6620c8ea
- should be ExonTranscript, not Exon · 03e2515a
  Magali Ruffier authored 9 years ago
  
  03e2515a
- correct capitalisation · 20c45bef
  Magali Ruffier authored 9 years ago
  
  20c45bef
Sep 10, 2015
- ENSCORESW-1439 : test additional methods · b144846c
  Magali Ruffier authored 9 years ago
  
  b144846c
- add tests for CDS and exon features · 012e41b3
  Magali Ruffier authored 9 years ago
  
  012e41b3
- Merge branch 'master' of https://github.com/Ensembl/ensembl · b2fd2f96
  Magali Ruffier authored 9 years ago
  
  b2fd2f96
Sep 09, 2015
- Merge branch 'experimental/alternative_sequence_stores' of... · e3b11aac
  Magali Ruffier authored 9 years ago
```
Merge branch 'experimental/alternative_sequence_stores' of https://github.com/Ensembl/ensembl into experimental/alternative_sequence_stores
```
  e3b11aac
- Pass $db into the constructor. · c9ea54ab
  Andy Yates authored 9 years ago
```
Seems by passing @_ onwards I broke later initalisation code. Thanks
Travis for picking that up :)
```
  c9ea54ab
- Forgot to add CDS prefix for non-trans-spliced cases... · e50776c7
  James Allen authored 9 years ago
  
  e50776c7
- Merge branch 'gff_trans_spliced' · 8f383153
  James Allen authored 9 years ago
  
  8f383153
- Fixed SequenceAdaptor::new() args and FileFaidx POD header. · 1d730ce1
  Andy Yates authored 9 years ago
```
Following on from Alessandro's comments from the pull request.
SequenceAdaptor can now control the cache size and FileFaidx's POD is
now correct.
```
  1d730ce1
- Merge pull request #87 from james-monkeyshines/master · 13025521
  Alessandro Vullo authored 9 years ago
```
Specify 5' or 3' UTR in the GTF file
```
  13025521
Sep 08, 2015
- dealing with uninitialised value · 961bff87
  Magali Ruffier authored 9 years ago
  
  961bff87