Commits · b1687015754682902a1687a3b29362810610d85b · ensembl-gh-mirror / ensembl

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Oct 23, 2014
- LSF profile file now optional for resubmission as well as initial submission · b1687015
  Kevin Howe authored 10 years ago
  
  b1687015
Oct 22, 2014
- Entries for spotted gar (Lepisosteous oculatus) and cave fish (Astyanax mexicanus). · 31458563
  Alessandro Vullo authored 10 years ago
```
Updated to ensembl ontology 78.
```
  31458563
- Correct the regex with which we get the type, label and long description of each record. · 1ca52f4c
  Alessandro Vullo authored 10 years ago
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The label is no longer truncated at the first 35 chars, as there does seem to be no
reason for that.
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  1ca52f4c
Oct 21, 2014
- Merge pull request #32 from ens-lgil/master · f037f587
  Kieron Taylor authored 10 years ago
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Make the method 'get_all_somatic_VariationFeatures' works the same way a...
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  f037f587
- Fix dodgy juettemann code, remove needless dependency on Regulation. · 4649ac7f
  Kieron Taylor authored 10 years ago
  
  4649ac7f
- Make the method 'get_all_somatic_VariationFeatures' works the same way as... · fb42bfa7
  Laurent Gil authored 10 years ago
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Make the method 'get_all_somatic_VariationFeatures' works the same way as 'get_all_VariationFeatures'
```
  fb42bfa7
Oct 16, 2014
- Merge pull request #30 from juettemann/master · 4778200f
  Kieron Taylor authored 10 years ago
```
Updated caching
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  4778200f
- ENSCORESW-389 : when processing pairs, process dependent xrefs as well · 6441270b
  Magali Ruffier authored 10 years ago
  
  6441270b
- Updated caching · 92f143db
  Thomas Juettemann authored 10 years ago
  
  92f143db
- updated uniprot parser to correctly fetch taxonomy with newly added evidence text · 8872775b
  Magali Ruffier authored 10 years ago
  
  8872775b
Oct 14, 2014
- Update table.sql · 833e3c3b
  Kieron Taylor authored 10 years ago
  
  833e3c3b
Oct 13, 2014
- [ENSCORESW-1033 ]. Parse long descriptions which spans several lines. · 794d86ea
  Alessandro Vullo authored 10 years ago
  
  794d86ea
Oct 10, 2014
- Forgot to apply patch 77_78b to table.sql · a847e9fd
  Kieron Taylor authored 10 years ago
  
  a847e9fd
- Specify registry configuration file in order to locate a production DB and get an adaptor for it. · 1351861a
  Alessandro Vullo authored 10 years ago
  
  1351861a
Oct 09, 2014
- Merge pull request #29 from juettemann/master · e23ff0ad
  Kieron Taylor authored 10 years ago
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Changed caching of unmapped reasons from new to store method to combat race conditions
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  e23ff0ad
- Correct way to get a production DB adaptor using the registry. · cc69acc6
  Alessandro Vullo authored 10 years ago
  
  cc69acc6
Oct 08, 2014
- [ENSCORESW-1057] Patch for get_overlapping_Genes for same-feature searches.... · c4601fdc
  Kieron Taylor authored 10 years ago
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[ENSCORESW-1057] Patch for get_overlapping_Genes for same-feature searches. Additional tests for this method added.
```
  c4601fdc
Oct 07, 2014
- Omitted ontology db version update · de0c54ca
  Kieron Taylor authored 10 years ago
  
  de0c54ca
- [ENSCORESW-1047] Altering column sizes for source in gene and transcript... · 814d3175
  Kieron Taylor authored 10 years ago
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[ENSCORESW-1047] Altering column sizes for source in gene and transcript tables. Also patch test databases.
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  814d3175
- The other schema patch. API version bump. · 51638038
  Kieron Taylor authored 10 years ago
  
  51638038
Oct 06, 2014
- Schema version patch · cca0b720
  Kieron Taylor authored 10 years ago
  
  cca0b720
Oct 02, 2014
- Changed caching of unmapped reasons from new to store method · 05b41335
  Thomas Juettemann authored 10 years ago
  
  05b41335
Sep 29, 2014
- [ENSCORESW-1050 ] Cure issues with get_nearest_Gene caused by minor invocation bugs. · 249fb779
  Kieron Taylor authored 10 years ago
  
  249fb779
Sep 23, 2014
- ENSCORESW-1024 : do not assign transcript names for LRGs · 9861ea20
  Magali Ruffier authored 10 years ago
  
  9861ea20
Sep 22, 2014
- ENSCORESW-524: coordinate overlap on refseq_import gene set · bee9e218
  Magali Ruffier authored 10 years ago
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include alternative sequences with correct start/end
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  bee9e218
- add version tag for all features, now available in gff format · 93c3ad25
  Magali Ruffier authored 10 years ago
  
  93c3ad25
- mispelt associcated · a9664d9e
  Magali Ruffier authored 10 years ago
  
  a9664d9e
- Merge branch 'master' of https://github.com/Ensembl/ensembl · cd70deaa
  Magali Ruffier authored 10 years ago
  
  cd70deaa
Sep 19, 2014
- get rid of unnecessary warnings about uninitialised values · 759e0747
  Magali Ruffier authored 10 years ago
  
  759e0747
- all go depdent xrefs should have a linkage_type · f6626b0f
  Magali Ruffier authored 10 years ago
  
  f6626b0f
Sep 18, 2014
- [ENSCORESW-1038] Fix bug in negative stranded assembly exceptions. Scoped... · 52badf39
  Kieron Taylor authored 10 years ago
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[ENSCORESW-1038] Fix bug in negative stranded assembly exceptions. Scoped variables were forgetting their new values and coming back undef.
```
  52badf39
- Code tidy in AssemblyExceptionFeatureAdaptor · 044f5660
  Kieron Taylor authored 10 years ago
  
  044f5660
Sep 10, 2014

: reinstate phase check · 5d49c39f

Magali Ruffier authored 10 years ago

ignoring phase creates more false positives than false negatives
also improves the overall exon mapping

5d49c39f

Sep 09, 2014
- ENSCORESW-978 : adding version for gene/transcript/protein/exon · 9fcdf2ee
  Magali Ruffier authored 10 years ago
  
  9fcdf2ee
- ENSCORESW-1028: source column displays source, not biotype · 4f87d3a5
  Magali Ruffier authored 10 years ago
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added transcript_biotype in attrib field
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  4f87d3a5
Sep 08, 2014
- Merge branch 'feature/getnearestgene' · 0f3112bb
  Kieron Taylor authored 10 years ago
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Convenience accessors in GeneAdaptor. Main code in BaseFeatureAdaptor. fetch_all_nearest_by_Feature provides an exhaustive mechanism for finding nearby features and ordering them by proximity.
```
  0f3112bb
- Update old overlapping genes code to match newer interface. Remove default feature limit. · a280aeef
  Kieron Taylor authored 10 years ago
  
  a280aeef
- Remove deprecation and provide one-feature return behaviour for get_nearest_Gene. · 86d2872d
  Kieron Taylor authored 10 years ago
  
  86d2872d
- ENSCORESW-1029 : added length to translation summary_as_hash · 8df142dc
  Magali Ruffier authored 10 years ago
  
  8df142dc
- Clean up the return type. · 96f125d9
  Kieron Taylor authored 10 years ago
  
  96f125d9