Commits · 8abe38aac4a6f14fac0925e2e195814668ba35fb · ensembl-gh-mirror / ensembl

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Dec 15, 2014
- Merge branch 'master' of https://github.com/Ensembl/ensembl · 8abe38aa
  Magali Ruffier authored 10 years ago
  
  8abe38aa
- [ENSCORESW-1190 ]. Parse GOA Uniprot release correctly. · 70110e27
  Alessandro Vullo authored 10 years ago
  
  70110e27
- UniGene source available for olive baboon · 93118178
  Magali Ruffier authored 10 years ago
  
  93118178
- ENSCORESW-1189 : group is a chromosome · f2ca00f5
  Magali Ruffier authored 10 years ago
  
  f2ca00f5
- use direct sql for checksum, as there are no identity xrefs for those · 564cbf8c
  Magali Ruffier authored 10 years ago
  
  564cbf8c
Dec 12, 2014
- some syntax errors · 68cb623c
  Magali Ruffier authored 10 years ago
  
  68cb623c
- ensure everyone gets emailed if travis build fails · 4161d648
  Magali Ruffier authored 10 years ago
  
  4161d648
- [ENSCORESW-1117 ]. Emptied table (not necessary) so that SQLite tests succeeds. · 7b9dd143
  Alessandro Vullo authored 10 years ago
  
  7b9dd143
- more \N removed · ae8c1bdf
  Magali Ruffier authored 10 years ago
  
  ae8c1bdf
- Revert "ENSCORESW-1116: first attempt at storing some form of scoring in the overlap mappings" · 3c79026d
  Magali Ruffier authored 10 years ago
```
overlap score is not identity score, we get the identity from the alignments instead
This reverts commit 26152269.
```
  3c79026d
- removed \N in description · c8db3919
  Magali Ruffier authored 10 years ago
  
  c8db3919
- ENSCORESW-1116 : keep alignment score even if overlap takes priority · a040bead
  Magali Ruffier authored 10 years ago
  
  a040bead
Dec 11, 2014
- SQLite table definition for the polyploid test database. · a12773e4
  Alessandro Vullo authored 10 years ago
  
  a12773e4
- MySQL < 5.5 compatible definition so that travis is happy. · 0de4ff0b
  Alessandro Vullo authored 10 years ago
  
  0de4ff0b
- Documentation. · d2e16dc7
  Alessandro Vullo authored 10 years ago
  
  d2e16dc7
- [ENSCORESW-1117 ]. Method to access the list of all top level slices for a given genome component. · 775da1f9
  Alessandro Vullo authored 10 years ago
  
  775da1f9
- [ENSCORESW-1117 ]. Test fetch_all_by_genome_component method. · 950d35f4
  Alessandro Vullo authored 10 years ago
  
  950d35f4
Dec 10, 2014
- [ENSCORESW-1117 ]. Get the list of genome components for a polyploid genome. · ea945dc6
  Alessandro Vullo authored 10 years ago
  
  ea945dc6
- [ENSCORESW-1117 ]. Test getting the list of genome components. · ce272c1e
  Alessandro Vullo authored 10 years ago
  
  ce272c1e
- [ENSCORESW-1117 ]. Test method in GenomeContainer to check genome polyploidy. · 6b3ea911
  Alessandro Vullo authored 10 years ago
  
  6b3ea911
- [ENSCORESW-1117 ]. Support loading core database to test polyploid genome support. · 248747af
  Alessandro Vullo authored 10 years ago
  
  248747af
- [ENSCORESW-1117 ]. Polyploidy test database extracted from Triticum aestivum (EG25). · 14711701
  Alessandro Vullo authored 10 years ago
  
  14711701
Dec 09, 2014
- [ENSCORESW-1117]. meta_key could be not defined. Polyploidy is defined with... · e683f1bd
  Alessandro Vullo authored 10 years ago
```
[ENSCORESW-1117]. meta_key could be not defined. Polyploidy is defined with more than two sets of paired chromosomes.
```
  e683f1bd
- Method to check whether a genome is polyploid or not. · 15b2f05f
  Alessandro Vullo authored 10 years ago
  
  15b2f05f
- [ENSCORESW-1117 ]. 'ploidy' is species-specific meta key. · 939906fe
  Alessandro Vullo authored 10 years ago
  
  939906fe
- utilsIo.t merged with io.t · 5090e673
  Alessandro Vullo authored 10 years ago
  
  5090e673
- ENSCORESW-1129: BEDSerializer added into Utils/IO directory · abb70f35
  Magali Ruffier authored 10 years ago
```
was used in REST View
```
  abb70f35
- added missing patches · 46626ab8
  Magali Ruffier authored 10 years ago
  
  46626ab8
Dec 08, 2014
- Merge pull request #47 from Anacode/mg13/ts_add_sf_fix_2 · f69010ab
  Magali Ruffier authored 10 years ago
```
Transcript->add_supporting_features(): fix cut-n-pasted throw() message.
```
  f69010ab
- Transcript->add_supporting_features(): fix cut-n-pasted throw() message. · c0e26c73
  Michael Gray authored 10 years ago
  
  c0e26c73
Dec 05, 2014
- ENSCORESW-1142 : add source RefSeq_ncRNA for NR_ transcripts · a854ce95
  Magali Ruffier authored 10 years ago
  
  a854ce95
- ENSCORESW-1130 : remove compara dbs from lookup · 79a9cbf5
  Magali Ruffier authored 10 years ago
  
  79a9cbf5
- ENSCORESW-1106 : retire overlapping_regions script · e7d262e5
  Magali Ruffier authored 10 years ago
  
  e7d262e5
- remove any accidental spaces at the end of sources rather than dying horribly · 1abdfaaa
  Magali Ruffier authored 10 years ago
  
  1abdfaaa
- remove evil blank spaces · 36563be7
  Magali Ruffier authored 10 years ago
  
  36563be7
- added config for amazon molly and sperm whale · 787e9c11
  Magali Ruffier authored 10 years ago
```
also added missing RefSeq_ncRNA source for otherfeatures import
```
  787e9c11
- if type is null, should be explicit \N in text file · 4c1416e9
  Magali Ruffier authored 10 years ago
  
  4c1416e9
- update master schema to release 79 · cfe26ad2
  Magali Ruffier authored 10 years ago
  
  cfe26ad2
- wrong taxonomy id for tasmanian devil · 3ad784b1
  Magali Ruffier authored 10 years ago
  
  3ad784b1
- Ontology test database patched. · 51dd37ae
  Alessandro Vullo authored 10 years ago
  
  51dd37ae