Commits · ce124519aad142f445dbede184b63ef38f58a000 · ensembl-gh-mirror / ensembl

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Sep 05, 2018
- Merge pull request #291 from Ensembl/feature/ucsc_parser · ce124519
  Kieron Taylor authored 6 years ago
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ENSCORESW-2792: one UCSC parser per species
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  Unverified
  
  ce124519
- ENSCORESW-2792 : one UCSC parser per species · bbb4a973
  Magali Ruffier authored 6 years ago
  
  bbb4a973
Sep 04, 2018
- Merge pull request #288 from Ensembl/feature/ucsc_parser · 09f9c7bd
  Kieron Taylor authored 6 years ago
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ENSCORESW-2792: separate mouse UCSC to avoid clashes
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  09f9c7bd
- Merge pull request #286 from wbazant/master · 2f39f152
  Kieron Taylor authored 6 years ago
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Test module for xref parsers, test WormbaseDirectParser
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  2f39f152
- Merge pull request #289 from Ensembl/bugfix/cleanup_dependent · 096ddc34
  Kieron Taylor authored 6 years ago
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ENSCORESW-2744: remove dependent_xref when removing master
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  096ddc34
- ENSCORESW-2744 : remove dependent_xref when removing master · 667e4c42
  Magali Ruffier authored 6 years ago
  
  667e4c42
- ENSCORESW-2792 : add documentation for future reference · 45632852
  Magali Ruffier authored 6 years ago
  
  45632852
Sep 03, 2018
- Merge pull request #287 from at7/var_tidyup_95 · 962bf859
  Kieron Taylor authored 6 years ago
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Remove deprecated Variation methods
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  962bf859
- remove AlignStrainSlice · f528f3b6
  Anja Thormann authored 6 years ago
  
  f528f3b6
- Remove AlignStrainSlice · ddc2c180
  Anja Thormann authored 6 years ago
  
  ddc2c180
- XrefParser::Database uses DBConnection · 93ad6e79
  Wojtek Bazant authored 6 years ago
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+ XrefParser::Database stores a DBConnection, setters delegate to it
+ New test database, for xrefs
+ Setup to test XrefParsers
+ Tests for WormbaseDirectParser
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  93ad6e79
Aug 31, 2018
- deleted for release/95 · 068d4b7a
  Anja Thormann authored 6 years ago
  
  068d4b7a
- deleted for release/95 · 15b281e9
  Anja Thormann authored 6 years ago
  
  15b281e9
- deleted for release/95 · 247da00f
  Anja Thormann authored 6 years ago
  
  247da00f
- remove deprecated code for release/95 · bfd37793
  Anja Thormann authored 6 years ago
  
  bfd37793
Aug 30, 2018
- ENSCORESW-2792 : separate mouse UCSC to avoid clashes · 522c72c1
  Magali Ruffier authored 6 years ago
  
  522c72c1
Aug 28, 2018
- Merge pull request #281 from Ensembl/bugfix/ENSCORESW2839 · 973776da
  Alessandro Vullo authored 6 years ago
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Update Bio::EnsEMBL::Exon->is_coding():
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  973776da
Aug 24, 2018
- Merge pull request #282 from Ensembl/feature/xref_config_cleanup · 59d1f52b
  Matthew Laird authored 6 years ago
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Feature/xref config cleanup
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  59d1f52b
Aug 22, 2018
- ENSCORESW-2805 : better source tracking · d3d59fc6
  Magali Ruffier authored 6 years ago
  
  d3d59fc6
- ENSCORESW-2805 : use more complete file and parser · 88768da7
  Magali Ruffier authored 6 years ago
  
  88768da7
- ENSCORESW-2805 : leftover gene_name sources · bb8c8c26
  Magali Ruffier authored 6 years ago
  
  bb8c8c26
- Update Bio::EnsEMBL::Exon->is_coding(): · afaf4c2f
  Matthew Laird authored 6 years ago
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- Update documentation on required parameters
- Throw an error if a Transcript isn't given
- Add a test for regression
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  afaf4c2f
Aug 20, 2018
- ENSCORESW-2805 : inherit default sources from vertebrates · 21f60e43
  Magali Ruffier authored 6 years ago
  
  21f60e43
- ENSCORESW-2805 : _gene_name sources not used · 1d5ddef0
  Magali Ruffier authored 6 years ago
  
  1d5ddef0
- ENSCORESW-2805 : simplify RefSeq sources · 3a7e40b3
  Magali Ruffier authored 6 years ago
  
  3a7e40b3
- ENSCORESW-2805 : remove commented out lines · 25e35240
  Magali Ruffier authored 6 years ago
  
  25e35240
- ENSCORESW-2818 : remove historical vega sources · 6c9eb151
  Magali Ruffier authored 6 years ago
  
  6c9eb151
Aug 17, 2018
- Merge pull request #280 from Ensembl/feature/division_xrefs · c0d38d06
  Magali Ruffier authored 6 years ago
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ENSCORESW-2725: can run for species, taxon or division
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  Unverified
  
  c0d38d06
- Merge pull request #279 from Ensembl/bugfix/official_naming · 74e90f3a
  Magali Ruffier authored 6 years ago
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Bugfix/official naming
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  74e90f3a
Aug 15, 2018
- Merge pull request #278 from Ensembl/feature/xref_test · b1df0fe8
  Tiago Grego authored 6 years ago
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ENSCORESW-2827: minimal test on xref config validity
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  Unverified
  
  b1df0fe8
Aug 13, 2018
- ENSCORESW-2830 : correct increment · 0887e6c9
  Magali Ruffier authored 6 years ago
  
  0887e6c9
- ENSCORESW-2725 : can run for species, taxon or division · ed1d7e9d
  Magali Ruffier authored 6 years ago
  
  ed1d7e9d
- explicitly add xref dependency · f50a8b8c
  Magali Ruffier authored 6 years ago
  
  f50a8b8c
- ENSCORESW-2827 : minimal test on xref config validity · 7662f2c7
  Magali Ruffier authored 6 years ago
  
  7662f2c7
- some cosmetic changes for better readibility · cba58f9b
  Magali Ruffier authored 6 years ago
  
  cba58f9b
- Merge pull request #275 from Ensembl/feature/clearer_mapping_stage · 7b3a74ce
  Tiago Grego authored 6 years ago
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ENSCORESW-2819: clean up steps in mapping
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  Unverified
  
  7b3a74ce
Aug 09, 2018
- Merge pull request #274 from Ensembl/feature/vega_cleanup · e065a3e4
  Magali Ruffier authored 6 years ago
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ENSCORESW-2818: remove vega from xref code
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  Unverified
  
  e065a3e4
- Merge pull request #277 from Ensembl/bugfix/pr_template · c6df1fa1
  Magali Ruffier authored 6 years ago
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[ENSCORESW-2820] Update links in pull request template
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  c6df1fa1
- [ENSCORESW-2820 ] Update links in pull request template · 4085f452
  Brandon Walts authored 6 years ago
  
  4085f452
Aug 08, 2018
- increment within loop · 74376e7e
  Magali Ruffier authored 6 years ago
  
  74376e7e