Commits · 5e04b1fca8b40a38fb6291bc2133b8b4c62fb56b · ensembl-gh-mirror / ensembl

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Dec 09, 2004
- added .0 to exonerate exe name · 5e04b1fc
  Ian Longden authored 20 years ago
  
  5e04b1fc
- peptide file now not prot · 75cf38aa
  Ian Longden authored 20 years ago
  
  75cf38aa
- Tidied up error message. · e2df72bb
  Glenn Proctor authored 20 years ago
  
  e2df72bb
- Added support for setting release. · ee4dc586
  Glenn Proctor authored 20 years ago
  
  ee4dc586
- Added -setrelease parameter. · 137de37c
  Glenn Proctor authored 20 years ago
```
Improved usage docs.
```
  137de37c
- Simplified synonym selection SQL due to table structure change. · 3d1c581a
  Glenn Proctor authored 20 years ago
  
  3d1c581a
- Synonym loading is simplified now that synonyms are stored as strings rather than xrefs. · 14a9cba9
  Glenn Proctor authored 20 years ago
  
  14a9cba9
- Changed synonym table to store synonyms as strings, not as "whole" xrefs. · f3c857c9
  Glenn Proctor authored 20 years ago
  
  f3c857c9
- Join description line components with a space 'cos that's how SP splits them. · ada092c0
  Glenn Proctor authored 20 years ago
  
  ada092c0
- Now deals correctly with multi-line AC and DE blocks. · a0e9d8f3
  Glenn Proctor authored 20 years ago
  
  a0e9d8f3
- Corrected bug that was resulting in old files not being deleted for first source downloaded. · 70cbf28e
  Glenn Proctor authored 20 years ago
  
  70cbf28e
- Renamed dump_xrefs to dump_core_xrefs to avoid conflict with similarly-named... · 85ce2e7f
  Glenn Proctor authored 20 years ago
```
Renamed dump_xrefs to dump_core_xrefs to avoid conflict with similarly-named but differntly-functioning dump_xref
```
  85ce2e7f
- tidy up of code · fd07aeca
  Ian Longden authored 20 years ago
  
  fd07aeca
Dec 08, 2004
- now removes supercontigs · 9b5849d1
  Steve Trevanion authored 20 years ago
  
  9b5849d1
- Removed debug and spurious exit() ... · 700ac809
  Glenn Proctor authored 20 years ago
  
  700ac809
- Changed xref dumping to generate SQL to retrieve only those xrefs we need. · a1411221
  Glenn Proctor authored 20 years ago
  
  a1411221
- trf condensing script · 1dfcadaa
  Arne Stabenau authored 20 years ago
  
  1dfcadaa
- Updated to use exonerate 0.9 · 838c24fa
  Glenn Proctor authored 20 years ago
  
  838c24fa
- change source_id -> linkage_source_id · 2239b76c
  Ian Longden authored 20 years ago
  
  2239b76c
- set_list to use all primary xrefs for humans as default · 64b9b0e1
  Ian Longden authored 20 years ago
  
  64b9b0e1
- source_id removed from synonym,dependent_xref and primary_xref this... · b0b66b4d
  Ian Longden authored 20 years ago
```
source_id removed from synonym,dependent_xref and primary_xref this information is available via the xref. linkage_source_id added to dependent xref. create_xrefs now also returns a hashref
```
  b0b66b4d
- Re-factored gene display xref calculation to make it clearer. · 620200c3
  Glenn Proctor authored 20 years ago
  
  620200c3
- snp_lite_density replaced by variation_density.pl · ea6c2f37
  Arne Stabenau authored 20 years ago
  
  ea6c2f37
- new run parameters. shouldnt really be in cvs I guess · 19497b97
  Arne Stabenau authored 20 years ago
  
  19497b97
- small changes. Got Coord system and assembly mapper now from chimp db instead... · 85ea4ef8
  Arne Stabenau authored 20 years ago
```
small changes. Got Coord system and assembly mapper now from chimp db instead of human. Made bigger mapper cache and did preload.
```
  85ea4ef8
- changed for the right assembly name, needs refactoring · fc290b5c
  Arne Stabenau authored 20 years ago
  
  fc290b5c
- Added gene display_xref calculation (not fully tested yet). · c58e700e
  Glenn Proctor authored 20 years ago
  
  c58e700e
Dec 07, 2004
- make get_valid_codes - return hashref · 5004b72c
  Ian Longden authored 20 years ago
  
  5004b72c
- Renamed upload_xrefs to more descriptive upload_xref_object_graphs · a32280aa
  Glenn Proctor authored 20 years ago
  
  a32280aa
Dec 06, 2004
- Updated regexp · e52ce5ec
  Abel Ureta-Vidal authored 20 years ago
  
  e52ce5ec
- *** empty log message *** · 35314ae9
  Abel Ureta-Vidal authored 20 years ago
  
  35314ae9
- Updated to new dbc calls, added few comments related to buggy refseq xrefs · c4abcff9
  Abel Ureta-Vidal authored 20 years ago
  
  c4abcff9
- Added monodelphis domestica and xenopus tropicalis. · e952912d
  Glenn Proctor authored 20 years ago
  
  e952912d
Dec 03, 2004
- Update the meta_coord table in core databases · 84533467
  Abel Ureta-Vidal authored 20 years ago
  
  84533467
- sources added etc · 1a7d9645
  Ian Longden authored 20 years ago
  
  1a7d9645
Nov 30, 2004
- Fixed typo AFYY->AFFY for ID 3116 · e9dcce1e
  Glenn Proctor authored 20 years ago
  
  e9dcce1e
- type fix. · ab18e771
  Ian Longden authored 20 years ago
  
  ab18e771
Nov 29, 2004
- · 7f6b5acc
  Jan-hinnerk Vogel authored 20 years ago
```
external db's for flybase added
```
  7f6b5acc
- changes method names in AnalysisAdaptor · 58ba593c
  Will Spooner authored 20 years ago
  
  58ba593c
Nov 26, 2004
- Spelling & typos · 20b98632
  Glenn Proctor authored 20 years ago
  
  20b98632