Commits · db65301fb494625cfc5883a782929c2a3014009a · ensembl-gh-mirror / ensembl

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Oct 27, 2011
- Make code do what its comments say. · db65301f
  Andreas Kusalananda Kähäri authored 13 years ago
  
  db65301f
- Minor corrections to pass the time while waiting for the farm to do its thing. · d2679435
  Kieron Taylor authored 13 years ago
  
  d2679435
- Added the possibility to parse a user parameter to connect to the database · 488780ee
  Arnaud Kerhornou authored 13 years ago
  
  488780ee
- · 3d7248c0
  Andreas Kusalananda Kähäri authored 13 years ago
```
Add gene_score_threshold (0.125).
```
  3d7248c0
- In score_matrix_from_flag_matrix(): add use of gene_score_threshold · 5e202176
  Andreas Kusalananda Kähäri authored 13 years ago
```
(zero by default in the code, but set to 0.125 in the default.conf
configuration file).
```
  5e202176
- In internal_id_rescore(): sort out possible bug. · f56e8405
  Andreas Kusalananda Kähäri authored 13 years ago
  
  f56e8405
- Update a comment. · 1dce067d
  Andreas Kusalananda Kähäri authored 13 years ago
  
  1dce067d
- Unify shebangs. · 67212a1d
  Andreas Kusalananda Kähäri authored 13 years ago
  
  67212a1d
Oct 26, 2011
- swap order · 67219a79
  Ian Longden authored 13 years ago
  
  67219a79
- reference -> is_ref · aec28f90
  Ian Longden authored 13 years ago
  
  aec28f90
- doc changes · ada79199
  Ian Longden authored 13 years ago
  
  ada79199
- HUGO is now HGNC · 6c6b37f6
  Ian Longden authored 13 years ago
  
  6c6b37f6
- Spelling improvements · 01f62de4
  Kieron Taylor authored 13 years ago
  
  01f62de4
Oct 25, 2011
- first draft of the document to help expalin the running of the xref system · ed3ef884
  Ian Longden authored 13 years ago
  
  ed3ef884
- example files from the xref pipeline · ac2ee655
  Ian Longden authored 13 years ago
  
  ac2ee655
- Throw an exception if the real species name for an alias can not be · 9825a9c1
  Andreas Kusalananda Kähäri authored 13 years ago
```
found in get_adaptor().  Suggested by jm18 on dev.

Also reformat get_alias() and get_DBAdaptor().
```
  9825a9c1
Oct 24, 2011
- now in docs directory · a21e9cf0
  Ian Longden authored 13 years ago
  
  a21e9cf0
- moved to docs directory · d9c6f802
  Ian Longden authored 13 years ago
  
  d9c6f802
- Old docs removed · f905ecc9
  Ian Longden authored 13 years ago
  
  f905ecc9
- Moved to docs directory · f8e86770
  Ian Longden authored 13 years ago
  
  f8e86770
- In equals(): Reorder so that the defined() test is first. Reformat. · 2151b2cc
  Andreas Kusalananda Kähäri authored 13 years ago
  
  2151b2cc
- only add direct xref if the ensembl id is okay · 48f64aca
  Ian Longden authored 13 years ago
  
  48f64aca
- sanity check · 7937b1bb
  Ian Longden authored 13 years ago
  
  7937b1bb
- unlink object xrefs doe dependents wherer the master is not the top priority · e5ad705b
  Ian Longden authored 13 years ago
  
  e5ad705b
Oct 21, 2011
- Remove the meta_key.only_for_species field and add the meta_key_species · 1b6321ef
  Andreas Kusalananda Kähäri authored 13 years ago
```
table to the SQL file.
```
  1b6321ef
Oct 20, 2011
- Added an extra source for gene and transcript names assignments · bdce78b4
  Arnaud Kerhornou authored 13 years ago
  
  bdce78b4
- Added an extra source · d38c7528
  Arnaud Kerhornou authored 13 years ago
  
  d38c7528
- Dump before sorting out meta_key.only_for_species vs. meta_key_species. · 63bf640a
  Andreas Kusalananda Kähäri authored 13 years ago
  
  63bf640a
- No apparent need for STRAIGHT JOIN. · 83a4709e
  Andreas Kusalananda Kähäri authored 13 years ago
  
  83a4709e
Oct 19, 2011
- Add · 1c3aadb0
  Andreas Kusalananda Kähäri authored 13 years ago
```
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype
to plugins to run.
```
  1c3aadb0
- Implement biotype() based on the method with the same name in · 37236884
  Andreas Kusalananda Kähäri authored 13 years ago
```
EnsemblGeneGeneric.pm
```
  37236884
- Implement biotype_transcript_rescore() based on the similarly named · 7e52b3aa
  Andreas Kusalananda Kähäri authored 13 years ago
```
method in GeneScoreBuilder.pm
```
  7e52b3aa
- Allow TinyTranscript to have biotype. · 8cea343d
  Andreas Kusalananda Kähäri authored 13 years ago
  
  8cea343d
- Fix SQL syntax error. · decde51d
  Andreas Kusalananda Kähäri authored 13 years ago
  
  decde51d
- In load_registry_from_multiple_dbs(): Initialize the hash with () rather · 3da13218
  Andreas Kusalananda Kähäri authored 13 years ago
```
than {}.
```
  3da13218
- Bug fixes for deprecate detection, truncated code sections · 58af92dd
  Kieron Taylor authored 13 years ago
  
  58af92dd
- Correct broken Sybase connection string. · 6094a8a8
  Andreas Kusalananda Kähäri authored 13 years ago
  
  6094a8a8
- Don't confuse user with %_stable_id tables. · a7810af3
  Andreas Kusalananda Kähäri authored 13 years ago
  
  a7810af3
- Better version. · 13625bd7
  Andreas Kusalananda Kähäri authored 13 years ago
  
  13625bd7
- merging changes from branch-ensembl-64 · ad3ae9e9
  Simon Brent authored 13 years ago
  
  ad3ae9e9