Commits · 82c1d3a1ffed9ad60f4dd7f4651f6f8c543e07e8 · ensembl-gh-mirror / ensembl

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Oct 18, 2004
- -dumpcheck option added which will not dump out the fasta files if they already exist · 82c1d3a1
  Ian Longden authored 20 years ago
  
  82c1d3a1
- updated pods · 97a51fd4
  Arne Stabenau authored 20 years ago
  
  97a51fd4
- Bug fix: was calling options() rather than $self->options() and so getting the... · 7d378dac
  Glenn Proctor authored 20 years ago
```
Bug fix: was calling options() rather than $self->options() and so getting the wrong set of options sometimes.
```
  7d378dac
- removed probeset from affy_feature · e69702ac
  Arne Stabenau authored 20 years ago
  
  e69702ac
- Shortened names of Genoscope_predicted_transcript and Genoscope_predicted_gene... · 91a19cf7
  Glenn Proctor authored 20 years ago
```
Shortened names of Genoscope_predicted_transcript and Genoscope_predicted_gene for mart compatibility.
```
  91a19cf7
- Changed max width of external_db.dbname to 27 for mart compatibility. · 81f466ac
  Glenn Proctor authored 20 years ago
  
  81f466ac
Oct 15, 2004
- Added storing of ensembl object types for dependent xrefs. · f3955264
  Glenn Proctor authored 20 years ago
  
  f3955264
- Added dumping of object_xref entries for dependent xrefs. · 087be40d
  Glenn Proctor authored 20 years ago
  
  087be40d
- removed probeset column from affy_feature table · 87ee1a96
  Arne Stabenau authored 20 years ago
  
  87ee1a96
- added Affy tables · ed55a5f0
  Arne Stabenau authored 20 years ago
  
  ed55a5f0
- uuups left one failing in there ... · 02121894
  Arne Stabenau authored 20 years ago
  
  02121894
- affy tables added, pre;liminary, no performance checks done yet · 019b57e2
  Arne Stabenau authored 20 years ago
  
  019b57e2
- more tests · 20c5c35c
  Arne Stabenau authored 20 years ago
  
  20c5c35c
- tests for affy adaptor functionality · 2fa1fc8e
  Arne Stabenau authored 20 years ago
  
  2fa1fc8e
- extensions/bugfixes · dc747ab5
  Arne Stabenau authored 20 years ago
  
  dc747ab5
- Implementing AffyAdaptors · 9821b80f
  Arne Stabenau authored 20 years ago
  
  9821b80f
- make AffyAdaptors available · 26d8988b
  Arne Stabenau authored 20 years ago
  
  26d8988b
- adding a general fetch_all() · 4f6ef05c
  Arne Stabenau authored 20 years ago
  
  4f6ef05c
- adding get_all_Affyfeatures · b2ff8a22
  Arne Stabenau authored 20 years ago
  
  b2ff8a22
Oct 13, 2004
- make sure path is absolute else lsf barfs when coping files back · 268cd12b
  Ian Longden authored 20 years ago
  
  268cd12b
- LSF job number is now stored in standard output and error file names to prevent ambiguities. · 2be298aa
  Glenn Proctor authored 20 years ago
  
  2be298aa
- Removed debug. · 96f6e54b
  Glenn Proctor authored 20 years ago
  
  96f6e54b
- Removed debug. · 3457b792
  Glenn Proctor authored 20 years ago
  
  3457b792
- Fixed dependent xref dumping SQL. · f693f3b3
  Glenn Proctor authored 20 years ago
  
  f693f3b3
- pass xref to method xref and no longer pass it as an argument in other methods · 7cdcfc14
  Ian Longden authored 20 years ago
  
  7cdcfc14
- add method to access xref obj instead of passing it around all over the place · 9dda83a5
  Ian Longden authored 20 years ago
  
  9dda83a5
- Exonerate output files now indude sequence type (dna or prot) to allow... · 41c621f9
  Glenn Proctor authored 20 years ago
```
Exonerate output files now indude sequence type (dna or prot) to allow determination of what sort of Ensembl objects to link them to when building the object_xref table.
```
  41c621f9
- Various changes to integrate better with config system. · 78b6a763
  Glenn Proctor authored 20 years ago
  
  78b6a763
Oct 12, 2004
- Added alt_allele table. Updated schema version to 26. · aeeab642
  Glenn Proctor authored 20 years ago
  
  aeeab642
- Updated to work with latest version of Saxon. · 838ab37f
  Glenn Proctor authored 20 years ago
  
  838ab37f
- store() now looks in correct directory for exonerate output files. · bd8a7bc6
  Glenn Proctor authored 20 years ago
```
Documentation.
```
  bd8a7bc6
Oct 11, 2004
- More tweaks - some places need path, some need just filename. · e1ad7a99
  Glenn Proctor authored 20 years ago
  
  e1ad7a99
- Minor tweaks to get it working with BasicMapper. · 74b10270
  Glenn Proctor authored 20 years ago
```
calculate_num_jobs now returns at least 1 job.
```
  74b10270
- Removed - functionality now in BasicMapper.pm · c70d4ffb
  Glenn Proctor authored 20 years ago
  
  c70d4ffb
- Added mapping stuff from old exonerate_prototype.pl · bc80daea
  Glenn Proctor authored 20 years ago
  
  bc80daea
- documentation and tidy up · 3bc4c26c
  Ian Longden authored 20 years ago
  
  3bc4c26c
Oct 08, 2004
- bugfix and adding of overlap_size method · 32dff732
  Arne Stabenau authored 20 years ago
  
  32dff732
- added test for suspected problem and for overlap size function · bc9c4ae5
  Arne Stabenau authored 20 years ago
  
  bc9c4ae5
- additional index for evidence table · 63dec523
  Steve Trevanion authored 20 years ago
  
  63dec523
Oct 07, 2004
- run_matching now needs xref to get the xref fasta files · f0153fec
  Ian Longden authored 20 years ago
  
  f0153fec