Commits · 935fe43caf22c6f8ad5e421fb8b5ef3891832045 · ensembl-gh-mirror / ensembl

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Jun 25, 2012
- Doh! If they're not the same then die. Not if they are the same · 935fe43c
  Andy Yates authored 12 years ago
  
  935fe43c
- Bad sprintf · 095aec57
  Andy Yates authored 12 years ago
  
  095aec57
- Wrong method call · 16da63c2
  Andy Yates authored 12 years ago
  
  16da63c2
- Adding a check to make sure we always have a fully populatted concatented gz file · 5894413b
  Andy Yates authored 12 years ago
  
  5894413b
- store description instead of accession in the label field... · c85cdf18
  Monika Komorowska authored 12 years ago
```
store description instead of accession in the label field http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-180
```
  c85cdf18
- don't parse Orphanet xrefs from UniProt http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-180 · 9395ce34
  Monika Komorowska authored 12 years ago
  
  9395ce34
- updated example for fetch_all_by_display_label · f7a8e65b
  Monika Komorowska authored 12 years ago
  
  f7a8e65b
- Additional patch to bring in version into the unique key for xref. Also apply... · e3b39cb6
  Andy Yates authored 12 years ago
```
Additional patch to bring in version into the unique key for xref. Also apply changes to gene and transcript
```
  e3b39cb6
Jun 23, 2012
- Adding type into the dir name. Makes it a lot easier to generate the different types of indexes · 8ad112e4
  Andy Yates authored 12 years ago
  
  8ad112e4
- Adding a softmasking blat indexer · a154aebb
  Andy Yates authored 12 years ago
  
  a154aebb
Jun 22, 2012
- More docs · a3ac663a
  Andy Yates authored 12 years ago
  
  a3ac663a
- release is a required parameter · 3953f0f7
  Andy Yates authored 12 years ago
  
  3953f0f7
- adding debug · bdd4a319
  Andy Yates authored 12 years ago
  
  bdd4a319
- Filter was not firing correctly · 81a03a93
  Andy Yates authored 12 years ago
  
  81a03a93
- switching from ok to is & Test::More · 2223def0
  Andy Yates authored 12 years ago
  
  2223def0
- RFAM::EG needs to use the CoreXrefParser · fb266ae2
  Monika Komorowska authored 12 years ago
  
  fb266ae2
- load registry in the main parser · 50996c8c
  Monika Komorowska authored 12 years ago
  
  50996c8c
- Ensembl version of the RFAMParser is not needed · ed1645c7
  Monika Komorowska authored 12 years ago
  
  ed1645c7
- RFAM xrefs need to be parsed using CoreXrefParser for EnsemblGenomes · 931f34a4
  Monika Komorowska authored 12 years ago
  
  931f34a4
- Missed dog and made more species alphabetical · f0f5d623
  Andy Yates authored 12 years ago
  
  f0f5d623
- removed warning in store_alt_alleles when none of the alt_alleles in a set is... · 77f20df7
  Monika Komorowska authored 12 years ago
```
removed warning in store_alt_alleles when none of the alt_alleles in a set is on reference sequence - this is a valid case and doesn't require a warning
```
  77f20df7
- changed miRBase to miRBase::MULTI · 9e5ca802
  Monika Komorowska authored 12 years ago
  
  9e5ca802
- changed miRBase to miRBase::MULTI · b770b554
  Monika Komorowska authored 12 years ago
  
  b770b554
- Allowing backups to go to a directory other than our current working... · 6fe52774
  Andy Yates authored 12 years ago
```
Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas
```
  6fe52774
- changed source definition for RNAMMER and TRNASCAN_SE · 33ae6905
  Monika Komorowska authored 12 years ago
  
  33ae6905
- RFAMParser which loads the registry with EnsemblGenomes databases · eb20db7a
  Monika Komorowska authored 12 years ago
  
  eb20db7a
- generic RFAMParser which RFAMParser_E and RFAMParser_EG inherit from · 4749b9f8
  Monika Komorowska authored 12 years ago
  
  4749b9f8
- RFAMParser which loads the registry with EnsEMBL databases · d8a1585c
  Monika Komorowska authored 12 years ago
  
  d8a1585c
- parser for xrefs from core which are generated by an analysis straight into a core db · 08911acf
  Monika Komorowska authored 12 years ago
  
  08911acf
- removed duplicate store method · b1608d60
  Magali Ruffier authored 12 years ago
```
does not store density feature with value of 0
```
  b1608d60
- updated the $option in repeat coverage case . Repeat coverage script now use... · 72f91cf9
  Thomas Maurel authored 12 years ago
```
updated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.
```
  72f91cf9
- updated the help, the script now use "-pattern" to find a database instead of "-p". · 2f97d9c6
  Thomas Maurel authored 12 years ago
  
  2f97d9c6
- Replaced "$option" from "-d" to "-pattern" for the percent_gc script. · 0df8692c
  Thomas Maurel authored 12 years ago
  
  0df8692c
Jun 21, 2012
- deleted unnecessary module import · e171eaab
  Monika Komorowska authored 12 years ago
  
  e171eaab
- when the band is at the end of the chromosome, make sure the two ends match · 4478c0dc
  Magali Ruffier authored 12 years ago
  
  4478c0dc
- I have added the softshell turtle ( psinensis ) to the projections. · dbc75ca6
  Thomas Maurel authored 12 years ago
  
  dbc75ca6
- Fixing a bug brought up by Nathan where we used version in the select for an xref_id. · fde3eb03
  Andy Yates authored 12 years ago
  
  fde3eb03
- fix module name · 2e97bb88
  Monika Komorowska authored 12 years ago
  
  2e97bb88
- added empty line after _store_or_fetch_xref_pod · 58eda2b0
  Nathan Johnson authored 12 years ago
  
  58eda2b0
- Missing xenopus from the execution order list · a676b36b
  Andy Yates authored 12 years ago
  
  a676b36b