Commits · 665249a9bb8017180654b8a97a72c5e3bd8292a5 · ensembl-gh-mirror / ensembl

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Aug 08, 2011
- Nope, those TODOs were wrong... Need to filter the parsed result. · 665249a9
  Andreas Kusalananda Kähäri authored 13 years ago
  
  665249a9
- write_filtered_exons(): Slight formatting and adding TODO comments so · 4973c513
  Andreas Kusalananda Kähäri authored 13 years ago
```
that I remmeber where I'm at tomorrow... or the next day.
```
  4973c513
- Added missing sources for the following species: microcebus_murinus, otolemur_garnettii, · 996b6d59
  Monika Komorowska authored 13 years ago
```
sorex_araneus
```
  996b6d59
- Reformat build_overlap_scores(). · c41192d5
  Andreas Kusalananda Kähäri authored 13 years ago
  
  c41192d5
- In build_overlap_scores(): Only add target if $add_target is non-zero, · 6b4713ec
  Andreas Kusalananda Kähäri authored 13 years ago
```
just as is done for adding source.
```
  6b4713ec
- Snapshot in the middle of the cycle for release 64. · 6a698848
  Andreas Kusalananda Kähäri authored 13 years ago
  
  6a698848
Aug 05, 2011
- Removed empty documentation tags (that might confuse the sql2html.pl script). · fb4878f5
  Andreas Kusalananda Kähäri authored 13 years ago
  
  fb4878f5
- Add a "Back to top" link for each table · a459b4d8
  Laurent Gil authored 13 years ago
  
  a459b4d8
Aug 04, 2011
- In parsing_finished_store_data(): · c16ff7c2
  Andreas Kusalananda Kähäri authored 13 years ago
```
If the table (either xref or object_xref) is empty, $max_val will be
undefined.  Make sure that we substitute 1 for it in this case when
calling add_meta_pair().
```
  c16ff7c2
- In fetch_files(): · 42a67c81
  Andreas Kusalananda Kähäri authored 13 years ago
```
Use -s to determine if a file previously fetched is not only there but
also if it's non-empty.  If the file is empty, unlink it and fetch it
again.

Also, clean-up.
```
  42a67c81
- Make sure the percent is an integer in run_exonerate(). · 4d979b1c
  Andreas Kusalananda Kähäri authored 13 years ago
  
  4d979b1c
- Modify the static meta table data for patches in release 64, and update · 988d905a
  Andreas Kusalananda Kähäri authored 13 years ago
```
schema version to 64 too.
```
  988d905a
Aug 02, 2011
- Added new species - sorex_araneus · 74887ae1
  Monika Komorowska authored 13 years ago
  
  74887ae1
- Correct bug in documentation. · c1381233
  Andreas Kusalananda Kähäri authored 13 years ago
  
  c1381233
- updated adaptors to handle analysis types for operons and their transcripts · 49bf7bab
  Dan Staines authored 13 years ago
  
  49bf7bab
Aug 01, 2011
- Added info_type is null condition to xref sql · 3bae0460
  Monika Komorowska authored 13 years ago
  
  3bae0460
- Added mouse lemur and bushbaby to species list · 593ee270
  Monika Komorowska authored 13 years ago
  
  593ee270
Jul 29, 2011
- If previous release of core defined in config, use it for tests · 79014fa9
  Monika Komorowska authored 13 years ago
  
  79014fa9
- Added previous release to xref_config.ini · e3b360a0
  Monika Komorowska authored 13 years ago
  
  e3b360a0
- Updated sources for c. intestinalis · d3cc5a46
  Monika Komorowska authored 13 years ago
  
  d3cc5a46
Jul 28, 2011
- Changed exec() to system() · f2ad3dd2
  Monika Komorowska authored 13 years ago
  
  f2ad3dd2
Jul 27, 2011
- Added taxon and species_prefix columns to species table. · 02c83f01
  Monika Komorowska authored 13 years ago
  
  02c83f01
- added method fetch_all_by_Operon and extended support to Operon and OperonTranscript · 23250db7
  Dan Staines authored 13 years ago
  
  23250db7
- Added defined condition before using value in calculations · 1f134247
  Monika Komorowska authored 13 years ago
  
  1f134247
- Updated sql to get only vega ids where accession and diplay label are different · 9fc48ab3
  Monika Komorowska authored 13 years ago
  
  9fc48ab3
Jul 26, 2011
- Added tests for defined values before using them in calculations · fe635f05
  Monika Komorowska authored 13 years ago
  
  fe635f05
Jul 25, 2011
- Get descriptions from _mRNA and _ncRNA · e36a6985
  Ian Longden authored 13 years ago
  
  e36a6985
- Added the new refseq sources _mRNA and _ncRNA · 3ac96484
  Ian Longden authored 13 years ago
  
  3ac96484
- update for release 64 · 68041e25
  Ian Longden authored 13 years ago
  
  68041e25
- Changed new species query to use db release instead of is_current, in case · 51a8ef93
  Monika Komorowska authored 13 years ago
```
the is_current field is not updated.
```
  51a8ef93
Jul 22, 2011
- $API_VERSION =~ s/63/64/ · c6688f85
  Miguel Pignatelli authored 13 years ago
  
  c6688f85
- deleted debug line · 49ae4a46
  Ian Longden authored 13 years ago
  
  49ae4a46
- fix for errors in getting a database connection when in... · e5d291dc
  Ian Longden authored 13 years ago
```
fix for errors in getting a database connection when in disconnect_when_inactive set and is being called to0 fast for the system to keep up with
```
  e5d291dc
Jul 21, 2011
- ensembl_object_type column is not null · 853ff6d3
  Magali Ruffier authored 13 years ago
  
  853ff6d3
- added is_ref to see if gene is the reference gene · a03738a6
  Ian Longden authored 13 years ago
  
  a03738a6
- changed is_ref to is_reference · cada933e
  Ian Longden authored 13 years ago
  
  cada933e
- is_ref added to alt_allele · 7e3e149b
  Ian Longden authored 13 years ago
  
  7e3e149b
Jul 20, 2011
- added is)ref to alt_allele table to say which is the reference allele · 50aecca5
  Ian Longden authored 13 years ago
  
  50aecca5
- patch to bring in operon model tables · 7b05e45f
  Dan Staines authored 13 years ago
  
  7b05e45f
Jul 14, 2011
- perlcritic level 5 fixes · 98a44bc7
  Ian Longden authored 13 years ago
  
  98a44bc7