Commits · b1608d60e7bdfece7f8435f89c2a67a587ff2b26 · ensembl-gh-mirror / ensembl

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Jun 22, 2012
- 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
May 10, 2012
- changes to provide multispecies support and also to use a unified command line... · ce96cdd8
  Dan Staines authored 12 years ago
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changes to provide multispecies support and also to use a unified command line processor (CliHelper)
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  ce96cdd8
May 08, 2012
- removed unnecessary array · aa3fa0c4
  Monika Komorowska authored 12 years ago
  
  aa3fa0c4
Apr 11, 2012
- store density features in batch · ca683575
  Monika Komorowska authored 12 years ago
  
  ca683575
- store density features in batch · 5cd7ec3b
  Monika Komorowska authored 12 years ago
  
  5cd7ec3b
- count only stored density features · 1fec175b
  Monika Komorowska authored 12 years ago
  
  1fec175b
- count only density features which have been stored · cde48eb3
  Monika Komorowska authored 12 years ago
  
  cde48eb3
- make sure dbs flagged as having variation positions changed have a variation db · 9cd98113
  Monika Komorowska authored 12 years ago
  
  9cd98113
Apr 10, 2012
- Setting small start to 0. This should be a safe thing to do looking at the currently logic usage. · d6247124
  Andy Yates authored 12 years ago
  
  d6247124
- This is an Ensembl script; defaults should reflect this & not other team's defaults · 6cff9789
  Andy Yates authored 12 years ago
  
  6cff9789
- added messages on how long each script takes to run on average · a171ed43
  Monika Komorowska authored 12 years ago
  
  a171ed43
- copy user and password from the first host, add memory limit of 2Gb · fe22129b
  Monika Komorowska authored 12 years ago
  
  fe22129b
Mar 06, 2012
- script can be executed from any directory · 6771a9c9
  Monika Komorowska authored 13 years ago
  
  6771a9c9
- script can be executed from any directory · b1fb38ca
  Monika Komorowska authored 13 years ago
  
  b1fb38ca
Jan 25, 2012
- Only allow a biotype if it had coding in there & not non_ which would negate the coding · 69895b28
  Andy Yates authored 13 years ago
  
  69895b28
Dec 08, 2011
- Updated the help wrt the production database commandline arguments · eb827e26
  Arnaud Kerhornou authored 13 years ago
  
  eb827e26
- Added commandline arguments for connecting ensembl_production db · 827fd6c2
  Arnaud Kerhornou authored 13 years ago
  
  827fd6c2
- added production database paramertes to make it work for Ensembl Genomes · 3c1bf83d
  Uma Maheswari authored 13 years ago
  
  3c1bf83d
Nov 30, 2011
- · 5096aae3
  Uma Maheswari authored 13 years ago
```
modified to add generic production database details
```
  5096aae3
- modified to add generic production database details · 83ed2b5f
  Uma Maheswari authored 13 years ago
  
  83ed2b5f
- Added muser, mhost and mport so we can pass as command arguments an... · 37515b04
  Arnaud Kerhornou authored 13 years ago
```
Added muser, mhost and mport so we can pass as command arguments an alternative server which hosts the ensembl_production database; updated the usage
```
  37515b04
Nov 02, 2011
- make them executable · 49f4f620
  Leo Gordon authored 13 years ago
  
  49f4f620
Nov 01, 2011
- disconnect from production database · d78004e9
  Monika Komorowska authored 13 years ago
  
  d78004e9
- populate analysis and analysis description if it's not already stored in the db · 3d13477a
  Monika Komorowska authored 13 years ago
  
  3d13477a
- disconnect from production database · 3dc1dd67
  Monika Komorowska authored 13 years ago
  
  3dc1dd67
- Corrected list of dbs for seq_region_stats snp count and variation_density. · 849d5fb3
  Monika Komorowska authored 13 years ago
```
The list will only contain species which have a variation db.
```
  849d5fb3
Sep 29, 2011
- Populating %attrib_codes hash from the biotype table in the production database · afd2cdde
  Monika Komorowska authored 13 years ago
  
  afd2cdde
Sep 27, 2011
- Don't delete the analysis and analysis description entries, update analysis creation date · 8b658086
  Monika Komorowska authored 13 years ago
  
  8b658086
- Don't delete the analysis and analysis description entries, update analysis creation date. · 06430119
  Monika Komorowska authored 13 years ago
  
  06430119
- added -s species to options · 9881f884
  Monika Komorowska authored 13 years ago
  
  9881f884
Sep 15, 2011
- Rolling back the code to 1.20 because of issues with re-binning the human Y... · 932cd31b
  Andy Yates authored 13 years ago
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Rolling back the code to 1.20 because of issues with re-binning the human Y chromsome density values resulting in a -ve value.
```
  932cd31b
Sep 14, 2011

Commit moved to HEAD from branch-64. Moved the slice fetch into the... · 4b4ab262

Andy Yates authored 13 years ago

Commit moved to HEAD from branch-64. Moved the slice fetch into the knowngenedensity/genedensity loop so we can continue to use shift to iterate through them

4b4ab262

Aug 16, 2011
- added new biotypes · a0df70c7
  Magali Ruffier authored 13 years ago
  
  a0df70c7
- when fetch all top level, fetch unpaired as well to include densities for the whole of chromosome Y · 8375391c
  Magali Ruffier authored 13 years ago
  
  8375391c
Aug 12, 2011
- Corrected syntax for loading dbs from the registry. · 93d8f73d
  Monika Komorowska authored 13 years ago
  
  93d8f73d
Jul 28, 2011
- Changed exec() to system() · f2ad3dd2
  Monika Komorowska authored 13 years ago
  
  f2ad3dd2
Jul 25, 2011
- Changed new species query to use db release instead of is_current, in case · 51a8ef93
  Monika Komorowska authored 13 years ago
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the is_current field is not updated.
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  51a8ef93