Commits · b1608d60e7bdfece7f8435f89c2a67a587ff2b26 · ensembl-gh-mirror / ensembl

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Jun 22, 2012
- removed duplicate store method · b1608d60
  Magali Ruffier authored 13 years ago
  b1608d60
- updated the $option in repeat coverage case . Repeat coverage script now use... · 72f91cf9
  Thomas Maurel authored 13 years ago
  72f91cf9
- updated the help, the script now use "-pattern" to find a database instead of "-p". · 2f97d9c6
  Thomas Maurel authored 13 years ago
  
  2f97d9c6
- Replaced "$option" from "-d" to "-pattern" for the percent_gc script. · 0df8692c
  Thomas Maurel authored 13 years ago
  
  0df8692c
Jun 21, 2012
- deleted unnecessary module import · e171eaab
  Monika Komorowska authored 13 years ago
  
  e171eaab
- when the band is at the end of the chromosome, make sure the two ends match · 4478c0dc
  Magali Ruffier authored 13 years ago
  
  4478c0dc
- I have added the softshell turtle ( psinensis ) to the projections. · dbc75ca6
  Thomas Maurel authored 13 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 13 years ago
  
  fde3eb03
- fix module name · 2e97bb88
  Monika Komorowska authored 13 years ago
  
  2e97bb88
- added empty line after _store_or_fetch_xref_pod · 58eda2b0
  Nathan Johnson authored 13 years ago
  
  58eda2b0
- Missing xenopus from the execution order list · a676b36b
  Andy Yates authored 13 years ago
  
  a676b36b
- Switch back to mydir so we don't use a person's own directory · 78bd5c7a
  Andy Yates authored 13 years ago
  
  78bd5c7a
- Cannot have an alias for print and we never did · 5ece2d5f
  Andy Yates authored 13 years ago
  
  5ece2d5f
- Switch to using get_all_GeneMembers() which is the supported API in 68 · b48c591d
  Andy Yates authored 13 years ago
  
  b48c591d
- added RFAM::EG source · 239893e8
  Monika Komorowska authored 13 years ago
  
  239893e8
- RFAM parser for ensembl genomes · df160679
  Monika Komorowska authored 13 years ago
  
  df160679
- Return 1 if we unlinked the file. Otherwise return 0 · bf90fd82
  Andy Yates authored 13 years ago
  
  bf90fd82
- Die if we had no files · acb18be4
  Andy Yates authored 13 years ago
  
  acb18be4
Jun 20, 2012
- fix to make sure that dbname takes priority over pattern · 319742e3
  Dan Staines authored 13 years ago
  
  319742e3
- no clone coordinate system in mouse exists in the new assembly, don't project... · f017c309
  Monika Komorowska authored 13 years ago
  f017c309
- fixed output message · 2e4b0861
  Monika Komorowska authored 13 years ago
  
  2e4b0861
- corrected file names - fix for Exonerate method override change · 3043d3eb
  Monika Komorowska authored 13 years ago
  
  3043d3eb
- new parser for RFAM xrefs, replaces use of ncRNA_DBParser in ensembl · 35cf179e
  Monika Komorowska authored 13 years ago
  
  35cf179e
- new parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensembl · 3c361f02
  Monika Komorowska authored 13 years ago
  
  3c361f02
- replaced source ncRNA::MULTI with RFAM::MULTI and miRBase::MULTI · d9482c27
  Monika Komorowska authored 13 years ago
  
  d9482c27
Jun 19, 2012
- Prefer sub ref to dereference · 01cb9d51
  Andy Yates authored 13 years ago
  
  01cb9d51
- Assignment bug; we did not want the cache assigned to the ID of the seq region... · 00d41af5
  Andy Yates authored 13 years ago
  00d41af5
- Fixed an inappropriate method of getting species aliases and changed a couple... · 5f353122
  Kieron Taylor authored 13 years ago
  5f353122
- Using the "best" HTTP client available i.e. avoid making people install LWP if... · 6ebe1736
  Andy Yates authored 13 years ago
  6ebe1736
- Asking if a dereferenced array ref is undefined is not testing what you think... · bcafe963
  Andy Yates authored 13 years ago
  bcafe963
Jun 18, 2012
- Removing seek() call and not using the filesystem. IO::String does the same job · 21c43846
  Andy Yates authored 13 years ago
  
  21c43846
- Stop accidental cleanup of databases during object cleanup · 5009ec78
  Andy Yates authored 13 years ago
  
  5009ec78
- correct type of compara db handle, method to remove duplicate attrib values · 080bd8ad
  Steve Trevanion authored 13 years ago
  
  080bd8ad
- added missing ncRNA sources · a50b9e98
  Magali Ruffier authored 13 years ago
  
  a50b9e98
- Change of content · 5ecbc0c4
  Andy Yates authored 13 years ago
  
  5ecbc0c4
- Simplification of the select. The query for select used fields which are not... · b3f7a9d0
  Andy Yates authored 13 years ago
  b3f7a9d0
Jun 15, 2012
- Missed the multiple mapping behaviour. Moved code inside the loop. · 13e51acd
  Kieron Taylor authored 13 years ago
  
  13e51acd
- Updating GFF parser tests · 64e00f69
  Andy Yates authored 13 years ago
  
  64e00f69
- support for empty lines and fasta sequence section · ee9aabdf
  Monika Komorowska authored 13 years ago
  
  ee9aabdf
- Rename of the schema · af53381b
  Andy Yates authored 13 years ago
  
  af53381b