Commits · aa7542e797bfb35469ef38ed86e7e4a041dcf8ce · ensembl-gh-mirror / ensembl · GitLab

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Feb 01, 2023.

09 Jan, 2015 1 commit
- update annual copyright to 2015 · aa7542e7
  Magali Ruffier authored Jan 09, 2015
  
  aa7542e7
07 Jan, 2015 6 commits
- ENSCORESW-764 : added Reactome source for all Ensembl species · 7824fe3c
  Magali Ruffier authored Jan 07, 2015
  
  7824fe3c
- ENSCORESW-764: new parser for reactome data · 12eef413
  Magali Ruffier authored Jan 07, 2015
```
this is a direct parser, as they already provide the links to Ensembl annotations
```
  12eef413
- ENSCORESW-764 : if uri is home page, create a name · 0a451857
  Magali Ruffier authored Jan 07, 2015
  
  0a451857
- if prefix exists, it needs to stay in the dbname · 80e729b0
  Magali Ruffier authored Dec 23, 2014
  
  80e729b0
- add a db_prefix option to correctly detect species and dbtype in presite databases · 4541c521
  Magali Ruffier authored Dec 23, 2014
  
  4541c521
- ENSCORESW-1193 : added is_empty method to check if there is genome data available · 80e8a271
  Magali Ruffier authored Jan 07, 2015
  
  80e8a271
23 Dec, 2014 6 commits
- when checking for duplicates, ignore version · 607d302f
  Magali Ruffier authored Dec 23, 2014
  
  607d302f
- updated test cases to include bam.bw extensions · 8adc0b52
  Magali Ruffier authored Dec 23, 2014
  
  8adc0b52
- ENSCORESW-1191 : added some example input · d43fa2e8
  Magali Ruffier authored Dec 23, 2014
  
  d43fa2e8
- Merge branch 'master' of https://github.com/Ensembl/ensembl · 280d878e
  Magali Ruffier authored Dec 23, 2014
  
  280d878e
- ENSCORESW-1191: regex updated to catch Name and Synonyms across multiple... · b61e8e62
  Magali Ruffier authored Dec 23, 2014
```
ENSCORESW-1191: regex updated to catch Name and Synonyms across multiple lines, with possible evidence codes
```
  b61e8e62
- if deleting everything from the table, use truncate as it is quicker · ef95d770
  Magali Ruffier authored Dec 23, 2014
  
  ef95d770
19 Dec, 2014 2 commits
- Merge pull request #49 from khowe/master · 26f380b5
  Kieron Taylor authored Dec 19, 2014
```
Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources
```
  26f380b5
- [ENSCORESW-1198 ]. Support for BigWIg BAM rnaseq data. · 33997813
  Alessandro Vullo authored Dec 19, 2014
  
  33997813
16 Dec, 2014 3 commits
- Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources · 95d7d298
  Kevin Howe authored Dec 16, 2014
  
  95d7d298
- Merge pull request #48 from khowe/master · 2007c4d8
  Alessandro Vullo authored Dec 16, 2014
```
Fixed bug with replacement of petpide ambiguity chars with X
```
  2007c4d8
- Fixed bug with replacement of petpide ambiguity chars with X · f0eff3b4
  Kevin Howe authored Dec 16, 2014
  
  f0eff3b4
15 Dec, 2014 8 commits
- ENSCORESW-1120 : added is_high_coverage flag for genome container · e148443a
  Magali Ruffier authored Dec 15, 2014
  
  e148443a
- ENSCORESW-1120 : new method to check if a genome has a karyotype (ie chromosomes) · f5421889
  Magali Ruffier authored Dec 15, 2014
  
  f5421889
- ENSCORESW-1127 : TSL and gencode_basic tags added to gtf dumps as per gencode specifications · 24d38fdb
  Magali Ruffier authored Dec 15, 2014
  
  24d38fdb
- Merge branch 'master' of https://github.com/Ensembl/ensembl · 8abe38aa
  Magali Ruffier authored Dec 15, 2014
  
  8abe38aa
- [ENSCORESW-1190 ]. Parse GOA Uniprot release correctly. · 70110e27
  Alessandro Vullo authored Dec 15, 2014
  
  70110e27
- UniGene source available for olive baboon · 93118178
  Magali Ruffier authored Dec 15, 2014
  
  93118178
- ENSCORESW-1189 : group is a chromosome · f2ca00f5
  Magali Ruffier authored Dec 15, 2014
  
  f2ca00f5
- use direct sql for checksum, as there are no identity xrefs for those · 564cbf8c
  Magali Ruffier authored Dec 15, 2014
  
  564cbf8c
12 Dec, 2014 7 commits
- some syntax errors · 68cb623c
  Magali Ruffier authored Dec 12, 2014
  
  68cb623c
- ensure everyone gets emailed if travis build fails · 4161d648
  Magali Ruffier authored Dec 12, 2014
  
  4161d648
- [ENSCORESW-1117 ]. Emptied table (not necessary) so that SQLite tests succeeds. · 7b9dd143
  Alessandro Vullo authored Dec 12, 2014
  
  7b9dd143
- more \N removed · ae8c1bdf
  Magali Ruffier authored Dec 12, 2014
  
  ae8c1bdf
- Revert "ENSCORESW-1116: first attempt at storing some form of scoring in the overlap mappings" · 3c79026d
  Magali Ruffier authored Dec 12, 2014
```
overlap score is not identity score, we get the identity from the alignments instead
This reverts commit 26152269.
```
  3c79026d
- removed \N in description · c8db3919
  Magali Ruffier authored Dec 12, 2014
  
  c8db3919
- ENSCORESW-1116 : keep alignment score even if overlap takes priority · a040bead
  Magali Ruffier authored Dec 12, 2014
  
  a040bead
11 Dec, 2014 5 commits
- SQLite table definition for the polyploid test database. · a12773e4
  Alessandro Vullo authored Dec 11, 2014
  
  a12773e4
- MySQL < 5.5 compatible definition so that travis is happy. · 0de4ff0b
  Alessandro Vullo authored Dec 11, 2014
  
  0de4ff0b
- Documentation. · d2e16dc7
  Alessandro Vullo authored Dec 11, 2014
  
  d2e16dc7
- [ENSCORESW-1117 ]. Method to access the list of all top level slices for a given genome component. · 775da1f9
  Alessandro Vullo authored Dec 11, 2014
  
  775da1f9
- [ENSCORESW-1117 ]. Test fetch_all_by_genome_component method. · 950d35f4
  Alessandro Vullo authored Dec 11, 2014
  
  950d35f4
10 Dec, 2014 2 commits
- [ENSCORESW-1117 ]. Get the list of genome components for a polyploid genome. · ea945dc6
  Alessandro Vullo authored Dec 10, 2014
  
  ea945dc6
- [ENSCORESW-1117 ]. Test getting the list of genome components. · ce272c1e
  Alessandro Vullo authored Dec 10, 2014
  
  ce272c1e