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Created with Raphaël 2.2.09Jan87421Dec20191817141312111076543230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun28272625added test cases for undefined objectsfetch_all_by_ method expanded to work even if no object is called onpatch submitted by ak4. --dumppath flag is not needed unless -dropbaks is onOnly use the coordinates with the smaller seq_region_id (usually 1-22,X,Y) to avoid mapping the LRG to the patch regionOnly use the coordinates with the smaller seq_region_id (usually 1-22,X,Y) to avoid mapping the LRG to the patch regionUses the new Net moduleKaryotype assigner. Don't like it being here but it's got to go in.Adding net based modulesAdded UniGene::* plants specific sources, and IPI::arabidopsis_thaliana sourceAdded UniGene::* plants specific sources, and IPI::arabidopsis_thaliana sourceInitial commit. Written by Mikkel. Mikkel is doing something kinky with source ids.Improved variable names. Mikkel is doing something kinky with source ids.Added gene_display_xref_sources subroutine.Add synonym sources for vectorbase species.Updated formatting for links to GO_REFNever allow someone to commit a MultiTestDB fileHave added all plants missing species, plus all gramene plants speciesHave added all plants missing species, plus all gramene plants speciesMove link for pub to PMC and stopped printing of extra evidence rows when it is redundant. For function get_extensionsHave replaced the deprecated "fetch_all_failed_jobs" by "fetch_all_by_analysis_id_status".New object to represent collections of alt alleles.check if source is HGNC or MGIdo not project all sourcesdo not add version numbers for uniprot gene namesnot all species have a common name, use production_name as a key insteadFixed an inaccurate value to be stored in the db.Fix to extension URLsTrying to improve the readmesVery basic gff serialiser testDo not add trailing ; since this is not part of the allowed specCopy is_patch onto branch 66 now that anacode have moved on. -- ds23cvs/release/ens…cvs/release/ensembl/66 release/66 upstream/release/66Update branch 66 now loutre is on 66 to allow empty params as not missing, asLoutre password is optional onto 66 because loutre is now on 66 schema.Add get_annotrack_params to branch 66 for loutre.Adding a no_error flag to allow for simple single value querying where the number of rows returned could be ambigiousGetting rid of a script which still refers to the contig tableGo through an object and make sure everything is populated once we go through a call of $gene->load().Added the method get_all_StructuralVariationFeatures_by_size_rangeAdding get_all_IntronSupportingEvidence()Adding documentation and also switching to using type