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Created with Raphaël 2.2.012Oct111076543230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar302928242322211816151411109874updated sources for S. mansoni and T. adhaerensstable_id merge changesFix SQL line with too much space in it.Specific logic for assignment of gene names and description valid for all Ensembl Genomes species at the exception of a few species (e.g. S. pombe or S. cer)Added a repeated warning suppression for absent adaptor or dbIDstable_id merge changesAdded EG11 plants and protists sources and species. Also added S. pombe sources and speciesuse POSIX.Mark two of the options as not currently implemented, until I implementanother name chnage in expr to match file name changeonly get species_id if doing official namingchange pass variable name to passive to make it more obvious. Bettere checking of ftp statusfile name changed so change expr to matchDump of the production database before genebuild handover for release 65.LSF dependencies removed. Correction of sql statement to get the list of cores.Dates changed in the copyright notice.Date and version changed.Bash script to compute the splicing events on a core database and to writeDocumentation to compute the alternative splicing events in one go.release file not neededDie with message if mysqldump fails.Formatting and dumping of existing analysis_description table using mysqldump.Formatting, mostly.Util library Makefile.amAlternative Splicing GFF parser library Makefile.amAlternative splicing library Makefile.amCPPFLAGS added (extra flags for includes)Updated for the 0.5.4 version of the toolkitExtra documentation on the installation process for the Ensembl team.Readablility.Be specific about what table 'created_date' and 'modified_date' are in.re-instated variation id dumpingadded release info for new refseq sourceschanged refseq_dna to refseq_mRNA and Refseq_ncRNADrop external_db_id from call to get_synonyms() as it is notIn map_stable_ids(): Only add mapping events if the stable ID hasadded another ignore sql statement for Uniprot/SPTREMBL priority_description protein_evidence_gt_3update ignore hashupdate ignore sql statement for EntrezGeneFixed ignore sql that was broken for ignoring entrezgene names if they came via refseq_predicted