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Created with Raphaël 2.2.010Nov9763231Oct252423201918111065327Sep252221201918131131Aug3024232117109872124Jul201917121110654328Jun27232116141396131May262419171110327Apr2013117428Mar232221171332128Feb2722151487131Jan30272625241817965415Dec139829Nov2421181611974228Oct2120141311754329Sep272623222120161514131286231Aug2625221918171615121153227Jul2521201911875128Jun2423171614109732131May2524171611109654329Apr251913118531Mar232118161510225Feb2423191817161512429Jan2625222118151211875418Dec1514111084321Merge pull request #220 from muffato/masterMade the script executableENSCORESW-2485: do not delete all possible mappingsMerge branch 'master' of https://github.com/Ensembl/ensemblkeep old mappings, always create new entrycapture mRNA for peptide informationkeep failed_cutoff to store alignment scoresbugfix: not all users require a passwordMerge pull request #219 from Ensembl/avullo-patch-1Create PULL_REQUEST_TEMPLATE.mdDelete PULL_REQUEST_TEMPLATE.md[ENSCORESW-2230]. Checking whether the same fragment is mapped to a different seq_region relies on checking[ENSCORESW-2428]. This is the full template with an added section about testing and improved formatting.[ENSCORESW-2428]. Use nested indentation properly.[ENSCORESW-2428]. PR template should be complete.Merge branch 'master' of https://github.com/Ensembl/ensembl[ENSCORESW-2428]. Initial skeleton template for PRs.Merge pull request #218 from ens-lgil/masterAdd tests for the method 'summary_as_hash'[ENSCORESW-2343]. Core triggers dependent build on Variation.Extra parameters for the REST endpoint 'overlap/translation'. Will be needed for a mapping to the PDB coordinates in a tool/feature using it[ENSCORESW-2343]. Core triggers dependent build on VEP.config update for 91separate VGNC parser, simplified from HGNCMerge branch 'master' into experimental/mapper_update[ENSCORESW-2276]. Documentation synched with reality.[ENSCORESW-2289]. Recalculate coordinates of projected slice segments using the values returned by invoking the[ENSCORESW-2289]. Consider returning original coordinates in all cases.[ENSCORESW-2289]. Match signature of ChainedAssemblyMapper.[ENSCORESW-2289]. Consider necessary option for Slice::project.[ENSCORESW-2289]. Call underlying mapper code to return original and mapped coordinates. More uniform function prototype to allow transparent calls from Slice project method.[ENSCORESW-2168]. Consider the indel case.[ENSCORESW-2168]. Use interval tree API, discard binary search.Merge branch 'master' into experimental/mapper_update[ENSCORESW-2168]. Use simplified interval tree API, discard binary search.[ENSCORESW-2168]. Simplified API, allow passing only boundaries.updates to Exon is_coding routine to handle cases where the coding region boundry falls within the exon boundry - ENSCORESW-2465[ENSCORESW-2168]. There can be zero coordinates.[ENSCORESW-2168]. Must allow zero coordinates but not undefined ones.[ENSCORESW-2168]. Return query results sorted by start coordinate to harmonise with mapper code.