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Created with Raphaël 2.2.012Jun11876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130NovHack smell appearing. We have to recreate and gunzip the created file to do the hardmaskingSwitching the logic around here. It makes sense if we are trying to read from a file which hasn't closed yet then maybe we're not going to get all the data into the file.Trying something more spectacular to avoid this horrible truncation of the filecopy is on targetBetter documentationAdding softmasked as a type of file and improving error reportingMissing softmasked dataForgot the repeat masked flowMethod is analysis() not get_Analysis()ENSCORESW-132. Bringing in the type of sequence into the headerIn calculate_version(): For translations, also look at the translatedFloating point comparison == 1 changed to > 0.9999.forgot to print the line to the filegave the wrong object. needed to give it a file path not a globSkip non chromsomes if we didn't have anycleaned up directory name issueReformat calculate_version(). No functional change.Fixing issues with the pipeline module usedChanging markup from Markdown to Textile as it supports table formatting which Markdown can only do via hardcoded HTML tablesAdding a no_scp modeENSCORESW-139, ENSCORESW-126, ENSCORESW-164 and ENSCORESW-132. This commit brings in support for stripping out the Y chromosome from Human for all dumps (if required). We also add support for deleting previous runs going into the same dump location. Softmasked sequence is now created by default; hard masked is generated from this. We also produce an email summary of the results of the pipeline.another attempt to accommodate multiple ensembl stable ids linking to the same vega stable idMissed POSIX import and added documentation as requestedMaking this a bit more like the other production scriptsCovering more cases with the execute_single_result() codeClassificaiton was not working as expectedRemoved fish from GO terms projections. Also double-checked order of execution code and added some explanatory comments.ENSCORESW-160. Committed with test cases checked in. Also manually verified the code works with transcripts (live as of v67 of Ensembl) ENST00000330803, ENST00000366472 and ENST00000318244Updated POD.Missed the done testing flagENSCORESW-171. Bringing in support for splice site work. We also had to change the intron table SQL as it was out of date.ENSCORESW-165. Adding support for intron_supporting_evidenceSchema was out of sync with the main tablesPatching issue with there being a difference between NULL and and empty string WRT description and also plugged a gap in the code when we were trying to query using a display_label which the api allows to be NULL but the DB does notENSCORESW-165. Committing the second attempt at the IntronSupportingEvidence API for genebuild RNASeq data.Removed elements from the meta table and updated sqlHelper.t accordingly so tests passBetter test case which reports what has gone wrongImproved error reporting. Nice to inform the user what has gone wrong with the given dataSkip now works.New test to load the Ensembl schema into a temporary database