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Created with Raphaël 2.2.022Jun212019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22changed miRBase to miRBase::MULTIAllowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotaschanged source definition for RNAMMER and TRNASCAN_SERFAMParser which loads the registry with EnsemblGenomes databasesgeneric RFAMParser which RFAMParser_E and RFAMParser_EG inherit fromRFAMParser which loads the registry with EnsEMBL databasesparser for xrefs from core which are generated by an analysis straight into a core dbremoved duplicate store methodupdated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.updated the help, the script now use "-pattern" to find a database instead of "-p".Replaced "$option" from "-d" to "-pattern" for the percent_gc script.deleted unnecessary module importwhen the band is at the end of the chromosome, make sure the two ends matchI have added the softshell turtle ( psinensis ) to the projections.Fixing a bug brought up by Nathan where we used version in the select for an xref_id.fix module nameadded empty line after _store_or_fetch_xref_podMissing xenopus from the execution order listSwitch back to mydir so we don't use a person's own directoryCannot have an alias for print and we never didSwitch to using get_all_GeneMembers() which is the supported API in 68added RFAM::EG sourceRFAM parser for ensembl genomesReturn 1 if we unlinked the file. Otherwise return 0Die if we had no filesfix to make sure that dbname takes priority over patternno clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse eitherfixed output messagecorrected file names - fix for Exonerate method override changenew parser for RFAM xrefs, replaces use of ncRNA_DBParser in ensemblnew parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensemblreplaced source ncRNA::MULTI with RFAM::MULTI and miRBase::MULTIPrefer sub ref to dereferencebugfix brought over from HEADAssignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.Using the "best" HTTP client available i.e. avoid making people install LWP if they are on a late enough version of Perl. HTTP::Tiny is very niceAsking if a dereferenced array ref is undefined is not testing what you think it is and is deprecated in Perl 5.16.0. You are seeing if the first element was defined when in actual fact you needed to assert if the array reference was undefined and act accordingly.Removing seek() call and not using the filesystem. IO::String does the same jobStop accidental cleanup of databases during object cleanup