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Created with Raphaël 2.2.015Jan12111098543221Dec201918161513128765130Nov29282724222120181716141310987632131Oct30272625242320191817161312104228Sep272625222120191815141312117654131Aug30292118171614119832131Jul282721191712111097654330Jun29282726232221201916151398762131May30262524221918171512111098543228Apr272624201813121110modified bug to map indelsremoved directory error left in by mistakechanged ncRNA to miRBaseadded fix for allele_stringBumped version number to 43.Added missing comma before peptide_archive_id_idxChanged release to source_release as row name for table source as release became a reserved word in MySQL5Row name change from release to source_release in source table, this change is done because release became a reserved word in MySQL5Modifed to code to make it MySQL5 friendly, the changes made were the addition of parenthesis in the LEFT JOIN queries, without the parenthesis the queries will just not work or give unexpected resultsChanged release to source_release as row name for table source as release became a reserved word in MySQL5Row name change from release to source_release in source table, this change is done because release became a reserved word in MySQL5Modifed to code to make it MySQL5 friendly, the changes made were the addition of parenthesis in the LEFT JOIN queries, without the parenthesis the queries will just not work or give unexpected resultsdocumentation clarificationssome documentation fixesadd index on gene_archive.peptide_archive_idAdded Illumina V2 (human only so far)Updated to deal with Illumina V2 sequence files. V1 dealt with by vanilla FastaParser.Added writing of unmapped entries to unmapped_object and unmapped_reason tables in xref database. Old entries are deleted (if -delete is specified).Only require external_db_id to be filled in if the type is xref.Incorporated changes for release 43.remove NOT NULL constraint on unmapped_object.external_db_idAdded UNMAPPED type as wellAdd PROBE to info_type enum in xref.don't create backup tablesAdded missing patch info to meta table.Add probe2transcript to type enum in unmapped_object.Added probe2transcript type to unmapped_object.type enum.added locus_tag for the gene synonym or more generally known name and also added a note that contains the description. This is all just for the gene.Fixed docs.added new type: complex_indel, for long variations affecting different coding regions in the same transcriptFix tests for unconventional transcript stuffAdded unconventional_transcript_association keys.Added optional argument to get_all_DBEntries and get_all_DBLinks which is the database name. Use like in sql statment so percentage sign can be used for wild cards etc.changed deprecated type to biotypeadded order as an optional argument to list_dbIDs, mosy useful for genes and transcripts so caching is maximisedfixed wrong data examplesFix number of tests.miRNA_Registry split into twp seperate sources now of miRBase and miRBase_predictedmade compatible for new and old formatsanoying print statement removed