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Created with Raphaël 2.2.028Nov272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211Use transcript display xrefs provided by FlyBaseNew biotype added for PC genes (IG_LV_gene)Simple code for sumamrising the exon/trasncript statisticsPass back no transcripts if we lacked a source IDget_alt_attrib_codes was added as a fresh dependency. This module missed it. We return nothing for this a we don't have alt_attrib codes for variationsAdded explicit call to use the $ENV proxy settings. LWP Simple did not do this by default.Added a sleep for web service retries.Missing sql alias added.Fixed an omission in taking hash keys on a reference.merging changes from branch-ensembl-69JGI version 2 should not be used, removed every reference to itcvs/release/ens…cvs/release/ensembl/64= does not work. We just assigned $type to 'cisred'. eq is what was wantedFinal changes to ensure the code works as expecteduse codes not namesAdd get_alignment to ConversionSupport.cvs/attic/branc…cvs/attic/branch-1000genomes-13-69 cvs/release/ensembl/69 release/69 upstream/release/69Documenting the hidden $to_slice argument in transform()array based attributes can be dodgy tooBringing in summaries as hashesadding new types for SOCounting all exons & transcripts nowClassy. Parent caller will abort looping if given a non-true value back.Used the wrong statementadding eval error checkingadding countshelp reworkedCan now compare transcripts and fixed some errors in the mapping codeBad old method left inUnlinked type cleanupUpdated the HTML code + display table colours in the tables listUpdated the HTML code and added the table colours in the tables listSupport locking of tables when doing thisAdding seq_region_end to the sortAnything in default_options() is not taken over to the pipeline by default. Pipeline wide parameters should be passed into the appropriate method to be set in metaSwitching the logic around a little bit here to get rid of single | or statements and an xor which I think has caused issues somewhere in our pipelinesmissed stderrmissed two printsmissed a message and got the time the wrong way aroundimport posixadding timesTrying to sort feature tables