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Created with Raphaël 2.2.025Apr2423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct282726252421201918cleanup importsfixing dependencies.t test case. Now works no matter where you run the test cases fromminor changes to regexes and layoutNow handles all component_type contigs which are not gapsAdded support for 'Active finishing' contigs. Removed hack for HG1211_PATCH unknown orientation (although GRC have bot provided a solution as yet) BUT added in a new hack for contig FP700111.21 which had to be retrieved from SVA (current version is FP700111.23).Note better than diag as otherwise we get whingy warnings all the timeMissed a WUModule locations not updatedPackage was wrongForgot the environment variables which is always neededForgot about the registry option given to the command lineAdding base_path as a reminder that we need to specify this otherwise everything goes pop!First pass documentationPOD correctionsPOD correctionsLeaving lots of parameters empty. The pipeline can deal with this now and will use the correct defaultsBetter target server empty detectionSupporting empty array specification and using the value specified in the param_defaultsPOD correctionsPOD correctionsFASTA dumper pipeline transfer from personal workspace. Consult the personal kt7 workspace for more detailed development notes.Update test count because I am too lazy to update it to use Test::MoreCopied fetch_all_by_biotype from GeneAdaptor to TranscriptAdaptor.Added support for SEE ALSO and further cleaned up code and text samples prior to doxygen processing.POD corrections*** empty log message ***correcting "End coord + 1 is less then start coord" error messagesAPI version upAllowing the API call to fetch back terms which have a distance of 0 i.e. linked at the current level. This is to be used with cautionPOD correctionsAllowing people to comment on web dataAdded the method "get_all_somatic_StructuralVariationFeatures"Cleaned up overly escaped code examples.Spelling of environment corrected in POD.In initial_stable_id():Really the user does not need to be able to do select into outfile. copy paste errorAppend accession number to the display label.Bug created and I didn't run the test cases.Do not do meta_coord calculations for the ditag table.Getter/setter for the header function