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Created with Raphaël 2.2.02May127Apr26252423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct2827262524212019Release not version.Added possibility to prevent --fix applying all patches since Anno Ensembland some more white space.Added whitespace to help POD filter.Add 'biotypes_include' and 'biotype_exclude' to list of options.This commit was manufactured by cvs2svn to create branch 'branch-Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd resultsImproved error checkingDon't give it an adaptor. Just causes warningsReturns default mappers from a class level. Makes serialisation using Storable possible without bringing in B::DeparseChanged to using Test::More and now use note instead of a warn to stop output contaminationaltered execute_into_hash to retain elements where value is 0 (as opposed to undef)Do not print. No needTesting the error message we get from the multiple alt_allele store methodCapturing the vague tests and asserting we will return the right kind of warning to the userFlagging up a todo in the test case to fixSwitched to using Test::MoreAdding a test case mode for quickly generating sets of ensembl-test compatible dumpsAdded link to AGP speccleanup 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.