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Created with Raphaël 2.2.019Jun181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec2221201914131298Fixed 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 cleanupcorrect type of compara db handle, method to remove duplicate attrib valuescorrect type of compara db handle, method to remove duplicate attrib valuesadded missing ncRNA sourcesChange of contentSimplification of the select. The query for select used fields which are not part of the unique key. We also get the API to issue a throw the moment we miss the xref id retrieval. This should be an impossible scenario to get into thoughMissed the multiple mapping behaviour. Moved code inside the loop.Updating GFF parser testssupport for empty lines and fasta sequence sectionRename of the schemaNew test case for applying the current release's patches. This downloads the last release of the core schema, finds all patches relevant to this release and patches the DB accordingly. The code requires access to CVSWEB and so supports proxies but can also skip the tests if the schema cannot be found. Failure of this test is not an issue for external users & so should not be punished as suchFirst draft of revised projections. Exclusions in place for inappropriate mammalian traits on birds and reptiles. Also platypus.Removed use of SeqDumper and replaced it with our own FASTASerializer.Corrected example code. It was misusing the wrap_array method.A more succient version of the method.logic was very wrong. we never closed a FH meaning lots of corrupted filesTranslation stable ID version incrementation only dependent onFirst pass of the flatfile documentationENSCORESW-132. Missed out the command line options for logic name adding/skippingImproving error reporting hopefullyDoc update for calculate_version().The penalty on the position-based score for exons when an exon had aMake sure we set no_scp correctlyformatting changesMissed this quite important change to avoid the closing of files when they can't beExtra unwanted @Document document documentBetter version. We now avoid gzipping which should give us a good speed boost and bring us closer to the original speedHack smell appearing. We have to recreate and gunzip the created file to do the hardmaskingSwitching the logic around here. It makes sense if we are trying to read from a file which hasn't closed yet then maybe we're not going to get all the data into the file.Trying something more spectacular to avoid this horrible truncation of the filecopy is on targetBetter documentationAdding softmasked as a type of file and improving error reportingMissing softmasked dataForgot the repeat masked flow