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Created with Raphaël 2.2.021Jun2019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec222120191413Return 1 if we unlinked the file. Otherwise return 0Die if we had no filesfix to make sure that dbname takes priority over patternno clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse eitherfixed output messagecorrected file names - fix for Exonerate method override changenew parser for RFAM xrefs, replaces use of ncRNA_DBParser in ensemblnew parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensemblreplaced source ncRNA::MULTI with RFAM::MULTI and miRBase::MULTIPrefer sub ref to dereferencebugfix brought over from HEADAssignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.Fixed 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 changes