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Created with Raphaël 2.2.017Jan11108713Dec1110528Nov2726232119161312629Oct161511984324Sep11Jun729May3Apr29Mar28272623212096213Feb12965231Jan292625823Oct9225Sep27Jan23Nov2212Sep20Apr28Jan9Nov727Oct26242226Aug1411Jun1022May2113627Jan234Nov323Oct4Sep19Aug1815149Jul25Jun15May986110Apr9874331Mar2827252421191413121119Feb18171312654331Jan302924222017141310613Dec105427Nov262120151275430Oct24231615141187123Sep2019181716131210964330Aug272221201916151413129631Jul3025241812111083227Jun262524Added additional ignore typeRemoved references to old sanger genedb chado databaseAdded scripts into Mac .app files to allow running from command line. Incremented release number in pom.Merge pull request #273 from ssjunnebo/644853_changelogMerge pull request #1 from sanger-pathogens/masterAutogenerate CHANGELOG.mdMerge pull request #272 from kpepper/gh-pagesAdded section on security warnings for MacsMerge pull request #271 from kpepper/gh-pagesChanged download links to point at v18.0.0 Github release artifacts. Removed note about Safari downloads.Merge pull request #270 from sanger-pathogens/build-process-upgrade-mergev18.0.0v18.0.0Merge pull request #269 from kpepper/build-process-upgrade-mergebuild-process-u…build-process-upgrade-mergeSmall performance improvement for some for-loopsUpgraded symlink resolution code, for Bioconda recipeUpdated release information and copyright datesUpdated unit test constantv18.0.0-RC1v18.0.0-RC1Updated Jacoco and Javadoc plugin versionsUpdated wording around pre-built releasesUpdated top level README with Java version infoRelease 18 documentation updatesRT Ticket 472601 - RPKM and read countsStandardise app icon behaviour across platformsRun InterPro search in a different thread to avoid event dispatcher blockingAdded additional file extension for drag/dropAdded exception catch for WindowsChanged some textChanged to use HTTP constantsRemoved a BamView mac optionFixed missing menu options for MacMade some variables privateRemoved unused importsAdded the ability to invoke an EBI InterPro sequence searchRemoved fasta36/fastx/Jalview/smart run ability, as these programs will no longer be supportedUpdated code references to Java 8Added recent changesAdded additional classUpdated for Java 9+Removed ability to run remote blast searches etc over SSH. This code is very old and will be iteratively retiredUpdated etc/run_ scripts to use later program versions, e.g. fasta36 and blast+. Removed the .sanger and .linux run scripts as these obviously have not been used for some time and were very out of datePorted local blast db setup script from Sanger general repo