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Created with Raphaël 2.2.013May12111027Apr26212018151413876531Mar3029282524232221181716151411109872128Feb2524232221181716151410126Jan131276521Dec2017151413976543230Nov2923181715102126Oct25242120198523Sep2119189127Aug1918161030Jul292623222120191372130Jun29282524232218151126May25242018171312117430Apr2928272623222019161513929Mar25232219171615109842126Feb252419943229Jan21191815141312876549Dec74130Nov26242320add commons-netadd commons-netuse FTPSeekableStream to support BAM files over FTPadditional constructors to handle files over http and ftpchanges to use FTPSeekableStream to support files over FTPisBCF() handles files over FTPuse FTPSeekableStream to support files over FTPapache commons-netFTPSeekableStream for BAM and BCF / VCFupdateuse filter when calculating overviewallow for Xallow for SP type change in bcftooolsadd TableViewer to display data in JTableset cursor to busy when count variant typesupdate versionmake class publicuse AbstractVCFReader.getNextRecord() and add variation overview optionfix for variants without a formatchanges for the "Create introns" function to transfer sys_id and allow for 3'UTR and 5'UTRupdateuse progress bar for read count calculationdisable analyse menus when no FeatureDisplayupdateupdaterpkm changesremove printchanges to filtering of readsload BAM/VCF using SwingWorkerfilter duplicatesjoin predicates togetherset visibility of flags to protectedreport number of mapped readsadd option to rpkm calculationVCF insertion colour is magentaupdateadd option to create features from variantschange to FileViewerchange to FileViewer to savechange to FileViewer