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Created with Raphaël 2.2.027Jan262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct302928272524232221201716151413109Switch Gatk pipeline and Basty to new multisample classesRenames and adds scala docsAdds finalBamFile functionMask yamsvp codeMove defaultsSwitch defaults to a def instead of a varRemove Queue command argsCNV pipeline for ExomeRemove queue args from pipelineRename functionAdded warning on use of old argumentRename functionAdded implicit Option[File] and Option[String]2 extra contructorsRemove outputDir from argumentsFix defaults for booleansAdded init functionsAdded init functionsSwitch to abstract init functionMoved init of varsAdded QUAL valueAdded VcfStats to executableFirst wrappers for kopisu #106Generate bamstats on the dedupMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvpFix xy plotWIP: abstract over processing unitsAdded plotsalso remove now completely redundant examples.jsonRemoved VCFFreqAnnotator (going to be vcfwithvcf annotator in own branch)Change Sage pipeline for multisample classesAdded defaultSample and defaultLibraryAdded a template as exampleChange sample to varSwitch Sage pipeline to new abstract classesNew abstract classes for samples and librariesFixed nullpointerChanges in format of heatmapChanging pipeline to improved multisampleQScriptSimplify multisampleQscript