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Created with Raphaël 2.2.028Jan27262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310Merge branch 'feature-improve_multisample' into 'develop'fix scala docs (again)Fix scala docsRenaming valuesRemove unused codeRenaming valuesChange color on heatmapSwitch 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 example