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Created with Raphaël 2.2.023Feb1918171615141312111096543230Jan292827262322212019161514131210986517Dec1611985432128Nov27252422Fixing seqstat usage of outDirMerge branch 'feature-seqstat-scala' into 'develop'Merge from developMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-cnvpipelineRScript commandline function wrapperAdded mroe docsAdde more docsSaver getChange data to statsMerge branch 'patch-sampletsvtojson' into 'develop'Fix for #117Added some scaladocsAdded scala docsFix formatMerge branch 'develop' into feature-summaryAdded scala docsMerge branch 'feature-toucan' into 'develop'Removing iml filesFixing expected info field test valuesafterGraph was deprecated, now beforeGraphrefactorsfixing missing cutadapt mock valuesAdded scala docsAdded scala docsMerge branch 'develop' into feature-toucanMerge branch 'develop' into feature-toucanExplode and standard in one function, no longer custom exceptions, CSQ tag by default removed.Fix insertsize metricsFreeC delayed config file writing, getting the nCoresRequest and adding the Kopisu pipeline to the executable jarMerge branch 'develop' into feature-summaryadd tool to executableChanged executables for summaryAdded Markduplicates to summaryMerge branch 'develop' into feature-gentrapMerge branch 'patch-flagstat_dirs' into 'develop'Remove version from summary and rename data to statsRename data to settingsAdd Cufflinks blind mode job and output filesAdd Cufflinks guided mode job and output filesOverride default sample directory path