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Created with Raphaël 2.2.04May130Apr2928232016151413121098764230Mar2726252423201918171615141312111098765432127Feb26242319Merge branch 'patch-AnnotateVcfWithBed' into 'develop'Fix flag handling and add some loggingAdded unit test for bammetricsChange bed files in summaryAdded plots for front page of reportAdded extension for stacked bar plotadd more info to tool helpMerge branch 'develop' into feature-reportMerge branch 'patch-rscript' into 'develop'Added some scala docsRefactor Rscript extensionAdded summary value classGears WIPAdded status logsGeneral rscript for stacked bar plotsGears for project 106 in Queue/BiopetAdded tool to extract a tsv file from a summaryAdded functions to get a value for all samples or librariesReport builder in now in parallelUpdate R script to accept commandline arguments with optparseChanged picard metrics output in jsonshift option had wrong var nameChange to non format json, save 90% of size of json fileChanged some of the tags for picard summariesAdded referenceFix summary for picardAdded stats from bam metrics to summaryAdded wgs metricsadded target pcr metricsFixed testsAdded rna metricsSwitch to multi metricsRefactor bed to intervalAccept multiple interval filesAdded BedToIntervalList extensionAdded a deprecated messageSafer class name, now checked by the compilerMerge update from developMerge branch 'path-style-fix' into 'develop'Merge branch 'patch-picard_summary' into 'develop'