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Created with Raphaël 2.2.029Jan2827262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct302928272524232221201716151413Add version commentbug fix in Carp pipelineAdded dendrogram plotChange color scale to fix clustering and added a dendrogram plotAdded changes for new sampling handlingMerge branch 'develop' into feature-Chipcapbug fixes in carp pipelinebug fixes for macs2 wrapperFix argsFix scala docs format errorAdded wigToBigWig extensionAdded allele overlap heatmapMerge branch 'develop' into feature-vcf_statsExtracted IGVTools from YamsvpUpdate on the pipeline, streamline and minimize the required arguments taken from the commandlineMerge 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 functions