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Created with Raphaël 2.2.06Mar5432127Feb2624231918171615141312111096543230Jan29Fix sickle wrapper bug causing by incorrect flag outputreleas notes modifications addedreleas notes modifications addedreleas notes modifications addedUpdate test for fragments_per_gene modeFurther trim down testsAdd convenience methods for creating sample configsTrim down general test to test for expMeasure and strandProtocol combinationsAdd more config options to test in GentrapTestFix duplicate value on valid cufflinks measuresRemove addAllJobs from CufflinksProducerRefactor Cufflinks jobs into its own traitAdd general heatmap plotting fallback when error is encounteredRename for consistencyFix picard version, only work with a picard jarChange getVersion to Option[String]Update formattingInitial update for GentrapTestAvoid NullPointerException when checking for R2 in GentrapAdded scala docs for picardPut all expression table outputs into a single directoryAdd heatmap plot jobs for all outputCreate fallback plot when data points for heatmap is not enoughAdded scala docs for macs2Added scala docs for igvtoolsAdded scala docs for bwaAdded scala docs for bedtoolsAdded scala docsAdded scala docs and and removed unused methodAdded scala docsChange output files handlingUse scalaz's implicit option for booleanInitial heat map plottingUpdate heatmap wrapperUpdate heatmap plot sizesadd scala docsUpdate heatmap plotting scriptreleas notes files addedMerge branch 'develop' into docs_v.0.3.0Merge branch 'patch_carp_summaryFix' into 'develop'