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Created with Raphaël 2.2.03Mar2127Feb2624231918171615141312111096543230Jan29282726232221201916151413121098Add conditional installation of required packages in aggr_base_count.RAdded option to add all info and format fieldsAdd jobs for base counting on gene and exonUpdate base count aggregator for easier use in the pipelineInitial jobs for base countingFix unit testAdded chromosome specific statsAdd -f and -F flags to samtools view wrapperUse proper repeat argument creationAdd check for input file and input labels sizeCheck that gene and/or exon output is set for base count aggregation scriptUpdate hist2count script wrapperUpdate base count aggregator script wrapperMove Gentrap-specific scripts and their wrappers to the Gentrap packageUpdate makeMergeTableFunction to return the created jobFix optional MergeTables flag errorsAdd merge jobs for cufflinks outputsAdd symlink jobs for cufflinks outputsDisabled some plots, we fix this laterAdded function to acces the qscript from a summarizeable to add multiple summarizeables to the qscriptAdded even more unit tests, now 1408 for gatk pipeline, sadly no 1337Added place holders for summaryMerge branch 'develop' into feature-shivaAdded unit test to gatk part of shivaAdded log4j to supress test outputAdded unit test to do some magicAdd MergeTable jobs for gene and exon fragment countsUpdate exon fragment count extensionAdd biopet wrapper for MergeTablesAdded more testsUpdate Gentrap with new Summarizable Sample and LibraryFix nameAdding basic unit testsChange memory of SeqStatFormatting fixAdd MergeTables to main tool executables listMerge branch 'develop' into feature-gentrapMerge branch 'patch-mutisample_summary' into 'develop'Change in scala docsFormat change