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Created with Raphaël 2.2.04Mar32127Feb2624231918171615141312111096543230Jan29282726232221201916Fix bug that omits md5sum calculation of Flexiprep filesUse GatherBam for merging per-strand jobsFix versionUse correct conditional for optional strand-specific jobsUse correct flag repetition for SamtoolsViewVersionfix on missing AD fieldFix chromosome statsAdded todoAdd strand-specific jobsfix versionfix executableadded bgzip and tabix to freebayesAdded index as input fileAdded tabixProperly enclose outputs in RawBaseCounterRename Ln.out => Ln.output and Ln.in => Ln.inputAdd wrapper for bgzipAdd isoforms output to summarychanges in output folder of MACS single sample runsSwitched Basty to Shivafix bugAdd wrapper for bgzipRemove default value from expressionMeasures optionUse '0' as fallback character when merging tables of countsRefactor Ln-or-MergeSamFiles job into a single factory functionUse symlink for strand-separation jobs for single-strand samplesFormatting updates and `add` function call updatefix bug on single sample callingremove unused importSwitch Basty to ShivaMake variantcaller publicRename pipelinesRemove non gatk version of shiva from the protected exeAdded haplotypeLength optionAdded freebayesAdd optional WipeReads jobUpdate WipeReads wrapperInitial flag and validation for rRNA removalUse structural typing to unify Ln and MergeSamFiles output access