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Created with Raphaël 2.2.04Mar32127Feb2624231918171615141312111096543230Jan29282726232221201916151413Make 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 accessAdd option to supply rRNA intervalsFix default tagsSpecify correct strand options in cufflinksAdd strand separation jobsSupply default arguments to samtools view wrapperMinor changes to optionsAdded args to queue extensionAdded excludeNonVariantsRequire sample libraries to have all single-end or paired-endFormatting updatesReorganize importsfix bugAdded check for incorrect variantcallersJava jobs now show diffrent version output in summarySkipping header in general statsAdd base counts per-sample output to summaryExpose merge jobs outside of multi sample jobs functionFix file nameAdding sample stats from vcfstats to summaryAdd base count table merge jobsAdd 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 script