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Created with Raphaël 2.2.022Jan21201918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct302928272625232221201916151413Added refflat support for base countingStart on basecounterFix empty default value for stripSuffixDisabled uncompilble codeMove Bam2Wig to multisample mappingChange ro preProcessBamFix compile issueMerge remote-tracking branch 'remotes/origin/develop' into feature-qiimeMajor upgrade to gentrap classMerge branch 'develop' into feature-small_rnaAdd pindel2vcf to pipelineMerge branch 'fix-260' into 'develop' Added cufflinksFixed typoAdded htseqCount jobAdded files to summaryFix bwa bug using freeVar=falseRevert "PindelVCF wrapper", does not belong to this branchPindelVCF wrapperPindelVCF wrapperAdded heatmap plotAdded general mergingMerge remote-tracking branch 'origin/feature-VarscanIntoShiva' into feature-VarscanIntoShivatypoMove script and init to main traitSet up more defaults.Merge branch 'fix-259' into 'develop' Style refactor of PindelCaller wrappersmallRNA pipelineIntegrating developRemove pindel from the list of default callersFixed unit testsAdded varscan_jar to test configRaise default memory for varscanAdded version to varscanAdded version to varscanFixed error message in bamutilsFixed styleMerge branch 'feature-update-cutadapt' into 'develop' add varscan test to shiva variantcalling test