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Created with Raphaël 2.2.025Jan232221201918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct3029282726252322212019161514Added tables and heatmaps to basecounterAdded tables and heatmaps to summaryRemove extra dot in filenameAdding sampleBamInsertSize (with some error, too be fixed later)Remove old codeImplement baseCounter in pipelineOptimize importsAdded tool extensionAdded transcript countsAdd documentationAdded output filesAdded gene exon and gene intron countsFixed squishAdded 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'