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Created with Raphaël 2.2.012Feb111096543230Jan292827262322212019161514131210986517Dec1611985432128Nov2725242221201918171412111087654Fix some config valuesAdded 128 unit tests to mapping pipelineFix typosFix "/" format errorsMake reference absoluteMake outputDir always absoluteBreakdancer vcf should output more headers, adding official header for SVsAdded asFileFix typoRemove unneeded "/"Format fixFix error messageMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-cnvpipelineFreeC wrapperChange name checkExecutable to preProcesExecutableRename afterGraph to beforeGraphFix some small bugsAdded flexiprep testingFix RPKM directory path from configChange globalConfig to defFormat fixChange outputDir to FileAdd exon read count modeAdd option to supply strandedness protocoladding VCFWithVCFAdd strandedness enum valuesUpdate general structureAdd possible expression measuresUpdate config retrievalRemove unused Gentrap valuesFormattingMerge branch 'develop' into feature-gentrapMerge branch 'develop' into feature-unittest_coreMerge branch 'feature-fix_missing_values' into 'develop'Add notesAdd commentMake a val for globalConfig, test should now be able to override it so unit test are not depending on a global varSimplify sortingRemove unused lineFix format