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Created with Raphaël 2.2.029Apr282726252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb2625242322211817161512111098754Merge branch 'develop' into fix-svcallers-vcfstyle fixesReduced number of test in shivaStyle fixesFixed testsMerge branch 'develop' into feature-bios_base_countsReduce number of testsFixed reportAdded varscan fake jarFixed testUsage of a filteredSet (applying mappability track)Updated test definition and add little comment what the code does.Added aggregate step againFix tinycap dirTemp commitFix compile errorsMerge remote-tracking branch 'remotes/origin/develop' into feature-queue_licenceMove public to rootRemove protected dirMove shiva testing to publicMove gatk variantcallers to correct packageFixed packageMove unit testing variantcalling to publicRemove protected executableMove preprocessing to publicMove variantcallers to publicMoved gatk extension to publicFixed extensions in testingSwitch to beforeGraphFixed compile errorsStyle fixesFixed indexesFixed indexesConvert more to biopet valuesConvert more to biopet valuesFixed typechanged default memoryChanged baserecalibrator to biopet config valuesAdded biopet config values to general gatk traitFixed type