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Created with Raphaël 2.2.029Apr282726252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb2625242322211817161512111098754Reduce 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 typeConvert analysis_type to abstract valueAdded biopet config valuesSetting default for haplotypecallerDisable gatheringAdded int lists and double list to config conversionsAdded method to get vcf index file