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Created with Raphaël 2.2.027Apr26252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb262524232221181716151211109875432Fix 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 fileFixed referenceAdding dbsnp automatic againRemoved complete dependency from protected modulesMake dict required for all gatk toolsFixed reference and added versionFixed cycle bugAdded gatk jarFix compile errorsFixed default scattercount