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Created with Raphaël 2.2.027Apr26252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb2625242322211817161512111098754321Move 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 scattercountRemove short name methodsAdded objects againMerge branch 'fix-script_run_time' into 'develop' Remove reverse complement adapter removal