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Created with Raphaël 2.2.027Apr26252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb262524232221181716151211109875432129JanFixed 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 removalSwitch to biopet scatteringConvert gatk extensionsConvert to biopet extensionsExclude gatk-toolsDisable scatteringRemove copy classConverting extensionsSwitch list to a set to speedup scriptFix clever vcf header and add sorting stepMerge branch 'develop' into fix-svcallers-vcf