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Created with Raphaël 2.2.027Apr26252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb262524232221181716151211109875432129Jan28Setting 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-vcfFix REF columnAdded exclusion for gatk toolsSwitch list to a set to speedup scriptAdded more logging to multisample pipelinesMerge branch 'fix-samplenames_qiime' into 'develop' Format fixedFixed tryreplace _ for -Merge branch 'feature-fixStarOptions' into 'develop' Merge branch 'fix-vcffilter_test' into 'develop' Merge branch 'fix-vcfstatssummary' into 'develop' Format fixFixed vcffilter test