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Created with Raphaël 2.2.01Sep29Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Added defaults for pipelinesAdded nested class, configContains() now replaced by config.contains()Added bedtools coverage to counts scriptAdded tagcounting to Sage pipelineMerge commit 'c1fa781e0f817244038ea756013dd7d581fe6a88' into peterPlaceholder for library tag countsMerge branch 'patch_names' into 'master'Rename 'runs' -> 'libraries' and 'resourses' -> 'resources' in summary data, 'Summarys' -> 'Summaries' in method namesremove old filesReplace SortSam to AddOrReplaceReadGroups for BowtieChanged default aligner to bowtieMoved aligners to functions and added BowtieAdded defaultAligner varAdded skipMarkduplicates on dedup stepFix on option on picardFix on final jobsFix deps for prefix JobFix bug on spaced files nameMerge commit '80ba94d1fe9ca4f77fe9235237a61980643b4676' into peterFix error in biopet-framework pom.xml fileFix bug on argsAdded Sage pipelineAdded -s and -S optionFix on args orderMoved scripts to general packageMerge peterMerge commit 'cfae9015423d5848a3228909821e3a2095553baa'OutputName changeMerge all maven packages into 1Added BiopetPackage as complete packageAdded single sample UnifiedGenotyperRemove old functionsconvert AddOrReplaceReadGroups to biopet functionconvert MergeSamFiles to biopet functionAdded skipMetrics optionAdded allSitePLs optionConvert SortSam to biopet functionMerge origin/sander into peterAdded BamOutput Option to HaplotypecallerMerge commit 'feeafebb314e1a73877c2b2ad665d3a6cc5875ad' into sander