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Created with Raphaël 2.2.024Sep2322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun292827262524Merge remote-tracking branch 'origin/develop' into feature-scoverageRemove some test from shiva-gatksamples testingfix sample showfix importbedfix samplesImportmove old classes for later useAdded Aggregate moduleMove breaking classestiny fixdata sources testfixadd cmd function to nicely format cmdLine in human readable formatFix importreformat some sentencesadded some extra information. Changed some typosadd root value to all children of ManweAdded FilePipesChanged menuannotate-bed and annotate-vcfManwe Datasources extensionsmove output argument to main Manwe class.manwe samplesAdding getting startedFix dirfix camelcaseChanged repo link of Gatkmanwe stubAdded support to have a pipe as input fileMerge branch 'fix-varscan' into 'develop' Remove count testsRefactor flexiprep, more pipes are used nowAdding a QC commandRemove intermediateFixed output pipelineReference is not used in hereBetter memory handling for pipesRemove old codeAdding classpath and memory to beforeGraphConvert mapping to sortsam for pipes