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Created with Raphaël 2.2.022Sep211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun2928272625242322Adding classpath and memory to beforeGraphConvert mapping to sortsam for pipesConvert pipe to SortSam againChange temp filesFix compile errorsMoved sam filestyle changeAdded a sum of memory and threadsAdded the -T argAdded executable to commandMerge remote-tracking branch 'origin/develop' into feature-pipeableUse piping after bwamemMade output of bwamem pipeableAdded samtools sortMade codeMemory readable from outsideAdded more to code styleStart on dev docsFix reference in varscanMerge branch 'feature-input_files_checking' into developMerge branch 'fix-remove_temp_files' into 'develop' Merge branch 'fix-sample_flag_summary_report' into 'develop' This will remove tempfiles on exitMerge branch 'feature-gatk_et_option' into 'develop' Still executes multisample jobs when all samples are given with --sample flagFix summary when --sample flag is used in multisample pipelinesMerge branch 'fix-report' into 'develop' Merge branch 'feature-external_examples' into 'develop' Fixed unit testsFastq sync is not intermediateFix protected packageAdd commentFixed case classChange nameAdd input files to pipelinesskip canRead when file does not existFastq sync is not intermediateDisable default toucanAdding input files to checkFix protected packageFix protected package