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Created with Raphaël 2.2.09Sep8532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Added samtools modulesMore concise codeExe no freeVar anymoreAdd mpileup to vcf scriptAdded target_bed as default to the intervals for all gatk functionsAdded gatk as sumodule for all general optionsAdded defaults to the contains functionConfig name changeMore efficient codeLast bam file not intermediate anymoreMerge branch 'peter' of git.lumc.nl:biopet/biopet into waiyiPipeline progress, for testing the mapping pipelineFixed chunking output dirsAdded variant recalibration as separated pipelineGive all gatk function there own classStart on yamsvp Scala versionFix typo in mapping pipelineAdded a general biopet trait for gatk extensionsAdded getFileList functionMoved samples to single root directoryThrow Exception when root is no flexiprepFix bug on inputFix on version regexfix output dir for taglibAdded seedmms optionAdded default values for bowtiefixed bug on default valueAdded more options for bowtieAdded 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 Bowtie