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Created with Raphaël 2.2.026Oct2523222120191615141312987652130Sep29282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643Fix existFix case classMove Executable function outside of classSet defaults for gc limitsAdded GenotypeConcordance to shivaAdded GenotypeConcordancefix compile errorFix failing test and codeMerge branch 'develop' into feature-vardaadd extra newlineMerge branch 'fix-Shiva_bcftools_calling' into 'develop' Merge remote-tracking branch 'remotes/origin/develop' into feature-generate_indexesMerge branch 'fix-sample-names' into 'develop' Typos and reformulating sentencesproper temp filesfix for #222Bugfix in KrakenReportToJson, include Root and Unclassified in any case.POM definition fix.Merge remote-tracking branch 'remotes/origin/develop' into fix-Shiva_bcftools_callingadded release notesrefactor memorylimitAdding tests for GearsSync with develop changesMerge with developSmall fixes in reportMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-docs-0.5.0Merge branch 'fix-typo-toolcommandfuntion' into 'develop' Adding examples for developers creating pipeline, tool, wrapper and reports.Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221Fix markup in codeChange to compressed outputFix sample and library flagchanged importsMerge branch 'fix-flexiprep_noext' into 'develop' Fix build issuesFix unit testingMore piping for target flagstatUse normal pipes instead of fifo pipesMerge remote-tracking branch 'remotes/origin/develop' into fix-coverage_pipingRemove fixme