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Created with Raphaël 2.2.027Oct262523222120191615141312987652130Sep29282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643Merge remote-tracking branch 'origin/feature-docs-0.5.0' into feature-docs-0.5.0Change titlesAn update on example pipelineSwitch -a and -b for bedtools coverageCode style fixesRemove file checkingFix summary keyFixed bcftools merge stepFixed unknown executablesStyle changesFix 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 code