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Created with Raphaël 2.2.020Nov1918171614111098754231Oct282726252421171413121110654329Sep2827262221201917161513102131Aug2625242322211817151110954129Jul28262522212019141387654129Jun2827242120171514131087632131May30292726252423201918171514131211109Simplify lineplot codeChanged reports summary valuesAdding mapping quality and clipping stats to summaryFixed unit testsMoving flagstats from bamstats to summaryFixed bamstats for single endAdded referenceFixed compile errorAdding output fileAdd basic version of bamstats to pipelineFixing BIOPET-353Fixing config filesFixed testMerge remote-tracking branch 'remotes/origin/develop' into feature_annotation_versionsAdded unit testsMerge branch 'fix-BIOPET-383' into 'develop' autostyle fixesMerge branch 'fix-BIOPET-458' into 'develop' fix testsFormat changeback to exceptionMerge remote-tracking branch 'remotes/origin/develop' into feature_annotation_versionsRemove redundant checksFixed nullpointerfix logger.errorslight improvement of message and autostyle fixesthrow error when no libraries in configMerge branch 'fix-jobreport' into 'develop' Fix jobreportMerge remote-tracking branch 'remotes/origin/develop' into feature_annotation_versionsMerge remote-tracking branch 'remotes/origin/fix-generate_indexes' into feature_annotation_versionsMerge branch 'feature-centrifuge_pipe' into 'develop' Fixed unit testsMerge branch 'develop' into feature-centrifuge_pipeMerge branch 'feature-full-fastq-to-gears' into 'develop' Merge branch 'feature-sanity_check_outputdir' into 'develop' Switch to fifo pipeMerge branch 'feature-vcfwithvcf-number' into 'develop' remove redundant imports, add scaladoc and autostyle fixes.Added thread correction