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Created with Raphaël 2.2.018Nov171614111098754231Oct282726252421171413121110654329Sep2827262221201917161513102131Aug2625242322211817151110954129Jul28262522212019141387654129Jun2827242120171514131087632131May30292726252423201918171514131211109Fixed 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 correctionAdded sanity checks for outputDirRemove unused importsFixing BIOPET-413 and BIOPET-416Merge branch 'feature-full-fastq-to-gears' into feature-centrifuge_pipeFixed unit testsadd test for numberRoutputfix fetching of secondary records