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Created with Raphaël 2.2.018May1715141312111098765432130Apr29282726252221181615141312111087654131Mar302925242321191817161514131110987Merge branch 'feature-singletons_flagstat' into 'develop' Fixed testMerge remote-tracking branch 'remotes/origin/develop' into biopet-biosMerge branch 'feature-index_generation' into 'develop' Merge remote-tracking branch 'origin/develop' into developAdded singletons to summaryStyle fixesAdded test to write configAdded test for gtf downFixed outputFix extensionstyle changesAdd gtf to refflatMerge branch 'feature-more_unit_tests' into 'develop' Fixed input errorAdd input annotationFixed typeStyle fixesMerge remote-tracking branch 'remotes/origin/develop' into feature-more_unit_testsAdded gtf to star index generationFix configStyle changesExtract gtf when neededMake curl pipableAdding gtf downloadMerge remote-tracking branch 'remotes/origin/develop' into feature-index_generationAdded mapping to gears testingFixed typoMerge branch 'feature-bed_check' into 'develop' Fixed testFix formatMerge branch 'fix-exit_calls' into 'develop' Merge branch 'fix-fifo_job_name' into 'develop' Added testing for start from bamThrow error whenever the arguments are not completeStyle fixesRemove old commentswitch to traitAdded basic testingRename file