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Created with Raphaël 2.2.017Oct1413121110654329Sep2827262221201917161513102131Aug2625242322211817151110954129Jul28262522212019141387654129Jun2827242120171514131087632131May302927262524232019181715141312111098765432130Aprtrimmed VersionCommand and test classMerge branch 'develop' into add-cnmops-kopisuautostyle and test fixget correct values for number=A and number=RMerge branch 'develop' into feature-vcfwithvcf-numberUpdateMerge branch 'feature-convenience-version' into 'develop' small extra com mentSimplify regex fetchingGeneral collector methodsemantic version convenience methodsAdded regex optionautostyleversion checkAdding genral feature for json extractionversion in rscript for cn mopsget method for output filesuse Option[File] for output dir in stead of StringRead all info from gitlabAdd paged methodAdded base tool to fetch issues from gitlabgracecully exitlimit wall clock time to max 2 hours per defaultraise default starting memoryMerge branch 'feature-centrifuge' into 'develop' Fix gzipFixed unit testMerge branch 'fix-must-have-variant' into 'develop' Merge branch 'develop' into add-cnmops-kopisuFixed inputstyle changesextra safeguards. potential genotype 1/. is still a call.Fix bugbetter way of finding these types of variantsFix styleAdded normalize fastaRemove defaultFixed output of centrifugeMerge branch 'feature-sage_unit_tests' into 'develop' User gtf has now higher prio