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Created with Raphaël 2.2.017May15141312111098765432130Apr29282726252221181615141312111087654131Mar30292524232119181716151413111098754Fixed 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 fileFix testFixed testsAdded amplicon testAdded amplicon testAdded test for referenceVcfMove WriteConfig to classAdded dbsnp to configAdded config for each genomeMerge remote-tracking branch 'origin/feature-index_generation' into feature-index_generationFixed testImproved messageAdding tests on normalize stepChanges arg parser with getOrElse(throw new IllegalArgumentException)Added a precheck when using bedfiles with wrong contig in there
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