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Created with Raphaël 2.2.018Nov17141211108765432131Oct30292827252423222120171615141310987630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29Original script from GATKFix typoAlow for multiple configs in BIOPET_CONFIG and BIO_CONFIG_SCATTERAdded option to skip AnalyzeCovariatesMerge branch 'feature-fix_disable_mpileup' into 'develop'Merge branch 'develop' into feature-fix_disable_mpileupStart to build from public branch of queueMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvpMerge branch 'feature-no_output_test' into 'develop'Merge branch 'feature-basty_generate_fasta' into 'develop'Added option to disable raw callerLogging layout is now done with properties filesMoved arg checkingAdded text to argsRemove Some()Fix typoMerge branch 'feature-gatk_jar' into 'develop'Changed default fill charfix on no known sites warningRemove unused importAdded useIndelRealigner and useBaseRecalibration optionFix endlines in fasta filesformatAdded collect consensusFix reference nameChange defaultsfix queue argsDocumentation change index file and split end-user and developers docuAdd gatk jar optionadded docsMerge branch 'feature-fixSingleSample' into 'develop'Fix singleSample commandline functionChange util to utilsAdded consensus fastas to pipelineChanged Queue wrapperAdded consensus + variants builderAdded consensus builderAdded scala maxthread optionAdded fillAllele functionAdded checks