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/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 13 lines | 13 code | 0 blank | 0 comment | 0 complexity | e92669b7d642af79e220c168f8a082e7 MD5 | raw file
 1GenomeAnalysisEngine - Strictness is SILENT
 2CountCovariatesWalker - The covariates being used here:
 3CountCovariatesWalker - 	ReadGroupCovariate
 4CountCovariatesWalker - 	QualityScoreCovariate
 5CountCovariatesWalker - 	CycleCovariate
 6CountCovariatesWalker - 	DinucCovariate
 7CountCovariatesWalker - 	HomopolymerCovariate
 8CountCovariatesWalker - 	MinimumNQSCovariate
 9CountCovariatesWalker - 	PositionCovariate
10TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
11CountCovariatesWalker - Writing raw recalibration data...
12CountCovariatesWalker - ...done!
13TraversalEngine - Total runtime