Mauricio Carneiro 68d0211fa1 Improved BQSR plotting and some new parameters ... * Refactored CycleCovariate to be a fragment covariate instead of a per read covariate * Refactored the CycleCovariateUnitTest to test the pairing information * Updated BQSR Integration tests accordingly * Made quantization levels parameter not hidden anymore * Added hidden option to keep intermediate plotting files for debug purposes (they're automatically deleted) * Added hidden option not to generate the plots automatically (important for scatter/gathering)		2012-04-19 09:31:41 -04:00
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sting	Improved BQSR plotting and some new parameters	2012-04-19 09:31:41 -04:00