Mark DePristo c8a06e53c1 DoC now properly handles reference N bases + misc. additional cleanups ... -- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage. -- Added option --includeRefNSites that will include them in the calculation -- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included -- Reorganized command line options, tagging advanced options with @Advanced		2012-02-25 11:32:50 -05:00
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broadinstitute/sting	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00