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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
..
R Improve variantCallQC.R 2012-04-13 17:00:37 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
doc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
java Improved BQSR plotting and some new parameters 2012-04-19 09:31:41 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala AggregateMetrics: 2012-04-17 11:45:32 -04:00
testdata continuing the BQSR triage... 2012-04-05 14:34:15 -04:00