gatk3的最后一个经典版本3.8

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
licensing	Licenses for GATK 1 and 2 beta	2012-04-17 11:40:02 +01:00
public	Improved BQSR plotting and some new parameters	2012-04-19 09:31:41 -04:00
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	Updated license year	2012-03-27 14:32:02 -04:00
build.xml	Added function to get bases from the current base forward in the window in ReferenceContext	2012-04-06 16:07:46 -04:00
ivy.xml	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00