gatk3的最后一个经典版本3.8

Eric Banks 31c3a6be48 BQSR optimization: getRequiredCovariates() and getOptionalCovariates() were creating a new List every time they were being called, and unfortunately getRequiredCovariates().size() is used as the stop condition in for-loops throughout the code. Just maintaining the original list of covariates results in a 15% reduction in runtime for BQSR.		2012-06-07 20:04:10 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java/src/org/broadinstitute/sting	build system overhaul	2012-05-17 15:16:29 -04:00
public	BQSR optimization: getRequiredCovariates() and getOptionalCovariates() were creating a new List every time they were being called, and unfortunately getRequiredCovariates().size() is used as the stop condition in for-loops throughout the code. Just maintaining the original list of covariates results in a 15% reduction in runtime for BQSR.	2012-06-07 20:04:10 -04:00
settings	Testing of BCF codec	2012-05-24 10:57:01 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00