gatk3的最后一个经典版本3.8

Mark DePristo a481d006f0 Optimizations for applying BQSR table with PrintReads ... -- Cleaned up code in updateDataForRead so that constant values where not computed in inner loops -- BaseRecalibrator doesn't create it's own fasta index reader, it just piggy backs on the GATK one -- ReadCovariates <init> now uses a thread local cache for it's int[][][] keys member variable. This stops us from recreating an expensive array over and over. In order to make this really work had to update recordValues in ContextCovariate so it writes 0s over base values its skipping because of low quality base clipping. Previously the values in the ReadCovariates keys were 0 because they were never modified by ContextCovariates. Now these values are actually zero'd out explicitly by the covariates.		2012-12-17 16:47:27 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Optimizations for applying BQSR table with PrintReads	2012-12-17 16:47:27 -05:00
public	Optimizations for applying BQSR table with PrintReads	2012-12-17 16:47:27 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Refactored entire NA12878KB to allow us to easily build a na12878kb.jar for IGV integration	2012-11-29 14:38:09 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Use build jars in test classpaths by default	2012-11-28 22:57:04 -05:00