gatk3的最后一个经典版本3.8

Mark DePristo dcc972a557 Usability cleanup for BQSR ... -- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private. -- Throw an exception if its required bintag argument is missing -- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate -- Show the type (Required, Experimental, Standard) of the covariates when running --list		2012-08-25 14:53:00 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Bug fix for popular _Duplicate allele added to VariantContext_ error reported on the forum. It seems to be due to lower case bases in the reference being treated as reference mismatches. We would try to turn these mismatches into SNP events, for example c/C. We now uppercase the result from IndexedFastaSequenceFile.getSubsequenceAt()	2012-08-22 14:39:35 -04:00
public	Usability cleanup for BQSR	2012-08-25 14:53:00 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00