gatk3的最后一个经典版本3.8

Eric Banks 3d476487c6 LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP.		2012-08-27 12:13:12 -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	LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP.	2012-08-27 12:13:12 -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