gatk3的最后一个经典版本3.8

Mark DePristo b7511c5ff3 Fixed long-standing bug in tribble index creation ... -- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write -- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index -- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils -- VCFWriter now requires the master sequence dictionary -- Updated walkers that create VCFWriters to provide the master sequence dictionary		2011-09-20 10:53:18 -04:00
public	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00
settings	Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.	2011-09-06 20:39:42 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.	2011-09-20 00:14:35 -04:00
ivy.xml	To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.	2011-09-20 00:14:35 -04:00