gatk3的最后一个经典版本3.8

Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects ... -- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples -- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type. -- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name) -- Integrationtests updated and all pass		2011-11-11 15:00:35 -05:00
public	VariantContext genotypes are now stored as GenotypeMap objects	2011-11-11 15:00:35 -05:00
settings	Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.	2011-11-09 15:24:29 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
ivy.xml	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00