gatk3的最后一个经典版本3.8

Guillermo del Angel 99ed64933f OK, I had it with the validation site selector running for 60 hours (due to speed of genotype reading/parsing) in gsa3 only to fail in OnTraversalDone() because of some silly operator issue. Break up validation site selection process by chromosome, pick # of sites in each chromosome proportional to chr length, (taking care of roundoff issues to ensure precisely requested number of sites is kept), and then CombineVariants in the end. This also makes the selector run comfortably under 2Gb and thus can be easily LSF'ed		2011-11-18 07:52:52 -05:00
public	One quick fix to previous commit	2011-11-14 14:42:12 -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