gatk3的最后一个经典版本3.8

Eric Banks 4bb7a99f08 Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.		2012-09-12 11:51:44 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings).	2012-09-12 11:24:53 -04:00
public	Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.	2012-09-12 11:51:44 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	More memory for gatkdocs and extracthelp targets	2012-09-05 15:45:22 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00