gatk3的最后一个经典版本3.8

Mark DePristo ff26f2bf68 HierarchicalMicroScheduler no longer attempts to wrap exceptions ... -- This behavior, which isn't obviously valuable at all, continued to grab and rethrow exceptions in the HMS that, if run without NT, would show up as more meaningful errors. Now HMS simply checks whether the throwable it received on error was a RuntimeException. If so, it is stored and rethrow without wrapping later. If it isn't, only in this case is the exception wrapped in a ReviewedStingException. -- Added a QC walker ErrorThrowingWalker that will throw a UserException, ReviewedStingException, and NullPointerException from map as specified on the command line -- Added IT that ensures that all three types are thrown properly (i.e., you catch a NullPointerException when you ask for one to be thrown) with and without threading enabled. -- I believe this will finally put to rest all of these annoying HMS captures.		2012-03-23 11:27:21 -04:00
public	HierarchicalMicroScheduler no longer attempts to wrap exceptions	2012-03-23 11:27:21 -04:00
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -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	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
ivy.xml	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00