gatk-3.8

Author	SHA1	Message	Date
Mauricio Carneiro	116885a450	Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.	2012-07-20 17:27:11 -04:00
Eric Banks	a42f90db11	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00
Mark DePristo	44bd9ae703	Restoring UninstantiableWalker, as it is not going to be possible to run ant test; ant gatkdocs without ant clean in between	2011-07-25 12:53:06 -04:00
Mark DePristo	acda8eb09c	Commented out test that causes new CommandLineGATK() to fail	2011-07-25 12:43:27 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00