Mark DePristo c2b97030a4 IntervalUtils for completely balanced locus-based scatter/gather ... -- scatterLocusIntervals master utility -- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc -- Util function for reversing a list (List<T> -> List<T>, unlike Collections version) -- DoC is PartitionType.INTERVAL -- Significant unit tests on new functionality (all passing) -- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work		2011-11-02 10:49:40 -04:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	IntervalUtils for completely balanced locus-based scatter/gather	2011-11-02 10:49:40 -04:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00