Eric Banks 6eb87bf58a RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.		2011-10-06 15:57:49 -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	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.	2011-10-06 15:57:49 -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jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	Merged bug fix from Stable into Unstable	2011-10-06 12:54:52 -04:00
BaseTest.java	TestDataProvider now can be named	2011-09-22 17:04:32 -04:00
MD5DB.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00
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