Mark DePristo 42bf9adede Initial version of "fast" FragmentPileup code ... -- Uses mayOverlapRoutine in ReadUtils -- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations -- PileupElement now comparable (sorts on offset than on start) -- Caliper microbenchmark to assess performance		2011-10-22 21:36:37 -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	Initial version of "fast" FragmentPileup code	2011-10-22 21:36:37 -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jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00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	Initial version of "fast" FragmentPileup code	2011-10-22 21:36:37 -04:00
BaseTest.java	Made the BaseTest.testDir absolute	2011-10-06 22:33:21 -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