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
..
R	Fixing errors in queueJobReport runtime unit	2011-10-07 12:04:53 -07:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Initial version of "fast" FragmentPileup code	2011-10-22 21:36:37 -04:00
packages	Enable testing of the jars produced by the packaging system.	2011-10-14 03:08:28 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	no sort order	2011-10-20 18:44:09 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00