Mark DePristo c7864c7256 Filter application order is now deterministic, in the order defined by the walker ... -- For no apparent reason we were using a HashSet to store the ReadFilters, so the order of operations was really arbitrarily applied. The order now is (1) the order of the walker intrinsic filters (2) read group black list (if provided) (3) command line filters (if provided)		2011-10-06 18:51:40 -07:00
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R	Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'.	2011-10-05 18:30:40 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	…
doc	…
java	Filter application order is now deterministic, in the order defined by the walker	2011-10-06 18:51:40 -07:00
packages	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	GATK read group requirement iron hand	2011-10-06 08:40:35 -07:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00