Mark DePristo 46e7370128 this.allele, getAlleles(), and getAltAlleles() now return List not set ... -- Changes associated code throughout the codebase -- Updated necessary (but minimal) UnitTests to reflect new behavior -- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC		2011-10-09 11:45:55 -07:00
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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	…
doc	…
java	this.allele, getAlleles(), and getAltAlleles() now return List not set	2011-10-09 11:45:55 -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