Eric Banks 8777288a9f Don't throw a UserException if too many alt alleles are trying to be genotyped. Instead, I've added an argument that allows the user to set the max number of alt alleles to genotype and the UG warns and skips any sites with more than that number.		2011-12-09 00:00:20 -05:00
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R	Compacting pdfs when running under R 2.13+.	2011-10-27 14:51:56 -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	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	Don't throw a UserException if too many alt alleles are trying to be genotyped. Instead, I've added an argument that allows the user to set the max number of alt alleles to genotype and the UG warns and skips any sites with more than that number.	2011-12-09 00:00:20 -05:00
packages	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Queue now outputs a GATK-like header with version number, build timestamp, etc.	2011-11-23 14:28:35 -05:00
testdata	Testdata for IntervalStratification	2011-11-10 11:08:34 -05:00