Mark DePristo 9f260c0dc1 Zero byte index bug fix for RandomlySplitVariants + cleanup ... -- vcfWriter2 was never being closed in onTraversalDone(), so the on the fly index file was being created but never actually properly written to the file. -- This bug is ultimately due to the inability of the GATK to allow multiple VCF output writers as @Output arguments, though -- Removed the unnecessary local variable iFraction, = 1000 * the input fraction argument. Now the system just uses a double random number and compares to the input fraction at all. Is there some subtle reason I don't appreciate for this programming construct?		2011-11-04 09:45:20 -04:00
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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	Zero byte index bug fix for RandomlySplitVariants + cleanup	2011-11-04 09:45:20 -04:00
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	Bug fix to avoid infinite loop in GATKScatterFunction	2011-11-02 16:20:42 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00