Mark DePristo 81bd7646d6 Fix for MISSING floats ... -- Restructured code to separate the MISSING value in java (currently everywhere a null) from the byte representation on disk (an int). -- Now handles correctly MISSING qual fields		2012-05-24 10:56:53 -04:00
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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
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	Fix for MISSING floats	2012-05-24 10:56:53 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	build system overhaul	2012-05-17 15:16:29 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Minor updates to pacbio data processing script to make it work with the latest bwa version/settings.	2012-05-22 10:24:45 -04:00
testdata	Extensive refactoring of the GATKReports. This was a beast.	2012-05-18 01:11:26 -04:00