Roger Zurawicki 538cdf9210 Created the FindCoveredIntervals ... Moved some stuff in the DiagnoseTargets walker to the more general ThresHolder class Minor tweaks FindCoveredIntervals supports Gathering FindCoveredIntervals outputs an interval list instead of GATKReport Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>		2012-06-13 11:15:25 -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	Created the FindCoveredIntervals	2012-06-13 11:15:25 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -04:00
testdata	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00