Roger Zurawicki c0c676590b First implementation of GATKReportGatherer ... - Added the GATKReportGatherer - Added private methods in GATKReport to combine Tables and Reports - It is very conservative and it will only gather if the table columns, match. - At the column level it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data. Added the gatherer functions to CoverageByRG Also added the scatterCount parameter in the Interval Coverage script Made some more GATKReport methods public The UnitTest included shows that the merging methods work Added a getter for the PrimaryKeyName Fixed bugs that prevented the gatherer form working Working GATKReportGatherer Has only the functional to addLines The input file parser assumes that the first column is the primary key Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>		2012-02-07 18:14:47 -05:00
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R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
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	First implementation of GATKReportGatherer	2012-02-07 18:14:47 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Small script to chunk up a VCF into equal-sized chunks	2012-02-02 12:29:03 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00