6 Commits (a648b5e65e8ce2f64fddc5fef4017d7de15f39fb)

Author	SHA1	Message	Date
Khalid Shakir	91cb654791	AggregateMetrics: ... - By porting from jython to java now accessible to Queue via automatic extension generation. - Better handling for problematic sample names by using PicardAggregationUtils. GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name. CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering. Added SelectHeaders walker for filtering headers for dbGAP submission. Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter. Latest WholeGenomePipeline. Other minor cleanup to utility methods.	2012-04-17 11:45:32 -04:00
Mark DePristo	67b022c34b	Cleanup for new SampleUtils function ... -- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase	2011-11-10 13:27:13 -05:00
Mark DePristo	178ba24c27	Move getSamplesForSamFile to SampleUtils ... -- A nearly identical piece of code already lived in SampleUtils. Now there are two functions, one taking a regular header and another grabbing the merged header from the GATK engine itself. Much cleaner	2011-09-30 10:28:18 -04:00
Mark DePristo	3e93f246f7	Support for sample sets in AssignSomaticStatus ... -- Also cleaned up SampleUtils.getSamplesFromCommandLine() to return a set, not a list, and trim the sample names.	2011-09-19 11:40:45 -04:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00