ebanks 83b9d63d59 1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files. ... 2. Used said mapping to implement N-way-in,N-way-out functionality in the new indel cleaner. Still needs more testing (to be done after vacation but preliminary tests look good). 3. Fixes to VCF validator: ignore case when testing VCF reference base against true reference base and allow quals of -1 (as per spec). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2773 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-04 04:12:49 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files.	2010-02-04 04:12:49 +00:00
test/org/broadinstitute/sting	some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach).	2010-02-02 23:13:10 +00:00