fromer 50f7f18cbd Changed ReadBackedPhasing default PQ threshold to 10 ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4166 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-30 21:26:15 +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	Changed ReadBackedPhasing default PQ threshold to 10	2010-08-30 21:26:15 +00:00
test	Improved interface to getting command line options. Now fully traverses all objects to get all internal argument collections. Preliminary (but disabled version) of phoning home (see -et argument for more information). Captures correct and erroring out runs and writes out gzipped, xml report with lots of useful information. Needs a bit more information but is approximately working. Reports going to /humgen/gsa-hpprojects/GATK/reports/ in submitted directory that will be collated by some external tool. Only operating if -et STANDARD or -et STDOUT are provided currently and REPORT_DIR contains a file called ENABLE. WalkerTest now adds -et NO_ET to tests to avoid populating the reports with tests.	2010-08-28 22:53:32 +00:00