depristo 3fd2392090 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4155 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-28 22:53:32 +00:00
..
alignment	Disabled AlignerIntegrationTest while addressing build machine memory issues.	2010-08-14 01:23:21 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Add the calculated lod value to the info field of each recalibrated VCF record.	2010-08-27 21:33:58 +00:00
oneoffprojects/walkers	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
playground	Cleaning up playground utils and tests	2010-08-27 01:25:47 +00:00
utils	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
BaseTest.java	Moving pointer to b36 reference from /broad/1KG to /humgen/1kg	2010-08-13 00:54:34 +00:00
WalkerTest.java	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