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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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rpoplin 0a06fbdb94 Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4288 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-15 16:45:03 +00:00
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arguments Removing the obsolete --hapmap and --hapmap_chip options 2010-08-31 16:57:05 +00:00
contexts/variantcontext Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
datasources Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis 2010-09-15 11:50:22 +00:00
executive A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
filters Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
iterators Eliminated -mrl option. 2010-08-26 21:38:03 +00:00
refdata Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
traversals Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +00:00
walkers Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt. 2010-09-15 16:45:03 +00:00