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gatk-3.8/java/test/org/broadinstitute/sting
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bthomas 96cccafb0d Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-28 02:16:25 +00:00
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alignment all fixed..thanks Matt! 2010-09-10 06:18:59 +00:00
commandline 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
datasources/pipeline Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
gatk Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +00:00
oneoffprojects/walkers The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 2010-09-21 18:21:22 +00:00
playground/gatk/walkers Recent changes to the build system make the build system complain loudly about 2010-09-24 22:09:12 +00:00
utils Recent changes to the build system make the build system complain loudly about 2010-09-24 22:09:12 +00:00
BaseTest.java 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
WalkerTest.java Added a back door so that integration tests can reset the sequence dictionary 2010-09-14 18:58:08 +00:00