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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
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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
R Ready for integration with queue script 2010-09-24 19:46:01 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java 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
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Fix for DoC issue with multiplexer -- will retire use of multiplexer when 2010-09-07 00:44:07 +00:00
perl Nightly test for Queue-based pipeline. 2010-09-27 05:24:58 +00:00
python Do this the right way 2010-09-19 04:30:48 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Default memory limit is now 4g (apparently necessary when testing on full 100-sample Autism_Daly dataset) 2010-09-27 05:43:08 +00:00
settings The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
shell Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Enhancements to build external projects for walker sharing. 2010-09-24 21:17:16 +00:00
ivy.xml Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00