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gatk-3.8/public/java/test/org/broadinstitute/sting
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Eric Banks 83e09b1f64 Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. 
Basically, it does 3 things (as opposed to having to call into 3 separate walkers):
1. merge the records at any given position into a single one with all alleles and appropriate PLs
2. re-genotype the record using the exact AF calculation model
3. re-annotate the record using the VariantAnnotatorEngine

In the course of this work it became clear that we couldn't just use the simpleMerge() method used
by CombineVariants; combining HC-based gVCFs is really a complicated process.  So I added a new
utility method to handle this merging and pulled any related code out of CombineVariants.  I tried
to clean up a lot of that code, but ultimately that's out of the scope of this project.

Added unit tests for correctness testing.
Integration tests cannot be used yet because the HC doesn't output correct gVCFs.
 		2013-12-31 12:07:56 -05:00
..
commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk Fixed bug in the filtering of lifted over variants where a deletion at the end of a contig could cause it to error out. 2013-12-11 14:07:18 -05:00
jna Fix pipeline tests that were not respecting the pipeline test dry run setting 2013-06-28 15:27:17 -04:00
utils Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. 2013-12-31 12:07:56 -05:00
BaseTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
ExampleToCopyUnitTest.java Add a class-based DataProvider 2013-12-03 13:31:01 -05:00
MD5DB.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
MD5Mismatch.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
WalkerTest.java Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy 2013-12-03 23:12:14 -05:00