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Valentin Ruano-Rubio 89c4e57478 gVCF <NON_REF> in all vcf lines including variant ones when –ERC gVCF is requested. 
Changes:
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  <NON_REF> likelihood in variant sites is calculated as the maximum possible likelihood for an unseen alternative allele: for reach read is calculated as the second best likelihood amongst the reported alleles.

  When –ERC gVCF, stand_conf_emit and stand_conf_call are forcefully set to 0. Also dontGenotype is set to false for consistency sake.

  Integration test MD5 have been changed accordingly.

Additional fix:
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  Specially after adding the <NON_REF> allele, but also happened without that, QUAL values tend to go to 0 (very large integer number in log 10) due to underflow when combining GLs (GenotypingEngine.combineGLs). To fix that combineGLs has been substituted by combineGLsPrecise that uses the log-sum-exp trick.

  In just a few cases this change results in genotype changes in integration tests but after double-checking using unit-test and difference between combineGLs and combineGLsPrecise in the affected integration test, the previous GT calls were either border-line cases and or due to the underflow.
 		2014-01-30 11:23:33 -05:00
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commandline Adding the functionality to enable users to input a file of VCFs for -V. 2014-01-08 00:45:00 -05:00
gatk Updated SAMPileup codec and pileup-related docs 2014-01-14 09:14:16 -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 gVCF <NON_REF> in all vcf lines including variant ones when –ERC gVCF is requested. 2014-01-30 11:23:33 -05:00
BaseTest.java Fix for the PairHMM transition probability miscalculation. 2014-01-26 16:30:36 -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