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gatk-3.8/public/java/test/org/broadinstitute/sting
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Eric Banks 9c0207f8ef Fixing BQSR/BAQ bug: 
If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would
fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases).
The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated.
Added a unit test to ensure that the tags are removed in such a case.
 		2013-01-31 11:03:17 -05:00
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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
BaseTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ExampleToCopyUnitTest.java UnitTesting example for copying 2013-01-30 11:19:08 -05:00
MD5DB.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
WalkerTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00