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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo f42bb86bdd e# This is a combination of 2 commits. 
Only try to clip adaptors when both reads of the pair are on opposite strands

-- Read pairs that have unusual alignments, such as two reads both oriented like:

  <-----
     <-----

where previously having their adaptors clipped as though the standard calculation of the insert size was meaningful, which it is not for such oddly oriented pairs.  This caused us to clip extra good bases from reads.
-- Update MD5s due change in adaptor clipping, which add some coverage in some places
 		2013-05-03 11:19:14 -04:00
..
commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk e# This is a combination of 2 commits. 2013-05-03 11:19:14 -04:00
jna Fix more tests that fail when run in parallel on the farm 2013-03-12 16:53:30 -04:00
utils e# This is a combination of 2 commits. 2013-05-03 11:19:14 -04:00
BaseTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -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 Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
WalkerTest.java Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00