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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo e19c24f3ee Bugfix for HaplotypeCaller error: Only one of refStart or refStop must be < 0, not both 
-- This occurred because we were reverting reads with soft clips that would produce reads with negative (or 0) alignment starts.  From such reads we could end up with adaptor starts that were negative and that would ultimately produce the "Only one of refStart or refStop must be < 0, not both" error in the FragmentUtils merging code (which would revert and adaptor clip reads).
-- We now hard clip away bases soft clipped reverted bases that fall before the 1-based contig start in revertSoftClippedBases.
-- Replace buggy cigarFromString with proper SAM-JDK call TextCigarCodec.getSingleton().decode(cigarString)
-- Added unit tests for reverting soft clipped bases that create a read before the contig
-- [delivers #50892431]
 		2013-06-04 10:33:46 -04:00
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commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk Check that -compress arguments are within range 0-9 2013-05-31 15:29:02 -04:00
jna Fix more tests that fail when run in parallel on the farm 2013-03-12 16:53:30 -04:00
utils Bugfix for HaplotypeCaller error: Only one of refStart or refStop must be < 0, not both 2013-06-04 10:33:46 -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 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 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 Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00