Eric Banks 573ed07ad0 Fixed reported bug in BQSR for RNA seq alignments with Ns. ... * ClippingOp updated to incorporate Ns in the hard clips. * ReadUtils.getReadCoordinateForReferenceCoordinate() updated to account for Ns. * Added test that covers the BQSR case we saw. * Created GSA-856 (for Mauricio) to add lots of tests to ReadUtils. * It will require refactoring code and not in the scope of what I was willing to do to fix this.		2013-03-14 11:26:52 -04:00
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commandline	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
gatk	Increase timeout for a test in the EngineFeaturesIntegrationTest	2013-03-12 23:53:26 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Fixed reported bug in BQSR for RNA seq alignments with Ns.	2013-03-14 11:26:52 -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	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00