David Roazen 5baf906c28 Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists ... -The algorithm for finding the intersection of two sets of intervals relies on the sortedness of the intervals within each set, but the engine was not sorting the intervals before attempting to find the intersection. -The result was that if one or both interval lists was unsorted / lexicographically sorted, we would often fail to find the intersection correctly. -Now the IntervalBinding sorts all sets of intervals before returning them, solving the problem. -Added an integration test for this case. GSA-909 #resolve		2013-04-02 14:01:52 -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	Refactored the het (polyploid) consensus creation in ReduceReads.	2013-03-25 09:34:54 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists	2013-04-02 14:01:52 -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