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gatk-3.8/public/java/test/org/broadinstitute/sting
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Eric Banks ebd5404124 Fixed the add functionality of GenomeLocSortedSet. 
* Fixed GenomeLocSortedSet.add() to ensure that overlapping intervals are detected and an exception is thrown.
 * Fixed GenomeLocSortedSet.addRegion() by merging it with the add() method; it now produces sorted inputs in all cases.
 * Cleaned up duplicated code throughout the engine to create a list of intervals over all contigs.
 * Added more unit tests for add functionality of GLSS.
 * Resolves GSA-775.
 		2013-02-28 23:31:00 -05:00
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commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
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 Extend default timeout to 20 minutes 2013-02-13 17:43:40 -08:00
WalkerTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00