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gatk-3.8/public/java/test/org/broadinstitute/sting
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Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 
* This version inherits from the original SW implementation so it can use the same matrix creation method.
   * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the
     right thing for indels at the edges of the alignments.
     * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy.
   * Lots of systematic testing added for this implementation.
   * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.
 		2013-05-13 09:36:39 -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 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -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