Eric Banks dadcfe296d Reworking of the dangling tails merging code. ... We now run Smith-Waterman on the dangling tail against the corresponding reference tail. If we can generate a reasonable, low entropy alignment then we trigger the merge to the reference path; otherwise we abort. Also, we put in a check for low-complexity of graphs and don't let those pass through. Added tests for this implementation that checks exact SW results and correct edges added.		2013-06-11 12:53:04 -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	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Reworking of the dangling tails merging code.	2013-06-11 12:53:04 -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