Ryan Poplin ac033ce41a Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference.		2013-01-31 11:32:19 -05:00
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commandline	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
gatk	More aggressive checking of AWS key quality upon startup in the GATK	2013-01-31 09:08:38 -05:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
utils	Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference.	2013-01-31 11:32:19 -05:00
BaseTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ExampleToCopyUnitTest.java	UnitTesting example for copying	2013-01-30 11:19:08 -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	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
WalkerTest.java	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00