David Roazen 07b369ca7e Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package ... This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.		2012-12-19 10:25:22 -05:00
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commandline	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
gatk	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
TestNGTestTransformer.java	Add custom TestNGTestTransformer that adds a maximum test runtime of 10 minutes to all testng tests	2012-11-01 15:34:12 -04:00
WalkerTest.java	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00