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gatk-3.8/public/java/src/org/broadinstitute/sting/gatk
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Mark DePristo 38969b9783 Prototype of RODBinding @Arguments instead of -B syntax 
Initial version of RodBinding class.
Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard).  Will need refactoring.
 		2011-07-26 11:09:06 -04:00
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arguments Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
contexts Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
datasources refdata directory cleanup 2011-07-25 13:21:52 -04:00
examples Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
executive Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
filters gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs 2011-07-23 20:00:35 -04:00
io Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
iterators Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
phonehome Enumerated types are working. 2011-07-24 18:14:21 -04:00
refdata refdata directory cleanup 2011-07-25 13:21:52 -04:00
report Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 2011-07-19 18:38:53 -04:00
traversals Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
walkers Prototype of RODBinding @Arguments instead of -B syntax 2011-07-26 11:09:06 -04:00
CommandLineExecutable.java Prototype of RODBinding @Arguments instead of -B syntax 2011-07-26 11:09:06 -04:00
CommandLineGATK.java Includes non-concrete classes in docs 2011-07-23 22:15:01 -04:00
DownsampleType.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
DownsamplingMethod.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeAnalysisEngine.java refdata directory cleanup 2011-07-25 13:21:52 -04:00
ReadMetrics.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
ReadProperties.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
WalkerManager.java Removed previous, and largely unused, help system extensions. 2011-07-22 09:42:44 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00