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Mark DePristo 6be5e82860 VariantEval scalability optimizations
-- StateKey no longer extends TreeMap.  It's now a final immutable data structure that caches it's toString and hashcode values.  TODO optimizations to entirely remove the TreeMap and just store the HashMap for performance and use the tree for the sorted tostring function.
-- NewEvaluationContext has a method makeStateKey() that contains all of the functionality that once was spread around VEUtils
-- AnalysisModuleScanner uses an annotationCache to speed up the reflections getAnnotations() call when invoked over and over on the same objects.  Still expensive to convert each field to a string for the cache, but the only way around that is a complete refactoring of the toTransversalDone of VE
-- VariantEvaluator base class has a cached getSimpleName() function
-- VEUtils: general cleanup due to refactoring of StateKey
-- VEWalker: much better iteration of map data structures.  If you need access to iterate over all key/value pairs use the Map.Entry construct with entrySet.  This is far better than iterating over the keys and calling get() on each key.
2012-03-26 16:28:48 -04:00
public VariantEval scalability optimizations 2012-03-26 16:28:48 -04:00
settings Rev. tribble to fix BED codec bug in tribble 51 2012-01-17 16:40:26 -05:00
.gitignore Minor additions to the shared .gitignore file, now that Mark has checked one in. 2011-10-26 12:24:28 -04:00
LICENSE One last test... 2011-06-28 19:18:17 -04:00
build.xml Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
ivy.xml S3 upload now directly creates the XML report in memory and puts that in S3 2012-01-29 15:14:58 -05:00