Mark DePristo 0f04485c24 NanoScheduler optimization: don't use a PriorityBlockingQueue for the MapResultsQueue ... -- Created a separate, limited interface MapResultsQueue object that previously was set to the PriorityBlockingQueue. -- The MapResultsQueue is now backed by a synchronized ExpandingArrayList, since job ids are integers incrementing from 0 to N. This means we avoid the n log n sort in the priority queue which was generating a lot of cost in the reduce step -- Had to update ReducerUnitTest because the test itself was brittle, and broken when I changed the underlying code. -- A few bits of minor code cleanup through the system (removing unused constructors, local variables, etc) -- ExpandingArrayList called ensureCapacity so that we increase the size of the arraylist once to accommodate the upcoming size needs		2012-12-24 13:35:56 -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	Added functionality of outputting sorted GATKReport Tables	2012-12-20 14:02:21 -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	NanoScheduler optimization: don't use a PriorityBlockingQueue for the MapResultsQueue	2012-12-24 13:35:56 -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