gatk-3.8/public
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
..
R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
doc
java NanoScheduler optimization: don't use a PriorityBlockingQueue for the MapResultsQueue 2012-12-24 13:35:56 -05:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00