gatk-3.8/public
Mark DePristo 295455eee2 NanoScheduler optimizations and simplification
-- The previous model was to enqueue individual map jobs (with a resolution of 1 map job per map call), to track the number of map calls submitted via a counter and a semaphore, and to use this information in each map job and reduce to control the number of map jobs, when reduce was complete, etc.  All hideously complex.
-- This new model is vastly simply.  The reducer basically knows nothing about the control mechanisms in the NanoScheduler.  It just supports multi-threaded reduce.  The NanoScheduler enqueues exactly nThread jobs to be run, which continually loop reading, mapping, and reducing until they run out of material to read, when they shut down.  The master thread of the NS just holds a CountDownLatch, initialized to nThreads, and when each thread exits it reduces the latch by 1.  The master thread gets the final reduce result when its free by the latch reaching 0.  It's all super super simple.
-- Because this model uses vastly fewer synchronization primitives within the NS itself, it's naturally much faster at getting things done, without any of the overhead obvious in profiles of BQSR -nct 2.
2012-12-24 13:35:57 -05:00
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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 optimizations and simplification 2012-12-24 13:35:57 -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