gatk3的最后一个经典版本3.8
 
 
 
 
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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
licensing Final final final version of the license. 2012-07-20 18:00:02 -04:00
protected/java Optimization of BQSR 2012-12-24 13:35:09 -05:00
public NanoScheduler optimizations and simplification 2012-12-24 13:35:57 -05:00
settings Final r119 tribble jar 2012-11-02 14:30:33 -04:00
.gitignore adding some directories to gitignore 2012-09-27 11:09:41 -04:00
build.xml Incorporating clover into build.xml 2012-12-24 13:35:57 -05:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
ivy.xml Use build jars in test classpaths by default 2012-11-28 22:57:04 -05:00