Mark DePristo c503884958 GSA-515 Nanoscheduler GSA-551 / Optimize nanoScheduling performance of UnifiedGenotyper ... -- I've rewritten the entire NS framework to use a producer / consumer model for input -> map and from map -> reduce. This is allowing us to scale reasonably efficiently up to 4 threads (see figure). Future work on the nano scheduler will be itemized in a separate JIRA entry. -- Restructured the NS code for clarity. Docs everywhere. -- This is considered version 1.0		2012-09-07 09:15:16 -04:00
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commandline	- New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs.	2012-09-04 16:41:44 -04:00
gatk	Downsampling: experimental engine integration	2012-09-06 15:03:27 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	GSA-515 Nanoscheduler GSA-551 / Optimize nanoScheduling performance of UnifiedGenotyper	2012-09-07 09:15:16 -04:00
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	…
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00