gatk3的最后一个经典版本3.8

Mark DePristo f277d7c09e Removing parallelism bottleneck in the GATK ... -- GenomeLocParser cache was a major performance bottleneck in parallel GATK performance. With 10 thread > 50% of each thread's time was spent blocking on the MasterSequencingDictionary object. Made this a thread local variable. -- Now we can run the GATK with 48 threads efficiently on GSA4! -- Running -nt 1 => 75 minutes (didn't let is run all of the way through so likely would take longer) -- Running -nt 24 => 3.81 minutes		2012-08-15 21:13:15 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Expanded the BQSR reporting script	2012-08-12 13:45:14 -04:00
public	Removing parallelism bottleneck in the GATK	2012-08-15 21:13:15 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Fix an issue with the classpath for external builds in build.xml	2012-08-15 16:08:21 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00