gatk3的最后一个经典版本3.8

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Mark DePristo d5dd3b23db Rev picard to get optimized tribble feature reads -- The previous version of TribbleIndexedFeatureReader.query() would open a RandomAccessFile each time the GATK crossed a shard boundary. When running with -L wex.intervals (or any time there were lots of intervals) we'd be opening and closing enormous numbers of files, radically slowing down the GATK. With these patched versions of Tribble we see something like the following performance improvements: SelectVariants with -L wex.intervals on my local machine against non-local file pre-patch => 3 hours post-patch => 30 seconds		2013-08-02 10:31:36 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Better caching for the HaplotypeCaller	2013-08-02 01:27:29 -04:00
public	Better caching for the HaplotypeCaller	2013-08-02 01:27:29 -04:00
settings	Rev picard to get optimized tribble feature reads	2013-08-02 10:31:36 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	build.xml: make ant -p output only important build targets	2013-07-19 14:35:00 -04:00
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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/