gatk3的最后一个经典版本3.8

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Karthik Gururaj 37526dfad5 1. Added the catch UnsatisfiedLinkError exception in PairHMMLikelihoodCalculationEngine.java to fall back to LOGLESS_CACHING in case the native library could not be loaded. Made VECTOR_LOGLESS_CACHING as the default implementation. 2. Updated the README with Mauricio's comments 3. baseline.cc is used within the library - if the machine supports neither AVX nor SSE4.1, the native library falls back to un-vectorized C++ in baseline.cc. 4. pairhmm-1-base.cc: This is not part of the library, but is being heavily used for debugging/profiling. Can I request that we keep it there for now? In the next release, we can delete it from the repository. 5. I agree with Mauricio about the ifdefs. I am sure you already know, but just to reassure you the debug code is not compiled into the library (because of the ifdefs) and will not affect performance.		2014-02-28 08:59:55 -08:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	1. Added the catch UnsatisfiedLinkError exception in	2014-02-28 08:59:55 -08:00
public	1. Added the catch UnsatisfiedLinkError exception in	2014-02-28 08:59:55 -08:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Native library part of git repo	2014-02-26 11:44:28 -08:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Add ability to run *KnowledgeBaseTests to maven	2014-02-11 14:08:24 -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
pom.xml	Moved private/scala/test to private/queue-private/src/test/scala	2014-02-22 01:21:35 +08:00

README.md

The Genome Analysis Toolkit

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