gatk3的最后一个经典版本3.8

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Karthik Gururaj 7180c392af 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the SSE compilation warning. 2. Added code to dynamically select between AVX, SSE4.2 and normal C++ (in that order) 3. Created multiple files to compile with different compilation flags: avx_function_prototypes.cc is compiled with -xAVX while sse_function_instantiations.cc is compiled with -xSSE4.2 flag. 4. Added jniClose() and support in Java (HaplotypeCaller, PairHMMLikelihoodCalculationEngine) to call this function at the end of the program. 5. Removed debug code, kept assertions and profiling in C++ 6. Disabled OpenMP for now.		2014-01-20 08:03:42 -08:00
PairHMM_JNI	1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the	2014-01-20 08:03:42 -08:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the	2014-01-20 08:03:42 -08:00
public	1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the	2014-01-20 08:03:42 -08:00
settings	Rev'ing the Variant jar to incorporate some patches to the BCF encoder that Menachem needs.	2014-01-02 23:33:17 -05:00
.gitignore	Added support for dynamic selection between AVX and un-vectorized C++,	2014-01-18 11:07:23 -08:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	1. Added support for JNI integration for LoglessCaching PairHMM AVX	2014-01-15 11:07:09 -08:00
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	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

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