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gatk3的最后一个经典版本3.8
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Intel Repocontact 0e4f2ac9e1 Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. 
C++ code has PAPI calls for reading hardware counters

Followed Khalid's suggestion for packing libVectorLoglessCaching into
the jar file with Maven

Native library part of git repo

1. Renamed directory structure from public/c++/VectorPairHMM to
public/VectorPairHMM/src/main/c++ as per Khalid's suggestion
2. Use java.home in public/VectorPairHMM/pom.xml to pass environment
variable JRE_HOME to the make process. This is needed because the
Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among
others). Assuming that the Maven build process uses a JDK (and not just
a JRE), the variable java.home points to the JRE inside maven.
3. Dropped all pretense at cross-platform compatibility. Removed Mac
profile from pom.xml for VectorPairHMM

Moved JNI_README

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.

1. Changed logger.info to logger.warn in PairHMMLikelihoodCalculationEngine.java
2. Committing the right set of files after rebase

Added public license text to all C++ files

Added license to Makefile

Add package info to Sandbox.java

Conflicts:
	protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
	protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
	protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java
	protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
	protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
	public/VectorPairHMM/src/main/c++/.gitignore
	public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc
	public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
	public/VectorPairHMM/src/main/c++/Makefile
	public/VectorPairHMM/src/main/c++/Sandbox.cc
	public/VectorPairHMM/src/main/c++/Sandbox.h
	public/VectorPairHMM/src/main/c++/Sandbox.java
	public/VectorPairHMM/src/main/c++/Sandbox_JNIHaplotypeDataHolderClass.h
	public/VectorPairHMM/src/main/c++/Sandbox_JNIReadDataHolderClass.h
	public/VectorPairHMM/src/main/c++/baseline.cc
	public/VectorPairHMM/src/main/c++/define-double.h
	public/VectorPairHMM/src/main/c++/define-float.h
	public/VectorPairHMM/src/main/c++/define-sse-double.h
	public/VectorPairHMM/src/main/c++/define-sse-float.h
	public/VectorPairHMM/src/main/c++/headers.h
	public/VectorPairHMM/src/main/c++/jnidebug.h
	public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
	public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
	public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
	public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
	public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc
	public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
	public/VectorPairHMM/src/main/c++/run.sh
	public/VectorPairHMM/src/main/c++/shift_template.c
	public/VectorPairHMM/src/main/c++/utils.cc
	public/VectorPairHMM/src/main/c++/utils.h
	public/VectorPairHMM/src/main/c++/vector_function_prototypes.h
 		2014-03-05 10:11:03 -08:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. 2014-03-05 10:11:03 -08:00
public Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. 2014-03-05 10:11:03 -08:00
settings/helpTemplates Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
.gitignore Adding the external example to the build. 2014-02-15 01:26:07 +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 Separate failsafe directories for each of the integration test types [#66515572] 2014-02-27 04:43:39 +08:00

README.md

The Genome Analysis Toolkit

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