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
..
VectorPairHMM	Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK.	2014-03-05 10:11:03 -08:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
external-example	Fixed mvn run for packagetests over external-example.	2014-02-22 01:21:34 +08:00
gatk-framework	Logger output should go to STDERR instead of STDOUT	2014-03-05 10:01:06 -05:00
gatk-package	Fixed scope for test-jar depedencies.	2014-02-22 01:21:34 +08:00
gatk-queue-extgen	Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script.	2014-02-03 13:50:46 -05:00
gsalib	Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution.	2014-02-06 08:25:38 -05:00
java/config	Moved files to maven directories.	2014-02-03 13:50:44 -05:00
package-tests	Separate failsafe directories for each of the integration test types [#66515572]	2014-02-27 04:43:39 +08:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
queue-framework	Added tests for cleaning up scattered .bai files, and using the log directory.	2014-02-26 02:11:28 +08:00
queue-package	Fixed scope for test-jar depedencies.	2014-02-22 01:21:34 +08:00
repo	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
sting-root	Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK.	2014-03-05 10:11:03 -08:00
sting-utils	Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK.	2014-03-05 10:11:03 -08:00
pom.xml	Adding the external example to the build.	2014-02-15 01:26:07 +08:00