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gatk-3.8/PairHMM_JNI
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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
..
.gitignore 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
JNI_README Same log message as before - forgot -a option 2014-01-16 21:40:04 -08:00
Makefile 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
avx_function_instantiations.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
baseline.cc Added support for dynamic selection between AVX and un-vectorized C++, 2014-01-18 11:07:23 -08:00
define-double.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
define-float.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
define-sse-double.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
define-sse-float.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
headers.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
pairhmm-1-base.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
pairhmm-template-kernel.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
pairhmm-template-main.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
run.sh 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
shift_template.c 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
sse_function_instantiations.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
template.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
utils.cc 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
utils.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
vector_defs.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00
vector_function_prototypes.h 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the 2014-01-20 08:03:42 -08:00