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gatk-3.8/PairHMM_JNI
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Karthik Gururaj 018e9e2c5f 1. Cleaned up code 
2. Split into DebugJNILoglessPairHMM and VectorLoglessPairHMM with base
class JNILoglessPairHMM. DebugJNILoglessPairHMM can, in principle,
invoke any other child class of JNILoglessPairHMM.
3. Added more profiling code for Java parts of LoglessPairHMM
 		2014-01-26 19:18:12 -08:00
..
.gitignore Deleted libJNILoglessPairHMM.so from git tracking 2014-01-21 15:01:09 -08:00
JNI_README Same log message as before - forgot -a option 2014-01-16 21:40:04 -08:00
LoadTimeInitializer.cc Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
LoadTimeInitializer.h Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
Makefile 1. Cleaned up code 2014-01-26 19:18:12 -08:00
avx_function_instantiations.cc Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately. 2014-01-21 09:30:15 -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 Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately. 2014-01-21 09:30:15 -08:00
define-float.h Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately. 2014-01-21 09:30:15 -08:00
define-sse-double.h Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately. 2014-01-21 09:30:15 -08:00
define-sse-float.h Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately. 2014-01-21 09:30:15 -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
jni_common.h 1. Cleaned up code 2014-01-26 19:18:12 -08:00
jnidebug.h 1. Cleaned up code 2014-01-26 19:18:12 -08:00
org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc 1. Cleaned up code 2014-01-26 19:18:12 -08:00
org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc 1. Cleaned up code 2014-01-26 19:18:12 -08:00
org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
pairhmm-1-base.cc 1. Converted q,i,d,c in C++ from int* to char* 2014-01-22 22:57:32 -08:00
pairhmm-template-kernel.cc Split the inner loop to avoid the overhead incurred when -fPIC flag is enabled. 2014-01-21 11:47:30 -08:00
pairhmm-template-main.cc Added support to transfer haplotypes once per region to the JNI 2014-01-22 10:52:41 -08:00
run.sh 1. Cleaned up code 2014-01-26 19:18:12 -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. Converted q,i,d,c in C++ from int* to char* 2014-01-22 22:57:32 -08:00
utils.cc Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
utils.h Temporary commit before moving to new native library 2014-01-24 16:29:35 -08:00
vector_defs.h Merge branch 'master' of /home/mozdal/git/hmm into intel_pairhmm 2014-01-21 12:43:16 -08:00
vector_function_prototypes.h 1. Inserted #define in sandbox pairhmm-template-main.cc 2014-01-21 09:57:14 -08:00