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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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Karthik Gururaj 8240ea826e Changes: 
1. Added TRISTATE_CORRECTION in pairhmm-template-kernel.cc (function
stripINITIALIZATION)
2. Added VEC_DIV macros to define-double.h and define-float.h
3. Edited initializeVectors to match Java
C++ original:
*(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
*(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
Modified:
*(ptr_p_MY+r-1) = ctx.ph2pr[_d];
*(ptr_p_YY+r-1) = ctx.ph2pr[_c];
 		2014-01-15 10:48:58 -08:00
.gitignore Changes: 2014-01-15 10:48:58 -08:00
CHEATSHEET First import of AVX-JNI to git 2014-01-14 17:26:55 -08:00
Makefile Changes: 2014-01-15 10:48:58 -08:00
README First import of AVX-JNI to git 2014-01-14 17:26:55 -08:00
define-double.h Changes: 2014-01-15 10:48:58 -08:00
define-float.h Changes: 2014-01-15 10:48:58 -08:00
hmm_mask.cc Changes: 2014-01-15 10:48:58 -08:00
org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc Changes: 2014-01-15 10:48:58 -08:00
org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h First import of AVX-JNI to git 2014-01-14 17:26:55 -08:00
pairhmm-1-base.cc First import of AVX-JNI to git 2014-01-14 17:26:55 -08:00
pairhmm-template-kernel.cc Changes: 2014-01-15 10:48:58 -08:00
pairhmm-template-main.cc Changes: 2014-01-15 10:48:58 -08:00
shift_template.c First import of AVX-JNI to git 2014-01-14 17:26:55 -08:00
template.h Changes: 2014-01-15 10:48:58 -08:00

README 

How to compile:
/opt/intel/bin/icc pairhmm-template-main.cc -o pairhmm-template-main.o -O3 -W -Wall -lm -xAVX

------------------------------------
How to run:
./pairhmm-template-main.o < ./test_data/largeTest.in > large.out
./pairhmm-template-main.o < ./test_data/mediumTest.in > medium.out
-------------------------------------
Results:
-------------------------------------
MEDIUM FLOAT:
AVX Read Time: 8019020
AVX Compute Time: 29270238
AVX Write Time: 242170
AVX Total Time: 37531428
# Double called: 0
-------------------------------------
MEDIUM HYBRID:
AVX Read Time: 7596629
AVX Compute Time: 29979220
AVX Write Time: 248485
AVX Total Time: 37824334
# Double called: 20329
-------------------------------------
LARGE FLOAT:
AVX Read Time: 111888586
AVX Compute Time: 408131806
AVX Write Time: 3477892
AVX Total Time: 523498284
# Double called: 0
-------------------------------------
LARGE HYBRID:
AVX Read Time: 109728994
AVX Compute Time: 419475317
AVX Write Time: 3575364
AVX Total Time: 532779675
# Double called: 310042