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

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How to run:
./pairhmm-template-main.o < ./test_data/largeTest.in > large.out
./pairhmm-template-main.o < ./test_data/mediumTest.in > medium.out
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Results:
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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
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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