gatk-3.8/PairHMM_JNI/headers.h

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <stdint.h>
#include <assert.h>
#include <ctype.h>

#include <sys/time.h>

#include <immintrin.h>
#include <emmintrin.h>
#include <omp.h>

#include <string>
#include <iostream>
#include <sstream>
#include <fstream>
#include <vector>
#include <map>
#include <cstdio>
#include <cstring>
#include <cstdlib>
#include <cmath>
Added support for dynamic selection between AVX and un-vectorized C++, still to include SSE code from Mohammad. Debug flags turned on in this commit. 2014-01-19 03:07:23 +08:00			`#include <stdio.h>`
			`#include <string.h>`
			`#include <stdlib.h>`
			`#include <math.h>`
			`#include <stdint.h>`
			`#include <assert.h>`
			`#include <ctype.h>`

			`#include <sys/time.h>`

			`#include <immintrin.h>`
			`#include <emmintrin.h>`
			`#include <omp.h>`

			`#include <string>`
			`#include <iostream>`
			`#include <sstream>`
			`#include <fstream>`
			`#include <vector>`
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. 2014-01-21 00:03:42 +08:00			`#include <map>`
Added support for dynamic selection between AVX and un-vectorized C++, still to include SSE code from Mohammad. Debug flags turned on in this commit. 2014-01-19 03:07:23 +08:00			`#include <cstdio>`
			`#include <cstring>`
			`#include <cstdlib>`
			`#include <cmath>`