gatk-3.8/public/c++/VectorPairHMM/template.h

#ifndef TEMPLATES_H_
#define TEMPLATES_H_

#include "headers.h"

#define MM 0
#define GapM 1
#define MX 2
#define XX 3
#define MY 4
#define YY 5

//#define MROWS  500
//#define MCOLS  1000

#define CAT(X,Y) X####Y
#define CONCAT(X,Y) CAT(X,Y)

#define ALIGNED __attribute__((aligned(32)))

typedef union __attribute__((aligned(32))) {
        ALIGNED __m256 ALIGNED d;
        ALIGNED __m128i ALIGNED s[2];
        ALIGNED float  ALIGNED f[8];
        ALIGNED __m256i ALIGNED i;
} ALIGNED mix_F ALIGNED;

typedef union __attribute__((aligned(32))) {
        ALIGNED __m128 ALIGNED d;
        ALIGNED __m64 ALIGNED s[2];
        ALIGNED float  ALIGNED f[4];
        ALIGNED __m128i ALIGNED i;
} ALIGNED mix_F128 ALIGNED;

typedef union ALIGNED {
  __m128i vec ;
  __m128 vecf ;
  uint32_t masks[4] ;
} MaskVec_F ;

typedef union ALIGNED {
  __m64 vec ;
  __m64 vecf ;
  uint32_t masks[2] ;
} MaskVec_F128 ;

typedef union ALIGNED
{
        ALIGNED __m128i ALIGNED i;
        ALIGNED __m128 ALIGNED f;
} ALIGNED IF_128f ALIGNED;

typedef union ALIGNED
{
        ALIGNED int    ALIGNED i;
        ALIGNED float  ALIGNED f;
} ALIGNED IF_32 ALIGNED;

typedef union __attribute__((aligned(32))) {
        ALIGNED __m256d ALIGNED d;
        ALIGNED __m128i ALIGNED s[2];
        ALIGNED double  ALIGNED f[4];
        ALIGNED __m256i ALIGNED i;
} ALIGNED mix_D ALIGNED;

typedef union __attribute__((aligned(32))) {
        ALIGNED __m128d ALIGNED d;
        ALIGNED __m64 ALIGNED s[2];
        ALIGNED double  ALIGNED f[2];
        ALIGNED __m128i ALIGNED i;
} ALIGNED mix_D128 ALIGNED;

typedef union ALIGNED {
  __m128i vec ;
  __m128d vecf ;
  uint64_t masks[2] ;
} MaskVec_D ;

typedef union ALIGNED {
  __m64 vec ;
  __m64 vecf ;
  uint64_t masks[1] ;
} MaskVec_D128 ;

typedef union ALIGNED
{
        ALIGNED __m128i ALIGNED i;
        ALIGNED __m128d ALIGNED f;
} ALIGNED IF_128d ALIGNED;

typedef union ALIGNED
{
        ALIGNED int64_t ALIGNED i;
        ALIGNED double  ALIGNED f;
} ALIGNED IF_64 ALIGNED;

template<class T>
struct Context{};

template<>
struct Context<double>
{
        Context()
        {
                for (int x = 0; x < 128; x++)
                        ph2pr[x] = pow(10.0, -((double)x) / 10.0);

                INITIAL_CONSTANT = ldexp(1.0, 1020.0);
                LOG10_INITIAL_CONSTANT = log10(INITIAL_CONSTANT);
                RESULT_THRESHOLD = 0.0;
        }

        double LOG10(double v){ return log10(v); }

        static double _(double n){ return n; }
        static double _(float n){ return ((double) n); }
        double ph2pr[128];
        double INITIAL_CONSTANT;
        double LOG10_INITIAL_CONSTANT;
        double RESULT_THRESHOLD;
};

template<>
struct Context<float>
{
        Context()
        {
                for (int x = 0; x < 128; x++)
                {
                        ph2pr[x] = powf(10.f, -((float)x) / 10.f);
                }

                INITIAL_CONSTANT = ldexpf(1.f, 120.f);
                LOG10_INITIAL_CONSTANT = log10f(INITIAL_CONSTANT);
                RESULT_THRESHOLD = ldexpf(1.f, -110.f);
        }

        float LOG10(float v){ return log10f(v); }

        static float _(double n){ return ((float) n); }
        static float _(float n){ return n; }
        float ph2pr[128];
        float INITIAL_CONSTANT;
        float LOG10_INITIAL_CONSTANT;
        float RESULT_THRESHOLD;
};


typedef struct
{
        int rslen, haplen;
	/*int *q, *i, *d, *c;*/
	/*int q[MROWS], i[MROWS], d[MROWS], c[MROWS];*/
	char *q, *i, *d, *c;
        char *hap, *rs;
	int *ihap;
	int *irs;
} testcase;

int normalize(char c);
int read_testcase(testcase *tc, FILE* ifp=0);


#define MIN_ACCEPTED 1e-28f
#define NUM_DISTINCT_CHARS 5
#define AMBIG_CHAR 4

class ConvertChar {

  static uint8_t conversionTable[255] ;

public:

  static void init() {
    assert (NUM_DISTINCT_CHARS == 5) ;
    assert (AMBIG_CHAR == 4) ;

    conversionTable['A'] = 0 ;
    conversionTable['C'] = 1 ;
    conversionTable['T'] = 2 ;
    conversionTable['G'] = 3 ;
    conversionTable['N'] = 4 ;
  }

  static inline uint8_t get(uint8_t input) {
    return conversionTable[input] ;
  }

};


#endif