jgtmat.h

/**
 * @file    jgtmat.h
 * @brief   header file for jgtmat.cpp
 * @details contains joint genotype matrix data structure (jgtmat_t) and associated functions 
 */
#ifndef __JGTMAT_H__
#define __JGTMAT_H__


/* INCLUDES ----------------------------------------------------------------- */
#include "dataStructs.h"
/* -------------------------------------------------------------------------- */

/* FORWARD DECLARATIONS ----------------------------------------------------- */
/* -------------------------------------------------------------------------- */

/* MACROS ------------------------------------------------------------------- */

// JGTMAT9
// calculations based on 3x3 matrix
// 		of pairwise genotype categories
// -------------------------------------
//
// 		MM	Mm	mm
// MM	A	D	G
// Mm	B	E	H
// mm	C	F	I
//
// linearized version:
// 		A D G B E H C F I
//      0 1 2 3 4 5 6 7 8
//

#define JGTMAT_LINEAR_IDXOF_A 0
#define JGTMAT_LINEAR_IDXOF_B 3
#define JGTMAT_LINEAR_IDXOF_C 6
#define JGTMAT_LINEAR_IDXOF_D 1
#define JGTMAT_LINEAR_IDXOF_E 4
#define JGTMAT_LINEAR_IDXOF_F 7
#define JGTMAT_LINEAR_IDXOF_G 2
#define JGTMAT_LINEAR_IDXOF_H 5
#define JGTMAT_LINEAR_IDXOF_I 8

#define JGTMAT_GET_DIJ (C + G + ((B + D + E + F + H) / 2.0))
#define JGTMAT_GET_SIJ (A + I + ((B + D + E + F + H) / 2.0))
#define JGTMAT_GET_FIJ (((2 * C) + (2 * G) - E) / ((2 * C) + (2 * G) + B + D + E + F + H))
#define JGTMAT_GET_IBS0 (C + G)
#define JGTMAT_GET_IBS1 (B + D + F + H)
#define JGTMAT_GET_IBS2 (A + E + I)
#define JGTMAT_GET_R0 ((C + G) / E)
#define JGTMAT_GET_R1 (E / (C + G + B + D + F + H))
#define JGTMAT_GET_KIN ((E - ((2 * C) + (2 * G))) / (B + D + F + H + (2 * E)))
/* END-OF-MACROS ------------------------------------------------------------ */

/* TYPEDEF-STRUCTS ---------------------------------------------------------- */
typedef struct jgtmat_t jgtmat_t;
struct jgtmat_t {

    // typically: nIndCmb (one matrix per ind pair)
    // or nIndCmb*(args->nBootstraps+1) (for each bootstrap replicate+the orig)
    size_t n;      // number of matrices

    // - 9 (3x3) for MM Mm mm
    // - 100 (10x10) for all genotype combinations
    size_t size;   // size of each matrix

    // probabilities
    // pm[n][size]
    double** pm;

    // counts
    // m[n][size]
    uint64_t** m;

    /// @var drop[n] - array of bool indicators for excluding specific matrices from downstream analyses
    /// @note allocated iff args->allow_mispairs==1
    /// @details if gl data, filled in em.cpp. if gt data, filled in vcfReader.cpp
    bool* drop;

};
/* END-OF-TYPEDEF-STRUCTS --------------------------------------------------- */

/* FUNCTION-DECLARATIONS ----------------------------------------------------- */
jgtmat_t* jgtmat_init(const size_t n);
void jgtmat_destroy(jgtmat_t* jgtmat);
/* END-OF-FUNCTION-DECLARATIONS ---------------------------------------------- */

#endif // __JGTMAT_H__