Rcpp::NumericVector rcpp_segInbreeding(std::string path1, std::string path2, int NFile1, int NFile2, const arma::ivec& ArmaIndex1, const arma::ivec& ArmaIndex2, int N1, int N2, int M, int minSNP, double minL, const arma::vec& ArmacM, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
int m, i, i0, j, rK, r, endoffile, gleich;
double L;
char str1[100];
char symB = stdsymB.at(0);
FILE *f1, *f2;
int N = N1 + N2;
int K = (minSNP<=60)?(minSNP/2):(30);
Rcpp::NumericVector ArmasegInbr(N/2);
size_t bufsize = 2*(NFile1+NFile2);
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
double* fROH = (double*)calloc(N/2,sizeof(double));
int* thisROH = (int*)calloc(N/2,sizeof(int));
int* thisAllel = (int*)calloc(N,sizeof(int));
int* prevAllel = (int*)calloc(N,sizeof(int));
double* cM = (double*)calloc(M+1,sizeof(double));
double* kb = (double*)calloc(M+1,sizeof(double));
int* index1 = (int*)calloc(N1,sizeof(int)); /* N1 - vector */
int* index2 = (int*)calloc(N2,sizeof(int)); /* N2 - vector */
if(fROH == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(thisAllel == NULL){error_return("Memory allocation failed.");};
if(prevAllel == NULL){error_return("Memory allocation failed.");};
if(cM == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
if(index1 == NULL){error_return("Memory allocation failed.");};
if(index2 == NULL){error_return("Memory allocation failed.");};
for(i=0;i<N1;i++){index1[i]=ArmaIndex1.at(i);}
for(i=0;i<N2;i++){index2[i]=ArmaIndex2.at(i);}
for(m=0;m<M+1;m++){
cM[m]=ArmacM.at(m);
kb[m]=Armakb.at(m);
}
f1 = fopen(path1.c_str(),"r");
if(f1 == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(f1)!='\n'){}
}
if(N2>0){
f2 = fopen(path2.c_str(),"r");
if(f2 == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(f2)!='\n'){}
}
}else{f2 = f1; /* avoid warnings */}
endoffile=0;
m=0;
while(!endoffile){
for(i=0; i<N;i++){
prevAllel[i] = thisAllel[i];
thisAllel[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(f1, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line, 2*NFile1, f1)==NULL;
if(endoffile){break;}
for(i=0; i<N1;i++){
if(Line[2*index1[i]]==symB){thisAllel[i]= thisAllel[i] | (1u<<rK);}
}
rK++;
}
if(N2>0){
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(f2, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line,2*NFile2,f2)==NULL;
if(endoffile){break;}
for(i=0; i<N2;i++){
if(Line[2*index2[i]]==symB){thisAllel[i+N1]= thisAllel[i+N1] | (1u<<rK);}
}
rK++;
}
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i0=0; i0<N/2;i0++){
i = 2*i0;
j = 2*i0+1;
if(thisAllel[i]==thisAllel[j]){
if(prevAllel[i]==prevAllel[j] && m>0){ /* ROH verlängern */
thisROH[i0] += rK;
}else{ /* neuer ROH */
thisROH[i0] = rK;
if(m>0){
gleich = ~(prevAllel[i] ^ prevAllel[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i0] += 1;
r--;
}
}
}
}else{
if(prevAllel[i]==prevAllel[j] && m>0){ /* ROH beenden */
gleich = ~(thisAllel[i] ^ thisAllel[j]);
r = 0;
while(r<rK && ((gleich>>r)&1u)){
thisROH[i0] += 1;
r++;
}
if(thisROH[i0]>=minSNP){
L = cM[m+r]-cM[m+r-thisROH[i0]];
if(L>=minL){fROH[i0] += (L*L/(a+L*L))*(kb[m+r]-kb[m+r-thisROH[i0]]);}
}
thisROH[i0] = 0;
}
}
Rcpp::NumericMatrix rcpp_segIBDandN(std::string pathThisBreed, std::string pathNative, int NFileC, int NFileN, const arma::ivec& ArmaIndexC, const arma::ivec& ArmaIndexN, int NC, int minSNP, double minL, const arma::vec& ArmaPos, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
/* ***** initialize variables ****** */
int m, i, j, r, r2, rK, endoffile, gleich;
double L;
char str1[100];
FILE *fC, *fN;
char symB = stdsymB.at(0);
Rcpp::NumericMatrix confROH(NC, NC);
int K = (minSNP<=60)?(minSNP/2):(30);
int M = Armakb.n_elem - 1;
size_t bufsize = 2*(NFileC+NFileN);
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
int** Nat = (int**)calloc(M,sizeof(int*)); /* M xNC - matrix */
double** fROH = (double**)calloc(NC,sizeof(double*)); /* NCxNC - matrix */
int** thisROH = (int**)calloc(NC,sizeof(int*)); /* NCxNC - matrix */
double** lSEG = (double**)calloc(NC,sizeof(double*)); /* NCxNC - matrix */
int* currAllelesC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* prevAllelesC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* indexC = (int*)calloc(NC,sizeof(int)); /* NC - vector */
int* indexN = (int*)calloc(NC,sizeof(int)); /* NC - vector */
double* Pos = (double*)calloc(ArmaPos.n_elem, sizeof(double)); /* M+1 - vector */
double* kb = (double*)calloc(Armakb.n_elem, sizeof(double)); /* M+1 - vector */
if(fROH == NULL){error_return("Memory allocation failed.");};
if(Nat == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(lSEG == NULL){error_return("Memory allocation failed.");};
if(currAllelesC== NULL){error_return("Memory allocation failed.");};
if(prevAllelesC== NULL){error_return("Memory allocation failed.");};
if(indexC == NULL){error_return("Memory allocation failed.");};
if(indexN == NULL){error_return("Memory allocation failed.");};
if(Pos == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
for(m=0;m<M+1;m++){
Pos[m] = ArmaPos.at(m);
kb[m] = Armakb.at(m);
}
for(i=0; i<NC;i++){
indexC[i] = ArmaIndexC.at(i);
indexN[i] = ArmaIndexN.at(i);
fROH[i] = (double*)calloc(i+1,sizeof(double));
thisROH[i]= (int*)calloc(i+1,sizeof(int));
lSEG[i] = (double*)calloc(i+1,sizeof(double));
if(fROH[i] == NULL){error_return("Memory allocation failed.");};
if(thisROH[i]== NULL){error_return("Memory allocation failed.");};
if(lSEG[i] == NULL){error_return("Memory allocation failed.");};
}
/* ******* Main part ******** */
fC = fopen(pathThisBreed.c_str(),"r");
fN = fopen(pathNative.c_str(),"r");
if(fC == NULL){error_return("File opening failed.");};
if(fN == NULL){error_return("File opening failed.");};
while(fgetc(fN)!='\n'){}
for(i=0;i<skip+1;i++){
while(fgetc(fC)!='\n'){}
}
endoffile=0;
m=0;
while(!endoffile){
/* *** Determine previous alleles and current alleles (K at a time) *** */
/* *** and native alleles for candidates *** */
for(i=0; i<NC;i++){
prevAllelesC[i] = currAllelesC[i];
currAllelesC[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(fC, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fscanf(fN, "%s ", str1)<1;
if(endoffile){break;}
endoffile = fgets(Line,2*NFileC,fC)==NULL;
if(endoffile){break;}
for(i=0; i<NC;i++){
if(Line[2*indexC[i]]==symB){currAllelesC[i]= currAllelesC[i] | (1u<<rK);}
}
endoffile = fgets(Line, 2*NFileN, fN)==NULL;
if(endoffile){break;}
Nat[m+rK] = (int*)calloc(NC,sizeof(int));
for(i=0; i<NC;i++){
Nat[m+rK][i] = ((Line[2*indexN[i]]=='1')?1:0);
}
rK++;
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i=0; i<NC;i++){
for(j=0; j<i+1; j++){
if(currAllelesC[i]==currAllelesC[j]){
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH verlängern */
thisROH[i][j] += rK;
for(r2=0;r2<rK;r2++){if(Nat[m+r2][i]*Nat[m+r2][j]>0){lSEG[i][j] += kb[m+r2+1]-kb[m+r2];}} /* !!!!! */
}else{ /* neuer ROH */
thisROH[i][j] = rK;
for(r2=0;r2<rK;r2++){if(Nat[m+r2][i]*Nat[m+r2][j]>0){lSEG[i][j] += kb[m+r2+1]-kb[m+r2];}} /* !!!!! */
if(m>0){
gleich = ~(prevAllelesC[i] ^ prevAllelesC[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
if(Nat[m-K+r][i]*Nat[m-K+r][j]>0){lSEG[i][j] += kb[m-K+r+1]-kb[m-K+r];} /* !!!!! */
r--;
}
}
}
}else{
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH beenden */
gleich = ~(currAllelesC[i] ^ currAllelesC[j]);
r = 0;
while(r<K && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
if(Nat[m+r][i]*Nat[m+r][j]>0){lSEG[i][j] += kb[m+r+1]-kb[m+r];} /* !!!!! */
r++;
}
if(thisROH[i][j]>=minSNP){
L = Pos[m+r]-Pos[m+r-thisROH[i][j]];
if(L>=minL){
fROH[i][j] += (L*L/(a+L*L))*lSEG[i][j];
}
}
thisROH[i][j] = 0;
lSEG[i][j] = 0.0;
}
}
}
Rcpp::NumericMatrix rcpp_segIBDandNVersion2(std::string pathThisBreed, int NFileC, int NC, const arma::ivec& ArmaIndexC, const arma::mat& ArmaNat, int minSNP, double minL, const arma::vec& ArmaPos, const arma::vec& Armakb, double a, std::string stdsymB, int skip, int cskip) {
int m, m2, i, j, r, rK, endoffile, gleich;
double L, w, lSEG ;
char str1[100];
char symB = stdsymB.at(0);
FILE *fC;
Rcpp::NumericMatrix confROH(NC, NC);
int K = (minSNP<=60)?(minSNP/2):(30);
int M = Armakb.n_elem - 1;
size_t bufsize = 2*NFileC;
char* Line = (char*)malloc(bufsize*sizeof(char));
if(Line == NULL){error_return("Memory allocation failed.");};
int** Nat = (int**)calloc(NC,sizeof(int*));
double** fROH = (double**)calloc(NC,sizeof(double*));
int** thisROH = (int**)calloc(NC,sizeof(int*));
int* currAllelesC = (int*)calloc(NC,sizeof(int));
int* prevAllelesC = (int*)calloc(NC,sizeof(int));
int* indexC = (int*)calloc(NC,sizeof(int));
double* Pos = (double*)calloc(ArmaPos.n_elem, sizeof(double));
double* kb = (double*)calloc(Armakb.n_elem, sizeof(double));
if(Nat == NULL){error_return("Memory allocation failed.");};
if(fROH == NULL){error_return("Memory allocation failed.");};
if(thisROH == NULL){error_return("Memory allocation failed.");};
if(currAllelesC == NULL){error_return("Memory allocation failed.");};
if(prevAllelesC == NULL){error_return("Memory allocation failed.");};
if(indexC == NULL){error_return("Memory allocation failed.");};
if(Pos == NULL){error_return("Memory allocation failed.");};
if(kb == NULL){error_return("Memory allocation failed.");};
for(m=0;m<M+1;m++){
Pos[m] = ArmaPos.at(m);
kb[m] = Armakb.at(m);
}
for(i=0; i<NC;i++){
indexC[i] = ArmaIndexC.at(i);
fROH[i] = (double*)calloc(i+1, sizeof(double));
thisROH[i]= (int*)calloc(i+1, sizeof(int));
Nat[i] = (int*)calloc(M, sizeof(int));
if(fROH[i] == NULL){error_return("Memory allocation failed.");};
if(thisROH[i] == NULL){error_return("Memory allocation failed.");};
if(Nat[i] == NULL){error_return("Memory allocation failed.");};
for(m=0; m<M;m++){
Nat[i][m] = ArmaNat.at(m,i);
}
}
fC = fopen(pathThisBreed.c_str(),"r");
if(fC == NULL){error_return("File opening failed.");};
for(i=0;i<skip+1;i++){
while(fgetc(fC)!='\n'){}
}
endoffile=0;
m=0;
while(!endoffile){
for(i=0; i<NC;i++){
prevAllelesC[i] = currAllelesC[i];
currAllelesC[i] = 0;
}
rK=0;
while(rK<K){
for(i=0; i<cskip; i++){
endoffile = fscanf(fC, "%s ", str1)<1;
if(endoffile){break;}
}
if(endoffile){break;}
endoffile = fgets(Line,2*NFileC,fC)==NULL;
if(endoffile){break;}
for(i=0; i<NC;i++){
if(Line[2*indexC[i]]==symB){currAllelesC[i]= currAllelesC[i] | (1u<<rK);}
}
rK++;
}
if(endoffile){Rprintf("M=%d\n",m+rK);}
if(rK==0){break;}
for(i=0; i<NC;i++){
for(j=0; j<i+1; j++){
if(currAllelesC[i]==currAllelesC[j]){
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH verlängern */
thisROH[i][j] += rK;
}else{ /* neuer ROH */
thisROH[i][j] = rK;
if(m>0){
gleich = ~(prevAllelesC[i] ^ prevAllelesC[j]);
r = K-1;
while(r>=0 && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
r--;
}
}
}
}else{
if(prevAllelesC[i]==prevAllelesC[j] && m>0){ /* ROH beenden */
gleich = ~(currAllelesC[i] ^ currAllelesC[j]);
r = 0;
while(r<K && ((gleich>>r)&1u)){
thisROH[i][j] += 1;
r++;
}
if(thisROH[i][j]>=minSNP){
L = Pos[m+r]-Pos[m+r-thisROH[i][j]];
if(L>=minL){
w = L*L/(a+L*L);
lSEG = 0.0;
for(m2=m+r-thisROH[i][j];m2<m+r;m2++){
if(Nat[i][m2]*Nat[j][m2]>0){lSEG += kb[m2+1]-kb[m2];}
}
fROH[i][j] += w*lSEG;
}
}
thisROH[i][j] = 0;
}
}
}
