int main(int argc, char** argv){
long i, m, l, j;
// verbose level
verbose=0;
verbose2=0;
verbose3=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"-v")==0){verbose2=100;verbose3=1;}}//atoi(argv[i+1]);}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"-V")==0){verbose2=100;verbose3=2;}}//atoi(argv[i+1]);}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"-Vv")==0){verbose2=100;verbose3=3;}}//atoi(argv[i+1]);}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"-VV")==0){verbose2=100;verbose3=4;}}//atoi(argv[i+1]);}}
// initilization for loading VCF files
if(init()==0){fprintf(stderr, "error on parseVCF\n"); return -1;};
if(verbose2>10){
fprintf(stderr, "\n");
fprintf(stderr, "#################################\n");
fprintf(stderr, "# RASQUAL v 1.0 #\n");
fprintf(stderr, "#################################\n");
fprintf(stderr, "\n");
}
// usage
if(argc==1){usage(); return -1;}//else{for(i=0;i<argc;i++){fprintf(stderr, "%s.", argv[i]);}}
// init hyper parameter setting
ab=10.001;
phiab=10.001;
ad = 1.01;
bd = 1.99;
kappa = 1.01*2.0;
omega = 0.1*2.0;
sigma2 = 10000.0;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-SIGMA")==0 && atof(argv[i+1])>0.){sigma2=(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-BETA")==0 && atof(argv[i+1])>0.){beta0 =(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-ABPHI")==0 && atof(argv[i+1])>0.){phiab=(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-ABPI")==0 && atof(argv[i+1])>0.){ab =(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-KAPPA")==0 && atof(argv[i+1])>0.){kappa=(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-OMEGA")==0 && atof(argv[i+1])>0.){omega=(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-ADELTA")==0 && atof(argv[i+1])>0.){ad=(double)atof(argv[i+1]);break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-BDELTA")==0 && atof(argv[i+1])>0.){bd=(double)atof(argv[i+1]);break;}}
if(verbose3>0){
fprintf(stderr, "Hyper-parameters :\n");
fprintf(stderr, " phiab : %lf\n", phiab);
fprintf(stderr, " ab : %lf\n", ab);
fprintf(stderr, " kappa : %lf\n", kappa);
fprintf(stderr, " omega : %lf\n\n", omega);
}
// fix parameters
fixParam=(int*)calloc(10,sizeof(int)); for(i=0; i<10; i++){fixParam[i]=0;}
for(i=0; i<argc; i++){if(strcmp(argv[i],"--fix-delta")==0){fixParam[1]=1; break;}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"--fix-phi")==0){fixParam[2]=1; break;}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"--fix-theta")==0){fixParam[4]=1; break;}}
//
// program arguments
//
// het type (0: ours 1: sun 2: mcv)
hetType=0;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-hetType")==0){hetType=atoi(argv[i+1]);}}
// force to fit model
int forced=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--force")==0){forced=1;}}//atoi(argv[i+1]);}}
// print result
int printAll=1;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--lead-snp")==0 || strcmp(argv[i],"-t")==0){printAll=0; break;}}
int printImprint=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--imprint")==0 || strcmp(argv[i],"-i")==0){printImprint=1; break;}}
// print VCF
int printVCF=0;
gzFile postVCF=NULL;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"--posterior-genotype")==0 || strcmp(argv[i],"-g")==0){printVCF=1; postVCF=gzopen(argv[i+1], "ab6f");break;}}
// for likelihood ratio ties
srand((unsigned)(time(NULL)+getpid()));
int rand0=rand(), rand1=0;
randomize=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"-r")==0 || strcmp(argv[i],"--random-permutation")==0){randomize=1;}}
// Usse ASE or not
ASE=1;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--population-only")==0){ASE=0;}}
for(i=0; i<argc; i++){if(strcmp(argv[i],"--as-only")==0){ASE=2;}}
// fit Null model only
Null=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--null")==0){Null=1;}}
// trans QTL mapping
transQTL=0;
char* chr0;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-trans")==0){transQTL=1; chr0=argv[i+1]; if(verbose3>0){fprintf(stderr, "Trans QTL Mapping\nChromosome=%s\n\n", chr0);} break;}}
// allelic prob from RSQ
allelicProbEstByErrorRate=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"-z")==0 || strcmp(argv[i],"--convert-imputation-score")==0){allelicProbEstByErrorRate=1; break;}}
// GL relaxation
double relaxGL=0.001;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--nominal-allelic-probability")==0){relaxGL=0.0; break;}}
// No prior genotype
int noPriorGenotype=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--population-allele-frequency")==0){noPriorGenotype=1; break;}}
// No genotype likelihood
noGL=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--fix-genotype")==0){noGL=1; break;}}
// posterior update
noPosteriorUpdate=0;
for(i=0; i<argc; i++){if(strcmp(argv[i],"--no-posterior-update")==0){noPosteriorUpdate=1; break;}}
if(verbose2>10){
if(noPosteriorUpdate>0)fprintf(stderr, "No posterior probability update\n");
if(allelicProbEstByErrorRate>0)fprintf(stderr, "Allelic probability has been estimated by error rate\n\n");
}
// data loading
long N=0;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-n")==0 || strcmp(argv[i],"--sample-size")==0){N=atoi(argv[i+1]); break;}}
if(N==0){fprintf(stderr, "Sample size is inappropriate\n"); return -1;}
// Sample weights
double* w;
w=(double*)calloc(N, sizeof(double));
for(i=0; i<N; i++){w[i]=1.0; }
//if(verbose>10){printDouble(w,N);}
// initial #snps
long M=0, L=0, K=0;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-m")==0 || strcmp(argv[i],"--number-of-fsnps")==0){M=atoi(argv[i+1]); break;}} // # of exon SNPs
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-l")==0 || strcmp(argv[i],"--number-of-testing-snps")==0){L=atoi(argv[i+1]); break;}} // # of Test SNPs
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-j")==0 || strcmp(argv[i],"--feature-id")==0){K=atoi(argv[i+1]); break;}} // Region ID {1..50K}
char* gid=NULL;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-f")==0 || strcmp(argv[i],"--feature-name")==0){gid=argv[i+1];}}
if(gid==NULL){gid=(char*)calloc(100,sizeof(char)); sprintf(gid, "%ld", K);}
//if(M==0 || L==0 || K==0){fprintf(stderr, "%s Numbers are inappropriate M=%ld L=%ld K=%ld!", gid, M, L, K); if(forced==0){fprintf(stderr, "\n"); return -1;}}
if(verbose2>10){
fprintf(stderr, "Sample Size : %ld\n", N);
fprintf(stderr, "Init No. fSNPs : %ld\n", M);
fprintf(stderr, "Init No. tested SNPs : %ld\n", L);
fprintf(stderr, "Kth feature : %ld\n\n", K);
}
FILE* fy=NULL; // total fragment counts
FILE* fk=NULL; // offset for Negative Binomial
FILE* fx=NULL; // covariates
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-y")==0 || strcmp(argv[i],"--feature-counts")==0){fy=fopen(argv[i+1],"rb"); break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-k")==0 || strcmp(argv[i],"--sample-offsets")==0){fk=fopen(argv[i+1],"rb"); break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-x")==0 || strcmp(argv[i],"--covariates")==0){fx=fopen(argv[i+1],"rb"); break;}}
if(fy==NULL || fk==NULL){fprintf(stderr, "imput files are not specified!\n"); return -1;}
int freadres;
long P=1;
double* X;
double tmp;
if(fx==NULL){
X = (double*)calloc(N, sizeof(double));
}else{
P = ncol(fx, N)+1;
X = (double*)calloc(N*P, sizeof(double));
freadres = fread(X+N, sizeof(double), N*(P-1), fx);
for(i=1; i<P; i++){
double m = mean(X+N*i, N);
//double ss = sd(X+N*i, N);
for(j=0; j<N; j++){
X[i*N+j] -= m;
//X[i*N+j] /= ss;
}
}
}
for(i=0; i<N; i++){ X[i] = 1.0; }
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-p")==0 || strcmp(argv[i],"--number-of-covariates")==0){P=atoi(argv[i+1])+1;}} // # of covs after change
double* y;
y = (double*)calloc(N, sizeof(double));
fseek(fy, N*(K-1)*sizeof(double), SEEK_SET);
freadres = fread(y, sizeof(double), N, fy);
double* ki;
ki= (double*)calloc(N+randomize*M*N, sizeof(double));
fseek(fk, N*(K-1)*sizeof(double), SEEK_SET);
freadres = fread(ki, sizeof(double), N, fk);
double totki = sum(ki, N)/(double)N;
for(i=0; i<N; i++){ki[i] /= totki;}
double tot = iwsum(y, ki, N);
// feature region(s)
char* sa=NULL;
char* sb=NULL;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-s")==0 || strcmp(argv[i],"--feature-starts")==0){sa=argv[i+1];}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-e")==0 || strcmp(argv[i],"--feature-ends")==0){sb=argv[i+1];}}
int nexon=0;
long* starts;
long* ends;
double cdnLen=0.0;
if(sa!=NULL){
nexon=countFields(sa);
}else{fprintf(stderr, "no feature region specified\n"); return -1;}
starts = (long*)calloc(nexon, sizeof(long));
ends = (long*)calloc(nexon, sizeof(long));
splitCSV(sa, nexon, starts);
splitCSV(sb, nexon, ends);
for(i=0;i<nexon;i++){ cdnLen+=(double)(ends[i]-starts[i]); }
if(verbose3>0)printLong(starts, nexon);
if(verbose3>0)printLong(ends, nexon);
// TSS
long TSS = (starts[0]+ends[nexon-1])/2;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-c")==0 || strcmp(argv[i],"--cis-midpoint")==0){TSS=atol(argv[i+1]);}}
long TSSPROX=270000000*2;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-w")==0 || strcmp(argv[i],"--cis-window-size")==0){TSSPROX=atol(argv[i+1])/2;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"--effective-feature-length")==0){cdnLen = (double)atol(argv[i+1]);}}
if(verbose2>10){fprintf(stderr, "Effective feature length : %.0lf\n\n", cdnLen);}
// SNP filter
double MAF=0.05;
double HWE=Qchisq(1.0e-8, 1.0);
double RSQ=0.7;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-a")==0 || strcmp(argv[i],"--minor-allele-frequency")==0){MAF=(double)atof(argv[i+1]); break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-h")==0 || strcmp(argv[i],"--hardy-weinberg-pvalue")==0){HWE=Qchisq((double)atof(argv[i+1]), 1.0); break;}}
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-q")==0 || strcmp(argv[i],"--imputation-quality")==0){RSQ=(double)atof(argv[i+1]); break;}}
double coverageDepth=0.05;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"-d")==0 || strcmp(argv[i],"--min-coverage-depth")==0){coverageDepth=(double)atof(argv[i+1]);break;}}
// loading VCF files
VCF_info vinfo;
int* dip;
double* gen;
double* gl;
double* ap;
long* ase;
long pos;
char* rs;
char* al;
dip=(int*)calloc(N*2, sizeof(int));
gen=(double*)calloc(N, sizeof(double));
gl =(double*)calloc(N*3, sizeof(double));
ap =(double*)calloc(N*2, sizeof(double));
ase=(long*)calloc(N*2, sizeof(long));
al = (char*)calloc(2, sizeof(char));
rs=(char*)calloc(1000, sizeof(char));
int genType=1;
double* Z=NULL;
Z = (double*)calloc(N*(L+M+1)*2, sizeof(double));
double* Y=NULL;
Y = (double*)calloc(N*M*2, sizeof(double));
double* km=NULL;
km = (double*)calloc(M, sizeof(double));
double* exon;
exon = (double*)calloc(L, sizeof(double));
long* poss; poss = (long*)calloc(L, sizeof(long));
double* afs; afs= (double*)calloc(L+2, sizeof(double));
double* hwes; hwes= (double*)calloc(L+2, sizeof(double));
double* ias; ias= (double*)calloc(L+2, sizeof(double));
double* rsq; rsq= (double*)calloc(L+2, sizeof(double));
double* crs; crs= (double*)calloc(L+2, sizeof(double));
char** rss=NULL; rss = (char**)calloc(L, sizeof(char*));
char** als; als = (char**)calloc(L, sizeof(char*));
char** chrs; chrs =(char**)calloc(L, sizeof(char*));
for(l=0; l<L; l++){//fprintf(stderr, "%ld ", l);
als[l] = (char*)calloc(2, sizeof(char));
rss[l] = NULL;
rss[l] = (char*)calloc(100, sizeof(char));
if(rss[l]==NULL){return -1;}
chrs[l] = (char*)calloc(100, sizeof(char));
}
if(Z==NULL || rss==NULL || Y==NULL){fprintf(stderr, "memory allocation error!");return -1;}
if(verbose2>10)fprintf(stderr, "\nMemory has been allocated...\n");
m=l=0;
numOfLoci=0;
double asgaf[2];
double asaf[2];
double Y1=0.0;
double Y0 = mean(y, N);
long l0=0;
double ep;
while(parseLine(chrs[l], &pos, rss[l], als[l], &vinfo, dip, gen, gl, ap, ase, N, genType)>0){
afs[l] = getAF(gen,w,N);// fprintf(stderr,"%lf ",afs[l]);
//hwes[l] = getHWE(dip,w,N);// fprintf(stderr,"%lf ",hwes[l]);
hwes[l] = getHWEfromAP(ap, dip, w, N);// fprintf(stderr,"%lf ",hwes[l]);
//ias[l] = getIA(gl,w,N); // fprintf(stderr,"%lf ",ias[l]);
ias[l] = getIAfromAP(ap, gl, w, N); // fprintf(stderr,"%lf ",ias[l]);
rsq[l] = vinfo.RSQ; // fprintf(stderr,"%lf ",rsq[l]);
if(rsq[l]<0.0){rsq[l]=ias[l];}
crs[l] = getCR(gen,w,N); // fprintf(stderr,"%lf ",crs[l]);
poss[l]=pos;
if(afs[l]>MAF && afs[l]<1.0-MAF && rsq[l]>RSQ && (hwes[l]<HWE||noPriorGenotype==1) && isTestReg(chrs[l], chr0, TSS, TSSPROX, pos)){// tested
exon[l]=1.0; numOfLoci++;
}else{exon[l]=-1.0;}// not tested
ep = afs[l]*(1-afs[l])*(1.0-rsq[l]); //if(ep<0.01){ep=0.01;}
if(noGL>0){ep=0.0;}
if(allelicProbEstByErrorRate>0 || noGL>0){
for(i=0; i<N; i++){
Z[l*2*N+i*2] = dip[i*2]==0 ?ep:(1.0-ep);
Z[l*2*N+i*2+1] = dip[i*2+1]==0?ep:(1.0-ep);
}
}else{
cblas_dcopy(2*N, ap, 1, Z+l*2*N, 1);
//for(i=0; i<N*2; i++){if(Z[l*2*N+i]>1-ep){Z[l*2*N+i]=1-ep;}else if(Z[l*2*N+i]<ep){Z[l*2*N+i]=ep;}} // ep adjust
//fprintf(stderr, "%s ", rss[l]); print(ap,2*N);
}
if(relaxGL>0.0){for(i=0; i<2*N; i++){
if(Z[l*2*N+i]>1.0-relaxGL){
Z[l*2*N+i] -= relaxGL;
}else if(Z[l*2*N+i]<relaxGL){
Z[l*2*N+i] += relaxGL;
}
}}
if(noPriorGenotype>0){
for(i=0; i<N*2; i++){Z[l*2*N+i] = afs[l];}
}
//if(strcmp("rs114814219",rss[l])==0){fprintf(stderr, "%s ", rss[l]); print(ap,2*N);}
//if(strcmp("rs2296475",rss[l])==0){fprintf(stderr, "%s ", rss[l]); print(ap,2*N);}
if(ASE>0 && isExon(pos, starts, ends, nexon) && afs[l]>0.005 && afs[l]<0.995 && rsq[l]>0. && isSameChr(chrs[l],chr0)>0){
km[m] = asgaf[0] = asgaf[1] = asaf[0] = asaf[1] = 0.0;
for(i=0; i<N; i++){
Y[m*2*N+i*2] = (double)ase[i*2];
Y[m*2*N+i*2+1] = (double)ase[i*2+1];
asgaf[0] += gen[i]*(Y[m*2*N+i*2]+Y[m*2*N+i*2+1])/ki[i];
asgaf[1] += 2.0*(Y[m*2*N+i*2]+Y[m*2*N+i*2+1])/ki[i];
asaf[0] += Y[m*2*N+i*2];
asaf[1] += Y[m*2*N+i*2+1];
km[m] += (Y[m*2*N+i*2]+Y[m*2*N+i*2+1])/ki[i]/((tot*150)/cdnLen);
Y1 += (Y[m*2*N+i*2]+Y[m*2*N+i*2+1])/(double)N/2.0;
}
//if((asaf[0]+asaf[1])>0.0){asaf[1]=asaf[1]/(asaf[0]+asaf[1]);}else{asaf[1]=0.0;};
asgaf[0]/=asgaf[1];
asaf[0]/=(asaf[0]+asaf[1]);
//km[m] /= tot;
if(verbose3>0){fprintf(stderr, "%s %ld km=%lf af=%lf hwe=%lf asgaf=%lf asaf=%lf\n", rss[l], pos, km[m], afs[l], hwes[l], asgaf[0], asaf[0]);}
if(km[m]>coverageDepth && asgaf[0]>0.005 && asgaf[0]<0.995 && asaf[0]>0.0 && asaf[0]<1.0){
if(verbose3>0){fprintf(stderr, "RSQ=%lf EP=%lf\n", rsq[l], ep);}
//if(m==0){ hoge++; }else{ if(poss[l]-poss[l0]<150){hoge += ((double)(poss[l]-poss[l0]))/150.0; }else{hoge++;} }
km[m]=1.0;
m++; // num of eSNPs
exon[l]*=2.0;
l0 = l;
}
}
if(exon[l]!=(-1)){l++;}
}
//if(m>0){ if(Y1>Y0){asNonasRatio=0.99/(double)(m);}else{asNonasRatio=Y1/Y0/(double)(m);} }else{ asNonasRatio=0.0; }
double effrlen = 150.0;
//if(m>0){ if(hoge*effrlen>cdnLen){asNonasRatio0=0.99;}else{asNonasRatio0=hoge*effrlen/cdnLen;} }else{ asNonasRatio0=0.0; }
asNonasRatio0=0.0;
//if(m>0){ if(((double)m)*75.0>(cdnLen-74.0)){asNonasRatio=0.99/(double)(m);}else{asNonasRatio=75.0/(cdnLen-74.0);} }else{ asNonasRatio=0.0; }
//for(l=0;l<m;l++){km[l]=asNonasRatio0;}asNonasRatio0=0.0;
//for(l=0;l<m;l++){if(m<6.0){km[l]=m;}else{km[l]=5.0;}}
//for(l=0;l<m;l++){ if(Y1>Y0){km[l]=0.99/(double)(m);}else{ km[l]=Y1/Y0/(double)(m);} }
//print(km, m);
//for(l=0;l<m;l++){for(i=0; i<N; i++){Y[i*2] += Y[m*2*N+i*2]; Y[i*2+1] += Y[m*2*N+i*2+1]; }}
//m = 1;
if(verbose2>10){
fprintf(stderr, "\nData has been loaded...\n\n\n");
fprintf(stderr, "No. fSNPs : %ld\n", m);
fprintf(stderr, "No. testing SNPs: %ld\n", numOfLoci);
fprintf(stderr, "No ase/ase ratio: %lf\n", asNonasRatio0);
//fprintf(stderr, "Effective no of eSNPs: %lf\n", hoge);
}//fprintf(stderr, "No. eSNPs : %d\n\n", m);
if(tot<=0.0){ printf("%s\trs\t%s\t0\tX\tX\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t0\t%ld\t%ld\t-1\t-1\t-1\t-1\t-1\t0\t0.0\n", gid, "0", m,numOfLoci); return 0;}
if(numOfLoci==0){printf("%s\trs\t%s\t0\tX\tX\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t0\t%ld\t%ld\t-1\t-1\t-1\t-1\t-1\t0\t0.0\n", gid, "0", m,numOfLoci); return 0;}
// average number of joint tests
NOfSigLoci=(double)numOfLoci;
for(i=0; i<argc-1; i++){if(strcmp(argv[i],"--number-of-significant-loci")==0){NOfSigLoci=(double)atof(argv[i+1]);break;}}
//fprintf(stderr, "num of sig=%lf\n", NOfSigLoci);
// ASEQTL
double* lkhdDiff;
double* randlkhdDiff;
double* ppi;
double* pdelta;
double* pphi;
double* pbeta;
double* ptheta;
double* pasr;
double* ptval;
double* pkld;
int* pitr;
int* pbound;
lkhdDiff = (double*)calloc(L+2, sizeof(double));
randlkhdDiff = (double*)calloc(L+2, sizeof(double)); for(i=0; i<L+1; i++){randlkhdDiff[i]=rand();}
ppi = (double*)calloc(L+2, sizeof(double));
pdelta = (double*)calloc(L+2, sizeof(double));
pphi = (double*)calloc(L+2, sizeof(double));
pbeta = (double*)calloc(L+2, sizeof(double));
ptheta = (double*)calloc(L+2, sizeof(double));
pasr = (double*)calloc(L+2, sizeof(double));
ptval = (double*)calloc(L+2, sizeof(double));
pkld = (double*)calloc(2*(L+2)+1, sizeof(double));
pitr = (int*)calloc(L+2, sizeof(int));
pbound = (int*)calloc(L+2, sizeof(int));
//fprintf(stderr,"%s ", gid);
ones = (double*)calloc(m, sizeof(double)); for(i=0; i<m; i++){ ones[i]=1.0; }
//if(randomize>0){randomise4(y, Y, ki, X, N, m, P);}
//if(m>0 || forced>0){
ASEQTLALL(y, Y, Z, X, P, ki, w, km, exon, L, N, m, rss, lkhdDiff, ppi, pdelta, pphi, pbeta, ptheta, pasr, pitr, pbound, ptval, pkld);
if(verbose3>0){fprintf(stderr, "ASEQTLALL finished.\n");}
//}else{fprintf(stderr,"No marker tested.\n"); return -1;}
//-------------- VCF start --------------
if(printVCF>0){
double *yx, *zx, *zc;
double *Zx;
Zx = Z+N*L*2;
zc = Zx+N*m*2;
l=maxCsnp;
int ll=0;
for(l=0;l<L;l++){
if(fabs(exon[l])>1.5){// feature snp
gzprintf(postVCF, "%s\t%ld\t%s\t%c\t%c\t.\t.\t%s\tGT:GL:AP:AS\t", chrs[l], poss[l], rss[l], als[l][0], als[l][1], gid);
zx = Zx+N*2*ll;
yx = Y+N*2*ll;
for(i=0; i<N; i++){
gzprintf(postVCF, "%d|%d:%lf,%lf,%lf:%lf,%lf:%.0lf,%.0lf",
zx[i*2]>0.5?1:0, zx[i*2+1]>0.5?1:0 ,
(1.0-zx[i*2])*(1.0-zx[i*2+1]), zx[i*2]*(1.0-zx[i*2+1])+(1.0-zx[i*2])*zx[i*2+1], zx[i*2]*zx[i*2+1],
zx[i*2], zx[i*2+1], yx[i*2], yx[i*2+1]);
if(i<N-1){gzprintf(postVCF, "\t");}else{gzprintf(postVCF, "\n");}
}
ll++;
}else if(l=maxCsnp){
gzprintf(postVCF, "%s\t%ld\t%s\t%c\t%c\t.\tLEAD_QTL_SNP\t%s\tGT:GL:AP:AS\t", chrs[l], poss[l], rss[l], als[l][0], als[l][1], gid);
for(i=0; i<N; i++){
gzprintf(postVCF, "%d|%d:%lf,%lf,%lf:%lf,%lf:%.0lf,%.0lf",
zc[i*2]>0.5?1:0, zc[i*2+1]>0.5?1:0 ,
(1.0-zc[i*2])*(1.0-zc[i*2+1]), zc[i*2]*(1.0-zc[i*2+1])+(1.0-zc[i*2])*zc[i*2+1], zc[i*2]*zc[i*2+1],
zc[i*2], zc[i*2+1], 0.0, 0.0);
if(i<N-1){gzprintf(postVCF, "\t");}else{gzprintf(postVCF, "\n");}
}
}
}
gzclose(postVCF);
}
//--------------- VCF end ---------------
double maxld=0.0;
int maxl = -1;
int maxlr = -1;
int numOfTies=0;
//fprintf(stderr,"TSS=%ldn",TSS);
afs[L]= afs[L+1] = 0.5; rsq[L] = rsq[L+1]=1.0; hwes[L]=hwes[L+1]=0.0;
if(Null==0){for(l=0; l<L; l++){
//if(exon[l]>=0.0)printf("%s\t%s\t%s\t%ld\t%c\t%c\t%lf\t%lf\t%lf\t%lf\t%3.22lf\t%lf\t%ld\t%ld\n", gid, rss[l], chr, poss[l], als[l][0], als[l][1], afs[l], hwes[l], ias[l], rsq[l], lkhdDiff[l], ppi[l], m, l);
if(afs[l]>MAF && afs[l]<1.0-MAF && rsq[l]>RSQ && (hwes[l]<HWE||noPriorGenotype==1) && isTestReg(chrs[l], chr0, TSS, TSSPROX, poss[l]) ){// && (pbound[l+1]+pbound[l+1+L])<1 && ptheta[l+1]<=ptheta[l+1+L]){
//printf("%ld %lf\n", poss[l],lkhdDiff[l]);
if(round(maxld*100000)<round(lkhdDiff[l]*100000)){
numOfTies=0;
rand0=rand();
maxld=lkhdDiff[l];
maxl=l;
maxlr=l;
}else if(round(maxld*100000)==round(lkhdDiff[l]*100000)){
numOfTies++;
if(abs(poss[l]-TSS)<abs(poss[maxl]-TSS)){
//maxld=lkhdDiff[l];
maxl=l;
}
rand1=rand();
//if(randlkhdDiff[maxlr]<randlkhdDiff[l]){
if(rand0<rand1){
maxlr=l;
rand0=rand1;
}
}
}
//printf("%s\t%ld\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", rss[l], poss[l], afs[l], hwes[l], ias[l], rsq[l], lkhdDiff[l], ppi[l]);
}
l=maxl; }else{l=L;}//null
if(printAll>0){
l=0;
for(l0=0; l0<L; l0++){
if(abs(exon[l0])>0.5){printf("%s\t%s\t%s\t%ld\t%c\t%c\t%lf\t%lf\t%lf\t%lf\t%.10lf\t%lf\t%lf\t%lf\t%lf\t%ld\t%ld\t%ld\t%d\t%d\t%ld\t%lf\t%d\t%lf\t%lf\n", gid, rss[l], chrs[l], poss[l], als[l][0], als[l][1], afs[l], hwes[l], ias[l], rsq[l], lkhdDiff[l],
ppi[l], pdelta[l], pphi[l], ptheta[l], l, m, numOfLoci, pitr[l], pitr[0], maxlr<0?-1:poss[maxlr], lkhdDiff[L+1], pbound[l]+pbound[L], pkld[l], pkld[l+L+2]);
l++;
}
}
}else{
if(l<0){// no max lkhd
printf("%s\trs\t%s\t0\tX\tX\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t-1.0\t%ld\t%ld\t%ld\t-1\t-1\t-1\t-1\t-1\t0.0\n", gid, chrs[0], l,m,numOfLoci);
}else if(l<L){// normal
printf("%s\t%s\t%s\t%ld\t%c\t%c\t%lf\t%lf\t%lf\t%lf\t%.10lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%ld\t%ld\t%d\t%d\t%ld\t%lf\t%d\t%lf\t%lf\n",
gid, rss[l], chrs[l], poss[l], als[l][0], als[l][1], afs[l], hwes[l], ias[l], rsq[l],
lkhdDiff[l], ppi[l], pdelta[l], pphi[l], ptheta[l], pbeta[l], m, numOfLoci, pitr[l], pitr[0],
maxlr<0?-1:poss[maxlr], lkhdDiff[L+1], pbound[l]+pbound[L], pkld[l], pkld[l+L+2]);
}else if(l==L){// null lkhd
printf("%s\tAI\t%s\t-1\tN\tN\t-1.0\t-1.0\t-1.0\t%lf\t%.10lf\t%lf\t%lf\t%lf\t%lf\t%ld\t%ld\t%ld\t%d\t%d\t%ld\t%lf\t%d\t%lf\t%lf\t%lf\n", gid, chrs[l], asNonasRatio0, lkhdDiff[L], ppi[L], pdelta[L], pphi[L], ptheta[L], l, m, numOfLoci, pitr[L], pitr[L], maxlr<0?-1:poss[maxlr], lkhdDiff[L+1], pbound[L], pkld[L], theta2, pkld[2*L+2]);
}
}
if(printImprint>0){
printf("%s\tIMP\t%s\t-1\tN\tN\t-1.0\t-1.0\t-1.0\t-1.0\t%.10lf\t%lf\t%lf\t%lf\t%lf\t%ld\t%ld\t%ld\t%d\t%d\t%ld\t%lf\t%d\t%lf\t%lf\n", gid, chrs[0], lkhdDiff[L+1], ppi[L+1], pdelta[L+1], pphi[L+1], ptheta[L+1], l, m, numOfLoci, pitr[L+1], pitr[L+1], maxlr<0?-1:poss[maxlr], ptheta[L+1], pbound[L+1]+pbound[L], pkld[L+1], pkld[2*L+3]);
}
return 1;
}
static void altGraphXDrawAt(struct track *tg, void *item, struct hvGfx *hvg,
int xOff, int yOff, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw an altGraphX at the specified location. */
{
int i = 0;
int s =0, e=0;
int heightPer = tg->heightPer;
int start = 0, end = 0;
struct altGraphX *ag = item;
int width = 0;
int x1, x2;
/* Create a link to hgc. */
if(tg->mapsSelf && tg->mapItem)
{
char name[256];
int nameWidth = 0;
int textX = 0;
start = max(winStart, ag->tStart);
end = min(winEnd, ag->tEnd);
width = (end - start) * scale;
x1 = round((double)((int) start - winStart)*scale) + xOff;
textX = x1;
if(width == 0)
width = 1;
/* If there isn't enough room on before the left edge snap the
label to the left edge. */
if(withLeftLabels && tg->limitedVis == tvPack)
{
safef(name, sizeof(name), "%s", tg->itemName(tg, ag));
nameWidth = mgFontStringWidth(font, name);
textX = textX - (nameWidth + tl.nWidth/2);
if(textX < insideX)
textX = insideX - nameWidth;
width = width + (x1 - textX);
}
tg->mapItem(tg, hvg, ag, "notUsed", "notUsed", ag->tStart, ag->tEnd, textX, yOff, width, heightPer);
}
/* Draw the edges (exons and introns). */
for(i= 0; i < ag->edgeCount; i++)
{
Color color2;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
color2 = MG_BLACK;
/* If you want to shade by number of transcripts uncomment next line. */
/* color2 = altGraphXColorForEdge(hvg, ag, i); */
if(isExon(ag, i))
{
if(vis == tvPack)
drawScaledBox(hvg, s, e, scale, xOff, yOff+heightPer/2, heightPer/2, color2);
else
drawScaledBox(hvg, s, e, scale, xOff, yOff, heightPer, color2);
}
else
{
int midX;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
x1 = round((double)((int) s - winStart)*scale) + xOff;
x2 = round((double)((int) e - winStart)*scale) + xOff;
if(vis == tvPack)
{
midX = (x1+x2)/2;
hvGfxLine(hvg, x1, yOff+heightPer/2, midX, yOff, color2);
hvGfxLine(hvg, midX, yOff, x2, yOff+heightPer/2, color2);
}
else
hvGfxLine(hvg, x1, yOff+heightPer/2, x2, yOff+heightPer/2, color2);
}
}
}
