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SMR_data_p3.cpp
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//
// SMR_data_p3.cpp
// SMR_CPP
//
// Created by Futao Zhang on 15/06/2016.
// Copyright (c) 2016 Futao Zhang. All rights reserved.
//
#include "SMR_data_p3.h"
namespace SMRDATA
{
void combine_esi(vector<snpinfolst> &snpinfo, vector<string> &smasNames, bool genouni)
{
long counter = 0;
map<string, int> rs_map;
map<string, int> rsbp_map;
long f2r=smasNames.size();
if(genouni) f2r=1;
for (int i = 0; i < f2r; i++)
{
eqtlInfo etmp;
string esifile = smasNames[i]+".esi";
read_esifile(&etmp, esifile);
for (int j = 0; j<etmp._snpNum; j++)
{
string crsbpstr=etmp._esi_rs[j]+":"+atos(etmp._esi_bp[j]);
rs_map.insert(pair<string, int>(etmp._esi_rs[j].c_str(), counter));
rsbp_map.insert(pair<string, int>(crsbpstr.c_str(), counter));
if(rs_map.size() != rsbp_map.size())
{
// SNP in one esi file has BP1 but in another esi file has BP2
printf("ERROR: inconsistent position for the SNP %s in different ESI files. Please check.\n", etmp._esi_rs[j].c_str()) ;
exit(EXIT_FAILURE);
}
if (counter < rs_map.size())
{
snpinfolst snpinfotmp;
counter = rs_map.size();
snpinfotmp.snpchr=etmp._esi_chr[j];
strcpy2(&snpinfotmp.snprs, etmp._esi_rs[j]);
snpinfotmp.bp=etmp._esi_bp[j];
snpinfotmp.gd=etmp._esi_gd[j];
strcpy2(&snpinfotmp.a1, etmp._esi_allele1[j]);
strcpy2(&snpinfotmp.a2, etmp._esi_allele2[j]);
snpinfotmp.freq=etmp._esi_freq[j];
snpinfo.push_back(snpinfotmp);
}
}
}
printf("Total %ld SNPs to be included from %ld esi files.\n",snpinfo.size(),f2r);
}
void combine_epi(vector<probeinfolst2> &probeinfo, vector<string> &smasNames)
{
long counter = 0;
map<string, int> prb_map;
map<string, int> prbbp_map;
map<string, int>::iterator iter;
for (int i = 0; i < smasNames.size(); i++)
{
eqtlInfo etmp;
string epifile = smasNames[i]+".epi";
read_epifile(&etmp, epifile);
for (int j = 0; j<etmp._probNum; j++)
{
string crsbpstr=etmp._epi_prbID[j]+":"+atos(etmp._epi_bp[j]);
prb_map.insert(pair<string, int>(etmp._epi_prbID[j].c_str(), counter));
prbbp_map.insert(pair<string, int>(crsbpstr.c_str(), counter));
if(prb_map.size() != prbbp_map.size())
{
printf("ERROR: inconsistent position for the probe %s in different EPI files. Please check.\n", etmp._epi_prbID[j].c_str()) ;
exit(EXIT_FAILURE);
}
if (counter < prb_map.size())
{
probeinfolst2 probinfotmp;
counter=prb_map.size();
probinfotmp.probechr=etmp._epi_chr[j];
strcpy2(&probinfotmp.probeId, etmp._epi_prbID[j]);
probinfotmp.bp=etmp._epi_bp[j];
probinfotmp.gd=etmp._epi_gd[j];
strcpy2(&probinfotmp.genename, etmp._epi_gene[j]);
probinfotmp.orien=etmp._epi_orien[j];
probinfotmp.vnum=0;
probinfotmp.rowid=NULL;
probinfotmp.beta_se=NULL;
probinfotmp.sinfo=NULL;
probinfotmp.besdpath.reserve(0x20);
probinfotmp.besdpath.push_back(smasNames[i]);
probeinfo.push_back(probinfotmp);
} else {
iter=prb_map.find(etmp._epi_prbID[j]);
if(iter!=prb_map.end())
{
probeinfo[iter->second].besdpath.push_back(smasNames[i]);
}
else
{
printf("ERROR: This would never happen. please help to report this bug.\n") ;
exit(EXIT_FAILURE);
}
}
}
}
printf("Total %ld probes to be included from %ld epi files.\n",probeinfo.size(),smasNames.size());
}
uint64_t countNotNullNum(vector<string> &smasNames, int &densefnum, int &sparsefnum)
{
uint64_t count=0;
for (int i = 0; i < smasNames.size(); i++)
{
eqtlInfo etmp;
string besdfile = smasNames[i]+".besd";
FILE *fptr=fopen(besdfile.c_str(), "rb");
if(!fptr)
{
printf ( "ERROR: Couldn't open file %s\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
uint32_t filetype=readuint32(fptr);
uint64_t valnum=0;
if(filetype==SPARSE_FILE_TYPE_3F || filetype==0x40000000) {valnum=readuint64(fptr); sparsefnum++;}
if(filetype==SPARSE_FILE_TYPE_3) {
for(int j=1;j<RESERVEDUNITS;j++) readint(fptr);
valnum=readuint64(fptr);
sparsefnum++;
}
if(filetype==0x3f800000) {valnum=(uint64_t)readfloat(fptr);sparsefnum++;}
if(filetype==DENSE_FILE_TYPE_1) {
densefnum++;
while(!feof(fptr))
{
float tmpfloat=readfloat(fptr);
if(fabs(tmpfloat+9)>1e-6) valnum++;
}
}
if(filetype==DENSE_FILE_TYPE_3) {
readint(fptr);
long esinum=readint(fptr);
long epinum=readint(fptr);
if(esinum==-9 || epinum==-9)
{
printf ( "ERROR: File is ruined %s\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
valnum=esinum*epinum;
densefnum++;
}
fclose(fptr);
count+=(valnum>>1);
}
return count;
}
void save_besds_dbesd(char* outFileName, vector<snpinfolst> &snpinfo, vector<probeinfolst2> &probeinfo, vector<string> &esi_rs,vector<string> &esi_a1,vector<string> &esi_a2, int addn)
{
map<string, int> esi_map;
for(int j=0;j<esi_rs.size();j++)
{
esi_map.insert(pair<string,int>(esi_rs[j],j));
}
// get esd info
long esiNum=snpinfo.size();
long epiNum=probeinfo.size();
string esdfile=string(outFileName)+string(".besd");
FILE * smr1;
smr1 = fopen (esdfile.c_str(), "wb");
if (!(smr1)) {
printf("ERROR: failed to open file %s.\n",esdfile.c_str());
exit(EXIT_FAILURE);
}
uint32_t ft2save=DENSE_FILE_TYPE_3;
uint64_t bsize=(uint64_t)esiNum<<1;
float* buffer=(float*)malloc (sizeof(float)*bsize);
if (NULL == buffer) {
printf("ERROR: failed to allocate write buffer for file %s.\n",esdfile.c_str());
exit(EXIT_FAILURE);
}
bool prtscr=false;
map<string, int>::iterator iter;
eqtlInfo eqtlinfo;
int ssck=-9;
for(int j=0;j<epiNum;j++)
{
printf("Saving... %3.0f%%\r", 100.0*j/epiNum);
fflush(stdout);
string prbname=probeinfo[j].probeId;
for(int k=0;k<bsize;k++) buffer[k]=-9; //init
for(int k=0;k<probeinfo[j].besdpath.size();k++)
{
string besdfilepre = probeinfo[j].besdpath[k];
vector<string> _rs;
vector<float> _beta;
vector<float> _se;
vector<int> _chr;
vector<string> _a1;
vector<string> _a2;
vector<int> _bp;
vector<float> _freq;
read_epifile(&eqtlinfo, string(probeinfo[j].besdpath[k])+".epi", prtscr);
extract_eqtl_single_probe(&eqtlinfo, prbname, prtscr);
read_esifile(&eqtlinfo, string(probeinfo[j].besdpath[k])+".esi", prtscr);
int tmp=shown(string(probeinfo[j].besdpath[k]));
if(tmp!=-9)
{
printf("The sample size is %d.\n",tmp);
if(ssck!=-9) {
ssck=tmp;
}
else
{
if(ssck!=tmp)
{
printf("ERROR: You are trying merge BESD files with different sample sizes.\n");
exit(EXIT_FAILURE);
}
}
}
read_besdfile(&eqtlinfo, string(probeinfo[j].besdpath[k])+".besd", prtscr);
if(eqtlinfo._rowid.empty() && eqtlinfo._bxz.empty())
{
//printf("No data included of probe %s from %s.\n",prbname.c_str(),probeinfo[j].besdpath[k].c_str());
continue;
}
if(eqtlinfo._valNum==0)
{
for(uint32_t jj=0;jj<eqtlinfo._snpNum;jj++)
{
float beta=eqtlinfo._bxz[0][jj];
float se=eqtlinfo._sexz[0][jj];
if(ABS(se+9)<1e-6) continue;
_beta.push_back(beta);
_se.push_back(se);
_rs.push_back(eqtlinfo._esi_rs[jj]);
_chr.push_back(eqtlinfo._esi_chr[jj]);
_a1.push_back(eqtlinfo._esi_allele1[jj]);
_a2.push_back(eqtlinfo._esi_allele2[jj]);
_bp.push_back(eqtlinfo._esi_bp[jj]);
_freq.push_back(eqtlinfo._esi_freq[jj]);
}
}
else
{
if(eqtlinfo._val.size()==0)
{
printf("Error: No data extracted from the input, please check.\n");
exit(EXIT_FAILURE);
}
for(uint32_t ii=0;ii<eqtlinfo._probNum;ii++)
{
uint64_t proid=eqtlinfo._include[ii];
uint64_t pos=eqtlinfo._cols[proid<<1];
uint64_t pos1=eqtlinfo._cols[(proid<<1)+1];
uint64_t num=pos1-pos;
for(int jj=0;jj<num;jj++)
{
double beta=eqtlinfo._val[pos+jj];
double se=eqtlinfo._val[pos+jj+num];
int rowid=eqtlinfo._rowid[pos+jj];
_beta.push_back(beta);
_se.push_back(se);
_rs.push_back(eqtlinfo._esi_rs[rowid]);
_chr.push_back(eqtlinfo._esi_chr[rowid]);
_a1.push_back(eqtlinfo._esi_allele1[rowid]);
_a2.push_back(eqtlinfo._esi_allele2[rowid]);
_bp.push_back(eqtlinfo._esi_bp[rowid]);
_freq.push_back(eqtlinfo._esi_freq[rowid]);
}
}
}
vector<int> rsid(_rs.size());
#pragma omp parallel for private(iter)
for (int l = 0; l<_rs.size(); l++){
iter = esi_map.find(_rs[l]);
if (iter != esi_map.end()) rsid[l]=iter->second;
else {
printf("ERROR: SNP %s is not in output SNP set. if you are using --geno-uni, please disable it then try again. Otherwise please report this bug.\n",_rs[l].c_str());
exit(EXIT_FAILURE);
}
}
for(int l=0;l<rsid.size();l++)
{
if(esi_a1[rsid[l]]==_a1[l] && esi_a2[rsid[l]]==_a2[l]){
buffer[rsid[l]]=_beta[l];
buffer[esiNum+rsid[l]]=_se[l];
} else if(esi_a1[rsid[l]]==_a2[l] && esi_a2[rsid[l]]==_a1[l]){
buffer[rsid[l]]=-1.0*_beta[l];
buffer[esiNum+rsid[l]]=_se[l];
} else {
printf("ERROR: inconsistent allele pairs of SNP %s found.\n",_rs[l].c_str());
printf("Discrepant Allele pairs: (%s,%s) with (%s,%s).\n",esi_a1[rsid[l]].c_str(), esi_a2[rsid[l]].c_str(),_a1[l].c_str(), _a2[l].c_str());
exit(EXIT_FAILURE);
//this part is for multi-allelic SNPs. since we don't save multi-allelic SNPs anymore, so we should disable it.
/*
int did=-9;
float sig=1.0;
for(int m=0;m<esi_rs.size();m++)
{
if(esi_rs[m]==_rs[l])
{
if(esi_a1[m]==_a1[l] && esi_a2[m]==_a2[l])
{
did=m;
break;
}
if(esi_a1[m]==_a2[l] && esi_a2[m]==_a1[l])
{
did=m;
sig=-1.0;
break;
}
}
}
if(did==-9)
{
printf("ERROR: This would not go to happen. Please report this bug.");
exit(EXIT_FAILURE);
}
buffer[did]=sig*_beta[l];
buffer[esiNum+did]=_se[l];
*/
}
}
}
if(j==0)
{
vector<int> ten_ints(RESERVEDUNITS);
ten_ints[0]=ft2save;
if(addn!=-9)
{
printf("Adding the sample size %d to the file %s.\n", addn, esdfile.c_str());
ten_ints[1]=addn;
} else if(ssck!=-9){
printf("Saving the sample size %d to the file %s.\n", ssck, esdfile.c_str());
ten_ints[1]=ssck;
} else {
ten_ints[1]=-9;
}
ten_ints[2]=(int)esiNum;
ten_ints[3]=(int)epiNum;
for(int i=4;i<RESERVEDUNITS;i++) ten_ints[i]=-9;
fwrite (&ten_ints[0],sizeof(int), RESERVEDUNITS, smr1);
}
fwrite (buffer,sizeof(float), bsize, smr1);
}
fclose (smr1);
free(buffer);
cout<<"Effect sizes (beta) and SE for "<<epiNum<<" probes and "<<esiNum<<" SNPs have been saved in a binary file [" + esdfile + "]." <<endl;
}
void save_besds_dbesd(char* outFileName, vector<snpinfolst> &snpinfo, vector<probeinfolst2> &probeinfo, int addn)
{
//because read only once .esi file. so the alleles of each SNP in every .esi should be the same and in the same alignment.
// get esd info
long esiNum=snpinfo.size();
long epiNum=probeinfo.size();
string esdfile=string(outFileName)+string(".besd");
FILE * smr1;
smr1 = fopen (esdfile.c_str(), "wb");
if (!(smr1)) {
printf("ERROR: failed to open file %s.\n",esdfile.c_str());
exit(EXIT_FAILURE);
}
uint32_t ft2save=DENSE_FILE_TYPE_3;
uint64_t sizeperprb=sizeof(float)*esiNum*2;
uint64_t bsize=0x7FFFFFC0;
float* buffer=(float*)malloc (bsize);
while(NULL == buffer && bsize>sizeperprb) {
buffer=(float*)malloc (bsize>>=1);
}
if(NULL == buffer)
{
printf("ERROR: Can't malloc the reading buffer for %llu MB.\n",(bsize>>20));
exit(EXIT_FAILURE);
} else {
printf("%llu MB memory has been allocated as the reading buffer.\n",(bsize>>20));
}
long prbperloop=bsize/sizeperprb;
bool prtscr=false;
map<string, int>::iterator iter;
eqtlInfo eqtlinfo;
read_esifile(&eqtlinfo, string(probeinfo[0].besdpath[0])+".esi", prtscr);
if(esiNum != eqtlinfo._snpNum)
{
printf("ERROR: the SNPs in the .esi files are not consistent. Please disable --geno-uni and have another try.\n");
exit(EXIT_FAILURE);
}
int loops=ceil(1.0*epiNum/prbperloop);
int ssck=-9;
for(int j=0;j<loops;j++)
{
printf("Saving... %3.0f%%\r", 100.0*j/loops);
fflush(stdout);
uint64_t numprbcurloop=prbperloop;
if(j==loops-1) numprbcurloop=epiNum-j*numprbcurloop;
uint64_t vnum=numprbcurloop*esiNum*2;
for(int k=0;k<vnum;k++) buffer[k]=-9; //init
map<string,int> fcurloop;
long fnum=0;
vector<F2Prb> f2prb;
for(int k=0;k<numprbcurloop;k++)
{
long curPrid=j*prbperloop+k;
if(curPrid>=probeinfo.size()) break;
string prbname=probeinfo[curPrid].probeId;
if(probeinfo[curPrid].besdpath.size()>1)
{
printf("ERROR: the probe %s is found in %ld BESD files. Please check whether the SNPs are in consistency among the .esi files, if yes, please remove one of the duplicate probe then have a try, if not, please disable --geno-uni, then have a try.\n",prbname.c_str(),probeinfo[curPrid].besdpath.size());
exit(EXIT_FAILURE);
}
iter=fcurloop.find(probeinfo[curPrid].besdpath[0]);
if(iter!=fcurloop.end())
{
f2prb[iter->second].pid.push_back(k);
} else {
fcurloop.insert(pair<string,int>(probeinfo[curPrid].besdpath[0],fnum));
F2Prb fptmp;
fptmp.besdpath=probeinfo[curPrid].besdpath[0];
fptmp.pid.push_back(k);
f2prb.push_back(fptmp);
fnum++;
}
}
for(int l=0;l<f2prb.size();l++)
{
string besdfilepre = f2prb[l].besdpath;
read_epifile(&eqtlinfo, besdfilepre+".epi", prtscr);
string besdfile = string(besdfilepre)+".besd";
FILE *fptr=fopen(besdfile.c_str(), "rb");
if(!fptr)
{
printf ( "ERROR: Couldn't open file %s\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
uint32_t filetype=readuint32(fptr);
int descriptive=1;
if(filetype==SPARSE_FILE_TYPE_3 || filetype==DENSE_FILE_TYPE_3) descriptive=RESERVEDUNITS;
uint64_t valNum=0;
uint64_t* ptr=NULL;
uint64_t rowSTART=0;
uint64_t valSTART=0;
if(filetype==SPARSE_FILE_TYPE_3F || filetype==SPARSE_FILE_TYPE_3)
{
uint64_t colNum=(eqtlinfo._probNum<<1)+1;
fseek(fptr, 0L, SEEK_END);
uint64_t lSize = ftell(fptr);
fseek(fptr, 0L, SEEK_SET);
readuint32(fptr);
if(filetype==SPARSE_FILE_TYPE_3)
{
int tmp=readint(fptr);
if(tmp!=-9)
{
printf("The sample size is %d.\n",tmp);
if(ssck!=-9) {
ssck=tmp;
}
else
{
if(ssck!=tmp)
{
printf("ERROR: You are trying merge BESD files with different sample sizes.\n");
exit(EXIT_FAILURE);
}
}
}
tmp=readint(fptr);
if(tmp!=eqtlinfo._snpNum)
{
printf("ERROR: The SNPs in your .esi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
tmp=readint(fptr);
if(tmp!=eqtlinfo._probNum)
{
printf("ERROR: The probes in your .epi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
for(int k=4;k<RESERVEDUNITS;k++) readint(fptr);
}
valNum=readuint64(fptr);
if(filetype==SPARSE_FILE_TYPE_3F) {
if( lSize - (sizeof(uint32_t) + sizeof(uint64_t) + colNum*sizeof(uint64_t) + valNum*sizeof(uint32_t) + valNum*sizeof(float)) != 0)
{
printf("ERROR: wrong value number. File %s is ruined.\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
}
else
{
if( lSize - (RESERVEDUNITS*sizeof(int) + sizeof(uint64_t) + colNum*sizeof(uint64_t) + valNum*sizeof(uint32_t) + valNum*sizeof(float)) != 0)
{
printf("ERROR: wrong value number. File %s is ruined.\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
}
uint64_t colsize=colNum*sizeof(uint64_t);
uint64_t* colbuf=(uint64_t*)malloc(colsize);
if(NULL == colbuf)
{
printf("ERROR: Can't malloc the reading cols buffer for %llu MB.\n",(colsize>>20));
exit(EXIT_FAILURE);
}
fread(colbuf,colNum,sizeof(uint64_t),fptr);
ptr=colbuf;
rowSTART=descriptive*sizeof(int) + sizeof(uint64_t) + colNum*sizeof(uint64_t);
valSTART=descriptive*sizeof(int) + sizeof(uint64_t) + colNum*sizeof(uint64_t)+valNum*sizeof(uint32_t);
for(int m=0;m<f2prb[l].pid.size();m++)
{
long curPrid=j*prbperloop+f2prb[l].pid[m];
string curprb=probeinfo[curPrid].probeId;
iter=eqtlinfo._probe_name_map.find(curprb);
if(iter!=eqtlinfo._probe_name_map.end())
{
uint64_t pid=iter->second;
uint64_t pos=*(ptr+(pid<<1)); //BETA START
uint64_t pos1=*(ptr+(pid<<1)+1); //SE START
uint64_t num=pos1-pos;
char* row_char_ptr;
row_char_ptr = (char*) malloc (sizeof(char)*2*num*sizeof(uint32_t));
if (row_char_ptr == NULL) {fputs ("Memory error",stderr); exit (1);}
char* val_char_ptr;
val_char_ptr = (char*) malloc (sizeof(char)*2*num*sizeof(float));
if (val_char_ptr == NULL) {fputs ("Memory error",stderr); exit (1);}
memset(row_char_ptr,0,sizeof(char)*2*num*sizeof(uint32_t));
memset(val_char_ptr,0,sizeof(char)*2*num*sizeof(float));
fseek(fptr, rowSTART+pos*sizeof(uint32_t), SEEK_SET);
fread(row_char_ptr, sizeof(uint32_t),2*num,fptr);
uint32_t* row_ptr=(uint32_t *)row_char_ptr;
fseek(fptr,valSTART+pos*sizeof(float),SEEK_SET);
fread(val_char_ptr,sizeof(float), 2*num,fptr);
float* val_ptr=(float*)val_char_ptr;
for(int j=0;j<num;j++)
{
uint32_t rid=*(row_ptr+j);
*(buffer+f2prb[l].pid[m]*esiNum*2+rid)=*(val_ptr+j);
*(buffer+f2prb[l].pid[m]*esiNum*2+rid+esiNum)=*(val_ptr+j+num);
}
free(row_char_ptr);
free(val_char_ptr);
}
}
free(colbuf);
}
else if(filetype==DENSE_FILE_TYPE_1 || filetype==DENSE_FILE_TYPE_3){
if(filetype==DENSE_FILE_TYPE_3)
{
int tmp=readint(fptr);
if(tmp!=-9)
{
printf("The sample size is %d.\n",tmp);
if(ssck!=-9) {
ssck=tmp;
}
else
{
if(ssck!=tmp)
{
printf("ERROR: You are trying merge BESD files with different sample sizes.\n");
exit(EXIT_FAILURE);
}
}
}
tmp=readint(fptr);
if(tmp!=eqtlinfo._snpNum)
{
printf("ERROR: The SNPs in your .esi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
tmp=readint(fptr);
if(tmp!=eqtlinfo._probNum)
{
printf("ERROR: The probes in your .epi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
for(int k=4;k<RESERVEDUNITS;k++) readint(fptr);
}
for(int m=0;m<f2prb[l].pid.size();m++)
{
long curPrid=j*prbperloop+f2prb[l].pid[m];
string curprb=probeinfo[curPrid].probeId;
iter=eqtlinfo._probe_name_map.find(curprb);
if(iter!=eqtlinfo._probe_name_map.end())
{
uint64_t pid=iter->second;
fseek(fptr,((pid<<1)*eqtlinfo._snpNum+descriptive)<<2, SEEK_SET);
float* wptr=buffer+f2prb[l].pid[m]*esiNum*2;
fread(wptr, sizeof(char),eqtlinfo._snpNum<<3,fptr);
}
}
}
else {
printf("Your file is in the old sparse format. please first re-make it by --beqtl-summary and --make-besd.\n");
exit(EXIT_FAILURE);
}
fclose(fptr);
}
if(j==0)
{
vector<int> ten_ints(RESERVEDUNITS);
ten_ints[0]=ft2save;
if(addn!=-9)
{
printf("Adding the sample size %d to the file %s.\n", addn, esdfile.c_str());
ten_ints[1]=addn;
} else if(ssck!=-9){
printf("Saving the sample size %d to the file %s.\n", ssck, esdfile.c_str());
ten_ints[1]=ssck;
} else {
ten_ints[1]=-9;
}
ten_ints[2]=(int)esiNum;
ten_ints[3]=(int)epiNum;
for(int i=4;i<RESERVEDUNITS;i++) ten_ints[i]=-9;
fwrite (&ten_ints[0],sizeof(int), RESERVEDUNITS, smr1);
}
fwrite (buffer,sizeof(float), vnum, smr1);
}
fclose (smr1);
free(buffer);
cout<<"Effect sizes (beta) and SE for "<<epiNum<<" probes and "<<esiNum<<" SNPs have been saved in a binary file [" + esdfile + "]." <<endl;
}
void save_besds_sbesd(char* outFileName, vector<snpinfolst> &snpinfo, vector<probeinfolst2> &probeinfo, vector<string> &esi_rs,vector<string> &esi_a1,vector<string> &esi_a2,vector<string> &smasNames, int addn)
{
//double init
/*
for(int j=0;j<probeinfo.size();j++)
{
probeinfo[j].vnum=0;
if(probeinfo[j].rowid!=NULL)
{
free(probeinfo[j].rowid);
probeinfo[j].rowid=NULL;
}
if(probeinfo[j].beta_se!=NULL)
{
free(probeinfo[j].beta_se);
probeinfo[j].beta_se=NULL;
}
}
*/
//
map<string, int> esi_map;
for(int j=0;j<esi_rs.size();j++)
{
esi_map.insert(pair<string,int>(esi_rs[j],j));
}
map<string, int> epi_map;
map<string,int>::iterator iter;
for(int j=0;j<probeinfo.size();j++)
{
epi_map.insert(pair<string,int>(probeinfo[j].probeId,j));
}
// get esd info
long esiNum=snpinfo.size();
long epiNum=probeinfo.size();
string esdfile=string(outFileName)+string(".besd");
FILE * smr1;
smr1 = fopen (esdfile.c_str(), "wb");
if (!(smr1)) {
printf("ERROR: failed to open file %s.\n",esdfile.c_str());
exit(EXIT_FAILURE);
}
uint32_t ft2save=SPARSE_FILE_TYPE_3;
bool prtscr=false;
eqtlInfo etmp;
printf("Reading besd files....\n");
int ssck=-9;
for (int i = 0; i < smasNames.size(); i++)
{
printf("Reading... %3.0f%%\r", 100.0*i/(smasNames.size()));
fflush(stdout);
string esifile = smasNames[i]+".esi";
read_esifile(&etmp, esifile, prtscr);
string epifile = smasNames[i]+".epi";
read_epifile(&etmp, epifile, prtscr);
string besdfile = smasNames[i]+".besd";
FILE *fptr=fopen(besdfile.c_str(), "rb");
if(!fptr)
{
printf ( "ERROR: Couldn't open file %s\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
uint32_t filetype=readuint32(fptr);
int descriptive=1;
if(filetype==SPARSE_FILE_TYPE_3 || filetype==DENSE_FILE_TYPE_3) descriptive=RESERVEDUNITS;
uint64_t valNum=0;
uint64_t* ptr=NULL;
uint64_t rowSTART=0;
uint64_t valSTART=0;
if(filetype==SPARSE_FILE_TYPE_3F || filetype==SPARSE_FILE_TYPE_3){
uint64_t colNum=(etmp._probNum<<1)+1;
fseek(fptr, 0L, SEEK_END);
uint64_t lSize = ftell(fptr);
fseek(fptr, 0L, SEEK_SET);
readuint32(fptr);
if(filetype==SPARSE_FILE_TYPE_3)
{
int tmp=readint(fptr);
if(tmp!=-9)
{
printf("The sample size is %d.\n",tmp);
if(ssck!=-9) {
ssck=tmp;
}
else
{
if(ssck!=tmp)
{
printf("ERROR: You are trying merge BESD files with different sample sizes.\n");
exit(EXIT_FAILURE);
}
}
}
tmp=readint(fptr);
if(tmp!=etmp._snpNum)
{
printf("ERROR: The SNPs in your .esi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
tmp=readint(fptr);
if(tmp!=etmp._probNum)
{
printf("ERROR: The probes in your .epi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
for(int k=4;k<RESERVEDUNITS;k++) readint(fptr);
}
valNum=readuint64(fptr);
if(filetype==SPARSE_FILE_TYPE_3F) {
if( lSize - (sizeof(uint32_t) + sizeof(uint64_t) + colNum*sizeof(uint64_t) + valNum*sizeof(uint32_t) + valNum*sizeof(float)) != 0)
{
printf("ERROR: wrong value number. File %s is ruined.\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
}
else
{
if( lSize - (RESERVEDUNITS*sizeof(int) + sizeof(uint64_t) + colNum*sizeof(uint64_t) + valNum*sizeof(uint32_t) + valNum*sizeof(float)) != 0)
{
printf("ERROR: wrong value number. File %s is ruined.\n", besdfile.c_str());
exit (EXIT_FAILURE);
}
}
uint64_t colsize=colNum*sizeof(uint64_t);
uint64_t* colbuf=(uint64_t*)malloc(colsize);
if(NULL == colbuf)
{
printf("ERROR: Can't malloc the reading cols buffer for %llu MB.\n",(colsize>>20));
exit(EXIT_FAILURE);
}
fread(colbuf,colNum,sizeof(uint64_t),fptr);
ptr=colbuf;
rowSTART=descriptive*sizeof(uint32_t) + sizeof(uint64_t) + colNum*sizeof(uint64_t);
valSTART=descriptive*sizeof(uint32_t) + sizeof(uint64_t) + colNum*sizeof(uint64_t)+valNum*sizeof(uint32_t);
for( int j=0;j<etmp._probNum;j++)
{
string curprb=etmp._epi_prbID[j];
iter=epi_map.find(curprb);
int prbindx=iter->second;
if(probeinfo[prbindx].besdpath.size()>1)
{
string bpaths=probeinfo[prbindx].besdpath[0];
for(int thid=1;thid<probeinfo[prbindx].besdpath.size();thid++) bpaths+=", "+probeinfo[prbindx].besdpath[thid];
printf("Reading summary data of the probe %s from %ld BESD files(%s).\n",curprb.c_str(),probeinfo[prbindx].besdpath.size(),bpaths.c_str());
}
uint64_t pos=*(ptr+(j<<1)); //BETA START
uint64_t pos1=*(ptr+(j<<1)+1); //SE START
uint64_t num=pos1-pos;
if(num>0)
{
uint32_t* ridbuff=(uint32_t*)malloc(num*2*sizeof(uint32_t));
if(NULL == ridbuff)
{
printf("ERROR: Memory allocation error when when reading the probe %s in the file %s.\n",curprb.c_str(),besdfile.c_str());
exit(EXIT_FAILURE);
}
memset(ridbuff,0,num*2*sizeof(uint32_t));
float* betasebuff=(float*)malloc(num*2*sizeof(float));
if(NULL == betasebuff)
{
printf("ERROR: Memory allocation error when when reading the probe %s in the file %s.\n",curprb.c_str(),besdfile.c_str());
exit(EXIT_FAILURE);
}
memset(betasebuff,0,num*2*sizeof(float));
fseek(fptr, rowSTART+pos*sizeof(uint32_t), SEEK_SET);
fread(ridbuff, sizeof(uint32_t),2*num,fptr);
fseek(fptr,valSTART+pos*sizeof(float),SEEK_SET);
fread(betasebuff,sizeof(float), 2*num,fptr);
vector<string> _rs;
vector<string> _a1;
vector<string> _a2;
_rs.reserve(num);
_a1.reserve(num);
_a2.reserve(num);
for(int l=0;l<num;l++) {
_rs.push_back(etmp._esi_rs[ridbuff[l]]);
_a1.push_back(etmp._esi_allele1[ridbuff[l]]);
_a2.push_back(etmp._esi_allele2[ridbuff[l]]);
}
#pragma omp parallel for private(iter)
for (int l = 0; l<_rs.size(); l++)
{
iter = esi_map.find(_rs[l]);
if (iter != esi_map.end())
{
int esiidx=iter->second;
ridbuff[l]=iter->second;
if(esi_a1[esiidx]==_a1[l] && esi_a2[esiidx]==_a2[l] )
{
} else if(esi_a1[esiidx]==_a2[l] && esi_a2[esiidx]==_a1[l] )
{
printf("WARING: switched the effect allele with the other allele of SNP %s found.\n", _rs[l].c_str());
betasebuff[l]=-1.0*betasebuff[l];
} else {
printf("ERROR: SNP %s with multiple alleles <%s,%s> and <%s,%s> does not pass the allele check.\n", _rs[l].c_str(),esi_a1[esiidx].c_str(),esi_a2[esiidx].c_str(),_a1[l].c_str(),_a2[l].c_str());
exit(EXIT_FAILURE);
}
}
else {
printf("ERROR: This can't happen. please report this bug.\n");
exit(EXIT_FAILURE);
}
}
//if geno in uniform, etmp._esi_rs identifies with esi_rs, ridbuff identifies with rsid
if(probeinfo[prbindx].vnum==0)
{
probeinfo[prbindx].rowid=ridbuff;
probeinfo[prbindx].beta_se=betasebuff;
probeinfo[prbindx].vnum=num;
} else {
map<int,int> rid_map;
for(int l=0;l<probeinfo[prbindx].vnum;l++)
{
rid_map.insert(pair<int,int>(probeinfo[prbindx].rowid[l],l));
}
int ridsize=rid_map.size();
vector<int> keepid;
for(int l=0;l<num;l++)
{
if(fabs(betasebuff[l+num]+9)>1e-6)
{
rid_map.insert(pair<int,int>(ridbuff[l],ridsize));
if(ridsize<rid_map.size())
{
keepid.push_back(l);
ridsize++;
} else {
printf("WARNING: duplicated SNP %s for the probe %s found in current summary data file\"%s\" and the besd file(s) read before. This one would be skipped. Please make sure they are the same.\n",_rs[l].c_str(),curprb.c_str(),besdfile.c_str());
}
} else {
printf("WARNING: SNP %s with \"NA\" value found and skipped.\n",_rs[l].c_str());
}
}
long num_new=probeinfo[prbindx].vnum+keepid.size();
uint32_t* rid_new=(uint32_t*)malloc(num_new*2*sizeof(uint32_t));
if(NULL == rid_new)
{
printf("ERROR: Memory allocation error when when merging data of probe %s.\n",curprb.c_str());
exit(EXIT_FAILURE);
}
memset(rid_new,0,num_new*2*sizeof(uint32_t));
float* betase_new=(float*)malloc(num_new*2*sizeof(float));
if(NULL == betase_new)
{
printf("ERROR: Memory allocation error when when merging data of probe %s.\n",curprb.c_str());
exit(EXIT_FAILURE);
}
memset(betase_new,0,num_new*2*sizeof(float));
if(keepid.size()<num)
{
memcpy(rid_new, probeinfo[prbindx].rowid, probeinfo[prbindx].vnum*sizeof(uint32_t));
for(int l=0;l<keepid.size();l++) *(rid_new+probeinfo[prbindx].vnum+l)=*(ridbuff+keepid[l]);
memcpy(rid_new+probeinfo[prbindx].vnum+keepid.size(),rid_new,(probeinfo[prbindx].vnum+keepid.size())*sizeof(uint32_t));
memcpy(betase_new, probeinfo[prbindx].beta_se,probeinfo[prbindx].vnum*sizeof(float));
for(int l=0;l<keepid.size();l++) *(betase_new+probeinfo[prbindx].vnum+l)=*(betasebuff+keepid[l]);
memcpy(betase_new+probeinfo[prbindx].vnum+keepid.size(), probeinfo[prbindx].beta_se+probeinfo[prbindx].vnum, probeinfo[prbindx].vnum*sizeof(float));
for(int l=0;l<keepid.size();l++) *(betase_new+2*probeinfo[prbindx].vnum+keepid.size()+l)=*(betasebuff+num+keepid[l]);
} else {
memcpy(rid_new, probeinfo[prbindx].rowid, probeinfo[prbindx].vnum*sizeof(uint32_t));
memcpy(rid_new+probeinfo[prbindx].vnum,ridbuff,num*sizeof(uint32_t));
memcpy(rid_new+probeinfo[prbindx].vnum+num,rid_new,(probeinfo[prbindx].vnum+num)*sizeof(uint32_t));
memcpy(betase_new, probeinfo[prbindx].beta_se,probeinfo[prbindx].vnum*sizeof(float));
memcpy(betase_new+probeinfo[prbindx].vnum, betasebuff, num*sizeof(float));
memcpy(betase_new+probeinfo[prbindx].vnum+num, probeinfo[prbindx].beta_se+probeinfo[prbindx].vnum, probeinfo[prbindx].vnum*sizeof(float));
memcpy(betase_new+2*probeinfo[prbindx].vnum+num, betasebuff+num, num*sizeof(float));
}
free(ridbuff);
free(betasebuff);
free(probeinfo[prbindx].rowid);
free(probeinfo[prbindx].beta_se);
probeinfo[prbindx].rowid=rid_new;
probeinfo[prbindx].beta_se=betase_new;
probeinfo[prbindx].vnum=num_new;
}
// no memory free here. later.
} else {
printf("Probe %s has no values in BESD file %s.\n",curprb.c_str(),besdfile.c_str());
}
}
free(colbuf);
}
else if(filetype==DENSE_FILE_TYPE_1 || filetype==DENSE_FILE_TYPE_3){
if(filetype==DENSE_FILE_TYPE_3)
{
int tmp=readint(fptr);
if(tmp!=-9)
{
printf("The sample size is %d.\n",tmp);
if(ssck!=-9) {
ssck=tmp;
}
else
{
if(ssck!=tmp)
{
printf("ERROR: You are trying merge BESD files with different sample sizes.\n");
exit(EXIT_FAILURE);
}
}
}
tmp=readint(fptr);
if(tmp!=etmp._snpNum)
{
printf("ERROR: The SNPs in your .esi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
tmp=readint(fptr);
if(tmp!=etmp._probNum)
{
printf("ERROR: The probes in your .epi file are not in consistency with the one in .besd file %s.\n", besdfile.c_str());
exit(EXIT_FAILURE);
}
for(int k=4;k<RESERVEDUNITS;k++) readint(fptr);
}
float* tmpbetase=(float*)malloc(sizeof(float)*etmp._snpNum<<1);
if(NULL == tmpbetase)
{
printf("ERROR: Can't malloc the reading cols buffer for %u MB.\n",(etmp._snpNum>>17));
exit(EXIT_FAILURE);
}
for( int j=0;j<etmp._probNum;j++)
{