void gcta::read_imp_info_beagle(string zinfofile)
{
_dosage_flag=true;
const int MAX_LINE_LENGTH = 1000;
char buf[MAX_LINE_LENGTH];
string str_buf, errmsg="Error: Reading SNP summary information filed? Please check the format of ["+zinfofile+"].";
string c_buf;
int i_buf;
double f_buf=0.0;
gzifstream zinf;
zinf.open( zinfofile.c_str() );
if(! zinf.is_open()) throw("Error: can not open the file ["+zinfofile+"] to read.");
cout<<"Reading summary information of the imputed SNPs (BEAGLE) ..."<<endl;
zinf.getline(buf, MAX_LINE_LENGTH, '\n'); // skip the header
while(1){
zinf.getline(buf, MAX_LINE_LENGTH, '\n');
if(zinf.fail() || !zinf.good()) break;
stringstream ss(buf);
string nerr=errmsg+"\nError line: "+ss.str();
if(!(ss>>i_buf)) throw(nerr);
_chr.push_back(i_buf);
if(!(ss>>str_buf)) throw(nerr);
_snp_name.push_back(str_buf);
if(!(ss>>i_buf)) throw(nerr);
_bp.push_back(i_buf);
if(!(ss>>c_buf)) throw(nerr);
_allele1.push_back(c_buf);
if(!(ss>>c_buf)) throw(nerr);
_allele2.push_back(c_buf);
if(!(ss>>str_buf)) throw(nerr);
if(!(ss>>str_buf)) throw(nerr);
if(!(ss>>str_buf)) throw(nerr);
if(!(ss>>f_buf)) throw(nerr);
if(!(ss>>f_buf)) throw(nerr);
if(!(ss>>f_buf)) throw(nerr);
_impRsq.push_back(f_buf);
if(!(ss>>f_buf)) throw(nerr);
if(!(ss>>f_buf)) throw(nerr);
if(ss>>f_buf) throw(nerr);
}
zinf.clear();
zinf.close();
_snp_num=_snp_name.size();
cout<<_snp_num<<" SNPs to be included from ["+zinfofile+"]."<<endl;
_genet_dst.resize(_snp_num);
_ref_A=_allele1;
_other_A=_allele2;
// Initialize _include
init_include();
}
void gcta::read_imp_info_mach(string zinfofile)
{
_dosage_flag=true;
int i=0;
const int MAX_LINE_LENGTH = 1000;
char buf[MAX_LINE_LENGTH];
gzifstream zinf;
zinf.open( zinfofile.c_str() );
if(! zinf.is_open()) throw("Error: can not open the file ["+zinfofile+"] to read.");
string str_buf, errmsg="Reading dosage data failed. Please check the format of the map file.";
string c_buf;
double f_buf=0.0;
cout<<"Reading map file of the imputed dosage data from ["+zinfofile+"]."<<endl;
zinf.getline(buf, MAX_LINE_LENGTH, '\n'); // skip the header
vector<string> vs_buf;
int col_num=StrFunc::split_string(buf, vs_buf);
if(col_num<7) throw(errmsg);
if(vs_buf[6]!="Rsq") throw(errmsg);
_snp_name.clear();
_allele1.clear();
_allele2.clear();
_impRsq.clear();
while(1){
zinf.getline(buf, MAX_LINE_LENGTH, '\n');
stringstream ss(buf);
string nerr=errmsg+"\nError occurs in line: "+ss.str();
if(!(ss>>str_buf)) break;
_snp_name.push_back(str_buf);
if(!(ss>>c_buf)) throw(nerr);
_allele1.push_back(c_buf);
if(!(ss>>c_buf)) throw(nerr);
_allele2.push_back(c_buf);
for(i=0; i<4; i++) if(!(ss>>f_buf)) throw(nerr);
_impRsq.push_back(f_buf);
if(zinf.fail() || !zinf.good()) break;
}
zinf.clear();
zinf.close();
_snp_num=_snp_name.size();
_chr.resize(_snp_num);
_bp.resize(_snp_num);
_genet_dst.resize(_snp_num);
_ref_A=_allele1;
_other_A=_allele2;
// Initialize _include
init_include();
cout<<_snp_num<<" SNPs to be included from ["+zinfofile+"]."<<endl;
}
void gcta::read_bimfile(string bimfile)
{
// Read bim file: recombination rate is defined between SNP i and SNP i-1
int ibuf=0;
string cbuf="0";
double dbuf=0.0;
string str_buf;
ifstream Bim(bimfile.c_str());
if(!Bim) throw("Error: can not open the file ["+bimfile+"] to read.");
cout<<"Reading PLINK BIM file from ["+bimfile+"]."<<endl;
_chr.clear();
_snp_name.clear();
_genet_dst.clear();
_bp.clear();
_allele1.clear();
_allele2.clear();
while(Bim){
Bim>>ibuf;
if(Bim.eof()) break;
_chr.push_back(ibuf);
Bim>>str_buf;
_snp_name.push_back(str_buf);
Bim>>dbuf;
_genet_dst.push_back(dbuf);
Bim>>ibuf;
_bp.push_back(ibuf);
Bim>>cbuf;
//StrFunc::to_upper(cbuf);
_allele1.push_back(cbuf);
Bim>>cbuf;
//StrFunc::to_upper(cbuf);
_allele2.push_back(cbuf);
}
Bim.close();
_snp_num=_chr.size();
_ref_A=_allele1;
_other_A=_allele2;
cout<<_snp_num<<" SNPs to be included from ["+bimfile+"]."<<endl;
// Initialize _include
init_include();
}
void init_preprocess(void)
{
int i;
char *cp;
init_symtbl();
for (i = 0; predefs[i]; i++)
{
cp = copyofstr("1");
check_os_malloc(cp);
define(predefs[i], -1, (unsigned char *) cp, DEF_PREDEF);
}
init_include();
keep_comments = 0;
no_line_lines = 0;
do_at_ctrls = 0;
incldep = 0;
willbefirst = 1;
quote = 0;
ifstack = 0;
n_skipped_ifs = 0;
}
