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output.cpp
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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2008 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <iomanip>
#include <climits>
#include <fstream>
#include <sstream>
#include <bitset>
#include <map>
#include "plink.h"
#include "options.h"
#include "perm.h"
#include "sets.h"
#include "helper.h"
#include "nlist.h"
extern ofstream LOG;
void Plink::printLOG(string s)
{
LOG << s;
LOG.flush();
if (!par::silent)
{
cout << s;
cout.flush();
}
}
void Plink::display_indivReport()
{
Individual * p1 = NULL;
int i1;
for (int i=0; i<n; i++)
{
if ( sample[i]->fid == par::indiv_report_fid &&
sample[i]->iid == par::indiv_report_iid )
{
p1 = sample[i];
i1 = i;
break;
}
}
if ( p1 == NULL )
error("Problem finding individual indicated in --report\n");
printLOG("\nReport for individual [ " + p1->fid + " " + p1->iid + " ]\n\n");
for ( int l = 0 ; l < nl_all ; l++)
{
stringstream s2;
s2 << setw(4) << locus[l]->chr << " "
<< setw(par::pp_maxsnp) << locus[l]->name << " "
<< setw(6) << genotype(*this,i1,l) << "\n";
printLOG( s2.str() );
}
}
void Plink::displayGenomePV()
{
ofstream PLO;
string f = par::output_file_name + ".plink2";
PLO.open(f.c_str(),ios::out);
printLOG("Writing genome-wide corrected PLINK results to [ " +f +" ] \n");
for (int i=0; i<original.size();i++)
{
for (int j=0; j<original[i].size(); j++)
{
double pv=0;
for (int k=0; k<maxr2.size(); k++)
if (maxr2[k] >= original[i][j]) pv++;
PLO << "G "
<< double(pv+1)/double(par::replicates+1)
<< "\n";
}
}
PLO.close();
}
void Plink::display_pairList()
{
if (par::SNP_major)
SNP2Ind();
string f = par::output_file_name + ".plist";
printLOG("Writing pair-list file to [ " + f + " ] \n");
ofstream PED(f.c_str(), ios::out);
PED.clear();
PED.precision(4);
// Find individuals
Individual * p1 = NULL;
Individual * p2 = NULL;
int i1, i2;
for (int i=0; i<n; i++)
{
if ( sample[i]->fid == par::plist_fid1 && sample[i]->iid == par::plist_iid1 )
{ p1 = sample[i]; i1 = i; }
if ( sample[i]->fid == par::plist_fid2 && sample[i]->iid == par::plist_iid2 )
{ p2 = sample[i]; i2 = i; }
}
if (p1 == NULL || p2 == NULL)
error("Problem finding individuals indicated in --plist\n");
PED << setw(4) << "CHR" << " "
<< setw(par::pp_maxsnp) << "SNP" << " "
<< setw(14) << "BP" << " "
<< setw(par::pp_maxfid+par::pp_maxiid) << (p1->fid+"/"+p1->iid) << " "
<< setw(par::pp_maxfid+par::pp_maxiid) << (p2->fid+"/"+p2->iid) << " "
<< setw(4) << "A1" << " "
<< setw(8) << "MAF" << " "
<< setw(4) << "IBS" << "\n";
for (int l=0; l<nl_all; l++)
{
PED << setw(4) << locus[l]->chr << " "
<< setw(par::pp_maxsnp) << locus[l]->name << " "
<< setw(14) << locus[l]->bp << " "
<< setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
<< setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
<< setw(4) << locus[l]->allele1 << " "
<< setw(8) << locus[l]->freq << " ";
bool a1 = p1->one[l];
bool a2 = p1->two[l];
bool b1 = p2->one[l];
bool b2 = p2->two[l];
bool ibs0 = false;
bool ibs1 = false;
bool miss = false;
if ( a1 == a2 &&
b1 == b2 &&
a1 != b1 ) ibs0 = true;
else if ( a1 && !(a2) ) miss = true;
else if ( b1 && !(b2) ) miss = true;
else if ( a1 != b1 ||
a2 != b2 ) ibs1 = true;
PED << setw(4);
if (ibs0) PED << "0" << "\n";
else if (ibs1) PED << "1" << "\n";
else if (miss) PED << "NA" << "\n";
else PED << "2" << "\n";
}
PED.close();
}
void Plink::display_listByAllele()
{
if (!par::SNP_major)
Ind2SNP();
// Create an output file that lists one allele per line
// N = number of individuals FID1 IID2 FID2 IID2 ... FIDN IIDN
// SNP ALLELE N { Individual list ( 2N entries) }
string f = par::output_file_name + ".list";
printLOG("Writing recoded list file to [ " + f + " ] \n");
ofstream PED(f.c_str(), ios::out);
PED.clear();
vector<CSNP*>::iterator s = SNP.begin();
vector<Locus*>::iterator loc = locus.begin();
while ( s != SNP.end() )
{
// Genotype 11
PED << (*loc)->chr << par::recode_delimit
<< (*loc)->name << par::recode_delimit
<< (*loc)->allele1 << (*loc)->allele1 ;
vector<bool>::iterator i1 = (*s)->one.begin();
vector<bool>::iterator i2 = (*s)->two.begin();
vector<Individual*>::iterator gperson = sample.begin();
while ( gperson != sample.end() )
{
if ( (!*i1) && (!*i2) )
PED << par::recode_delimit << (*gperson)->fid
<< par::recode_delimit << (*gperson)->iid ;
i1++;
i2++;
gperson++;
}
PED << "\n";
// Genotype 12
PED << (*loc)->chr << par::recode_delimit
<< (*loc)->name << par::recode_delimit
<< (*loc)->allele1 << (*loc)->allele2 ;
i1 = (*s)->one.begin();
i2 = (*s)->two.begin();
gperson = sample.begin();
while ( gperson != sample.end() )
{
if ( (!*i1) && *i2 )
PED << par::recode_delimit << (*gperson)->fid
<< par::recode_delimit << (*gperson)->iid ;
i1++;
i2++;
gperson++;
}
PED << "\n";
// Genotype 22
PED << (*loc)->chr << par::recode_delimit
<< (*loc)->name << par::recode_delimit
<< (*loc)->allele2 << (*loc)->allele2 ;
i1 = (*s)->one.begin();
i2 = (*s)->two.begin();
gperson = sample.begin();
while ( gperson != sample.end() )
{
if ( *i1 && *i2 )
PED << par::recode_delimit << (*gperson)->fid
<< par::recode_delimit << (*gperson)->iid ;
i1++;
i2++;
gperson++;
}
PED << "\n";
// Genotype 00
PED << (*loc)->chr << par::recode_delimit
<< (*loc)->name << par::recode_delimit
<< "00";
i1 = (*s)->one.begin();
i2 = (*s)->two.begin();
gperson = sample.begin();
while ( gperson != sample.end() )
{
if ( *i1 && !*i2 )
PED << par::recode_delimit << (*gperson)->fid
<< par::recode_delimit << (*gperson)->iid ;
i1++;
i2++;
gperson++;
}
PED << "\n";
// Next SNP
s++;
loc++;
}
PED.close();
}
void make2LTable(ofstream & TWOL, Plink & P, int m1, int m2, vector_t count, bool percent)
{
vector_t margA(4);
vector_t margB(4);
double total = 0;
for (int i=0; i<16; i++)
total += count[i];
if (percent)
{
for (int i=0; i<16; i++)
count[i] /= total;
total = 1;
}
margA[0] = count[0]+count[1]+count[2]+count[3];
margA[1] = count[4]+count[5]+count[6]+count[7];
margA[2] = count[8]+count[9]+count[10]+count[11];
margA[3] = count[12]+count[13]+count[14]+count[15];
margB[0] = count[0]+count[4]+count[8]+count[12];
margB[1] = count[1]+count[5]+count[9]+count[13];
margB[2] = count[2]+count[6]+count[10]+count[14];
margB[3] = count[3]+count[7]+count[11]+count[15];
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << " " << " "
<< " " << par::twolocus_snp2 << "\n";
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << " " << " "
<< setw(6) << (P.locus[m2]->allele1+"/"+P.locus[m2]->allele1) << " "
<< setw(6) << (P.locus[m2]->allele1+"/"+P.locus[m2]->allele2) << " "
<< setw(6) << (P.locus[m2]->allele2+"/"+P.locus[m2]->allele2) << " "
<< setw(6) << "0/0" << " "
<< setw(6) << "*/*" << "\n";
TWOL << setw(par::pp_maxsnp) << par::twolocus_snp1 << " "
<< setw(4) << (P.locus[m1]->allele1+"/"+P.locus[m1]->allele1) << " ";
TWOL << setw(6) << count[0] << " "
<< setw(6) << count[1] << " "
<< setw(6) << count[2] << " "
<< setw(6) << count[3] << " "
<< setw(6) << margA[0] << "\n";
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << (P.locus[m1]->allele1+"/"+P.locus[m1]->allele2) << " ";
TWOL << setw(6) << count[4] << " "
<< setw(6) << count[5] << " "
<< setw(6) << count[6] << " "
<< setw(6) << count[7] << " "
<< setw(6) << margA[1] << "\n";
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << (P.locus[m1]->allele2+"/"+P.locus[m1]->allele2) << " ";
TWOL << setw(6) << count[8] << " "
<< setw(6) << count[9] << " "
<< setw(6) << count[10] << " "
<< setw(6) << count[11] << " "
<< setw(6) << margA[2] << "\n";
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << "0/0" << " ";
TWOL << setw(6) << count[12] << " "
<< setw(6) << count[13] << " "
<< setw(6) << count[14] << " "
<< setw(6) << count[15] << " "
<< setw(6) << margA[3] << "\n";
TWOL << setw(par::pp_maxsnp) << " " << " "
<< setw(4) << "*/*" << " ";
TWOL << setw(6) << margB[0] << " "
<< setw(6) << margB[1] << " "
<< setw(6) << margB[2] << " "
<< setw(6) << margB[3] << " "
<< setw(6) << total << "\n";
TWOL << "\n";
}
void Plink::display_twolocus()
{
if (!par::SNP_major)
Ind2SNP();
// Find the two SNPs
// Write to file a contingency table, possibly stratified
// by phenotype
string f = par::output_file_name + ".twolocus";
printLOG("Writing two-locus table for "
+ par::twolocus_snp1 + " by "
+ par::twolocus_snp2 + " to [ " + f + " ] \n");
ofstream TWOL(f.c_str(), ios::out);
TWOL.clear();
TWOL.precision(3);
int m1 = getMarkerNumber(*this,par::twolocus_snp1);
int m2 = getMarkerNumber(*this,par::twolocus_snp2);
if (m1<0) error("Marker "+par::twolocus_snp1+" not found\n");
if (m2<0) error("Marker "+par::twolocus_snp2+" not found\n");
vector<CSNP*>::iterator sa = SNP.begin()+m1;
vector<CSNP*>::iterator sb = SNP.begin()+m2;
vector<Locus*>::iterator loc1 = locus.begin()+m1;
vector<Locus*>::iterator loc2 = locus.begin()+m2;
vector<bool>::iterator ia1 = (*sa)->one.begin();
vector<bool>::iterator ia2 = (*sa)->two.begin();
vector<bool>::iterator ib1 = (*sb)->one.begin();
vector<bool>::iterator ib2 = (*sb)->two.begin();
vector<Individual*>::iterator person = sample.begin();
int gtype = 0;
vector_t c_all(16);
vector_t c_case(16);
vector_t c_control(16);
while ( person != sample.end() )
{
if ( (!*ia1) && (!*ia2) )
{
if ( (!*ib1) && (!*ib2) ) gtype=0;
else if ( (!*ib1) && *ib2 ) gtype=1;
else if ( *ib1 && *ib2 ) gtype=2;
else if ( *ib1 && (!*ib2) ) gtype=3;
}
else if ( (!*ia1) && *ia2 )
{
if ( (!*ib1) && (!*ib2) ) gtype=4;
else if ( (!*ib1) && *ib2 ) gtype=5;
else if ( *ib1 && *ib2 ) gtype=6;
else if ( *ib1 && (!*ib2) ) gtype=7;
}
else if ( *ia1 && *ia2 )
{
if ( (!*ib1) && (!*ib2) ) gtype=8;
else if ( (!*ib1) && *ib2 ) gtype=9;
else if ( *ib1 && *ib2 ) gtype=10;
else if ( *ib1 && (!*ib2) ) gtype=11;
}
else if ( *ia1 && (!*ia2) )
{
if ( (!*ib1) && (!*ib2) ) gtype=12;
else if ( (!*ib1) && *ib2 ) gtype=13;
else if ( *ib1 && *ib2 ) gtype=14;
else if ( *ib1 && (!*ib2) ) gtype=15;
}
c_all[gtype]++;
if ( ! (*person)->missing )
{
if ( (*person)->aff )
c_case[gtype]++;
else
c_control[gtype]++;
}
ia1++;
ia2++;
ib1++;
ib2++;
person++;
}
TWOL << "\nAll individuals\n===============\n";
make2LTable(TWOL,*this,m1,m2,c_all,false);
TWOL.setf(ios::fixed);
make2LTable(TWOL,*this,m1,m2,c_all,true);
TWOL.unsetf(ios::fixed);
TWOL << "\nCases\n=====\n";
make2LTable(TWOL,*this,m1,m2,c_case,false);
TWOL.setf(ios::fixed);
make2LTable(TWOL,*this,m1,m2,c_case,true);
TWOL.unsetf(ios::fixed);
TWOL << "\nControls\n========\n";
make2LTable(TWOL,*this,m1,m2,c_control,false);
TWOL.setf(ios::fixed);
make2LTable(TWOL,*this,m1,m2,c_control,true);
TWOL.unsetf(ios::fixed);
TWOL << "\n";
TWOL.close();
}
void Plink::extractExcludeSet(bool exclude)
{
// Make map of locus name with 'l' number
map<string,int> mlocus;
vector<bool> del(nl_all);
for (int l=0;l<nl_all;l++)
{
mlocus.insert(make_pair(locus[l]->name,l));
if (exclude) del[l] = false; // start off all included
else del[l] = true; // start off all excluded
}
map<string,int>::iterator ilocus;
//////////////////////////////////
// Either extract a certain "GENE"
if (par::dump_gene)
{
// Temporarily read sets -- these will get updated later
readSet();
bool found_gene = false;
int c=0;
for (int s=0; s<setname.size(); s++)
{
if ( setname[s] == par::dump_genename )
{
// Retain just these SNPs
for (int l=0; l<snpset[s].size(); l++)
del[snpset[s][l]] = false;
found_gene = true;
c = snpset[s].size();
break;
}
if (found_gene) break;
}
if (found_gene)
printLOG(int2str(c) + " SNPs selected from [ "
+ par::dump_genename + " ]\n");
else
printLOG("WARNING: ** Could not find [ "
+ par::dump_genename + " ] in [ "
+ par::setfile + " ]\n");
}
/////////////////////////////////////
// OR get a list of SNPs form the command line
else if ( par::snp_include_from_cl )
{
NList nl(nl_all);
vector<int> lst = nl.deparseStringList( par::snp_include_range, & mlocus );
for (int l=0; l<lst.size(); l++)
del[ lst[l] ] = false;
printLOG("Extracting " + int2str(lst.size() ) +" SNPs\n");
}
/////////////////////////////////////
// OR get a list of ranges from a file
else if ( par::snp_range_list )
{
string filename = exclude ? par::exclude_file : par::extract_file;
set<int> slist;
// Read list of ranges
map<string, set<Range> > ranges;
map<int,set<Range*> > snp2range;
makeScaffold( *this );
mapRangesToSNPs( filename ,
ranges,
snp2range );
map<int,set<Range*> >::iterator i1 = snp2range.begin();
while ( i1 != snp2range.end() )
{
del[ i1->first ] = exclude ? true : false;
slist.insert( i1->first );
++i1;
}
if ( exclude )
printLOG("Excluding " + int2str( slist.size() ) + " SNPs\n");
else
printLOG("Extracting " + int2str( slist.size() ) + " SNPs\n");
}
/////////////////////////////////////
// OR get a list of SNPs from a file
else
{
string filename = par::extract_file;
if (exclude)
filename = par::exclude_file;
checkFileExists(filename);
ifstream INFILE(filename.c_str(),ios::in);
INFILE.clear();
printLOG("Reading list of SNPs ");
if (exclude)
printLOG("to exclude [ "
+ par::exclude_file + " ] ... ");
else
printLOG("to extract [ "
+ par::extract_file + " ] ... ");
int c=0;
while (!INFILE.eof())
{
string m;
INFILE >> m;
if (m=="") continue;
ilocus = mlocus.find(m);
if (ilocus != mlocus.end())
{
if (exclude) del[ilocus->second] = true;
else del[ilocus->second] = false;
c++;
}
}
INFILE.close();
printLOG(int2str(c)+" read\n");
}
////////////////////////////////////////
// Remove selected loci from locus list,
deleteSNPs(del);
}
void Plink::removeIndividuals(bool keep)
{
//////////////////////////////////
// Make map of individuals FID/IID
map<string,int> mperson;
map<string,int>::iterator iperson;
vector<bool> del(n);
for (int i=0;i<n;i++)
{
mperson.insert(make_pair(sample[i]->fid+"_"+sample[i]->iid,i));
if (!keep) del[i] = false; // start off all included
else del[i] = true; // start off all excluded
}
///////////////////////////
// Read list of individuals
string filename = par::remove_indiv_list;
if (keep)
filename = par::keep_indiv_list;
checkFileExists(filename);
ifstream INFILE(filename.c_str(),ios::in);
INFILE.clear();
printLOG("Reading individuals ");
if (keep) printLOG("to keep [ "+par::keep_indiv_list + " ] ... ");
else printLOG( "to remove [ "+par::remove_indiv_list + " ] ... ");
int c=0;
while (!INFILE.eof())
{
vector<string> s = tokenizeLine( INFILE );
if ( s.size() == 1 )
error("Problem with line:\n"+s[0]);
else if (s.size() == 0 )
continue;
string fid = s[0];
string iid = s[1];
iperson = mperson.find(fid+"_"+iid);
if (iperson != mperson.end())
{
if (!keep) del[iperson->second] = true;
else del[iperson->second] = false;
c++;
}
}
INFILE.close();
printLOG(int2str(c)+" read\n");
////////////////////////////////////
// Remove individuals as appropriate
int n_removed = deleteIndividuals(del);
printLOG(int2str(n_removed)+" individuals removed with ");
if (keep) printLOG("--keep option\n");
else printLOG("--remove option\n");
}
void Plink::keep2SetsForGenome()
{
//////////////////////////////////
// Make map of individuals FID/IID
map<string,int> mperson;
map<string,int>::iterator iperson;
vector<bool> del(n);
for (int i=0;i<n;i++)
{
mperson.insert(make_pair(sample[i]->fid+"_"+sample[i]->iid,i));
del[i] = true; // start off all excluded
}
///////////////////////////
// Read list of individuals
checkFileExists(par::genome_setlist1);
checkFileExists(par::genome_setlist2);
ifstream INFILE1(par::genome_setlist1.c_str(),ios::in);
INFILE1.clear();
ifstream INFILE2(par::genome_setlist2.c_str(),ios::in);
INFILE2.clear();
int c=0;
while (!INFILE1.eof())
{
string fid,iid;
INFILE1 >> fid >> iid;
if (fid=="" || iid=="") continue;
iperson = mperson.find(fid+"_"+iid);
if (iperson != mperson.end())
{
del[iperson->second] = false;
gset1.insert(sample[iperson->second]);
c++;
}
}
INFILE1.close();
printLOG(int2str(c)+" read from [ "+par::genome_setlist1 +" ]\n");
c=0;
while (!INFILE2.eof())
{
string fid,iid;
INFILE2 >> fid >> iid;
if (fid=="" || iid=="") continue;
iperson = mperson.find(fid+"_"+iid);
if (iperson != mperson.end())
{
del[iperson->second] = false;
gset2.insert(sample[iperson->second]);
c++;
}
}
INFILE2.close();
printLOG(int2str(c)+" read from [ "+par::genome_setlist2 +" ]\n");
////////////////////////////////////
// Remove individuals as appropriate
int n_removed = deleteIndividuals(del);
}
void Plink::zeroOnCluster()
{
// Make map of locus name with 'l' number
map<string,int> mlocus;
vector<bool> del(nl_all);
for (int l=0;l<nl_all;l++)
mlocus.insert(make_pair(locus[l]->name,l));
map<string,int>::iterator ilocus;
///////////////////////////////////////////
// Get a list of SNPs/clusters from a file
string filename = par::zero_cluster_filename;
checkFileExists(filename);
ifstream INFILE(filename.c_str(),ios::in);
INFILE.clear();
printLOG("Reading list of SNP/clusters to zero out [ ");
printLOG(par::zero_cluster_filename + " ]\n");
int c=0;
while (!INFILE.eof())
{
string m;
string k;
INFILE >> m >> k;
if (m=="") continue;
ilocus = mlocus.find(m);
if (ilocus != mlocus.end())
{
int l = ilocus->second;
map<string,int>::iterator ki = kmap.find(k);
if ( ki == kmap.end() )
{
continue; // cluster does not exist
//printLOG("Cluster [ "+k+" ] not found \n");
}
else
{
int k2 = ki->second;
// Zero out the following
for (int i=0; i<n; i++)
{
if ( sample[i]->sol == k2 )
{
if ( par::SNP_major )
{
SNP[l]->one[i] = true;
SNP[l]->two[i] = false;
}
else
{
sample[i]->one[l] = true;
sample[i]->two[l] = false;
}
c++;
}
}
}
}
}
INFILE.close();
printLOG(int2str(c)+" genotypes zeroed\n");
}
void Plink::setObligMissing()
{
// Temporaily use the cluster (sol) variables to store information
// about oblig missing (i.e. call this *before* we read any
// subsequent cluster variables
printLOG("Reading list of SNP/clusters that are obligatory missing [ ");
printLOG(par::oblig_missing_filename + " ]\n");
printLOG("Reading the clusters that define obligatory missingness [ ");
printLOG(par::oblig_clusters_filename + " ]\n");
string stored_name = par::include_cluster_filename;
par::include_cluster_filename = par::oblig_clusters_filename;
readClusterFile();
par::include_cluster_filename = stored_name;
// Make map of locus name with 'l' number
map<string,int> mlocus;
vector<bool> del(nl_all);
for (int l=0;l<nl_all;l++)
mlocus.insert(make_pair(locus[l]->name,l));
map<string,int>::iterator ilocus;
///////////////////////////////////////////
// Get a list of SNPs/clusters from a file
string filename = par::oblig_missing_filename;
checkFileExists(filename);
ifstream INFILE(filename.c_str(),ios::in);
INFILE.clear();
int c=0;
while (!INFILE.eof())
{
string m;
string k;
INFILE >> m >> k;
if (m=="") continue;
ilocus = mlocus.find(m);
if (ilocus != mlocus.end())
{
int l = ilocus->second;
map<string,int>::iterator ki = kmap.find(k);
if ( ki == kmap.end() )
continue; // cluster does not exist
else
{
int2 p;
p.p1 = l;
p.p2 = ki->second;
oblig_missing.insert(p);
++c;
}
}
}
INFILE.close();
printLOG(int2str(c)+" SNP/cluster combinations set as obligatory missing\n");
}
void Plink::display_recoded_PEDFILE()
{
string f = par::output_file_name + ".ped";
printLOG("Writing recoded ped file to [ " + f + " ] \n");
ofstream PED(f.c_str(), ios::out);
PED.clear();
string missingCode = par::out_missing_phenotype;
if ( par::recode_HV )
missingCode = "0";
for (int i=0;i<n;i++)
{
Individual * person = sample[i];
PED << person->fid << par::recode_delimit
<< person->iid << par::recode_delimit
<< person->pat << par::recode_delimit
<< person->mat << par::recode_delimit
<< person->sexcode << par::recode_delimit;
if ( person->missing )
{
PED << missingCode;
}
else
{
if (par::bt)
PED << (int)person->phenotype;
else
PED << person->phenotype;
}
for (int l=0;l<nl_all;l++)
PED << genotypeToFile( *this , i, l );
PED << "\n";
}
PED.close();
// And we also need a new map file
if (par::recode_HV)
{
f = par::output_file_name + ".info";
printLOG("Writing HaploView-format map file [ " + f + " ] \n");
}
else
{
f = par::output_file_name + ".map";
printLOG( "Writing new map file to [ " + f + " ] \n");
}
ofstream MAP(f.c_str(), ios::out);
MAP.clear();