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genome.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 <fstream>
#include <sstream>
#include <vector>
#include <map>
#include <cmath>
#include <iterator>
#include "plink.h"
#include "options.h"
#include "helper.h"
#include "stats.h"
#include "cfamily.h"
#include "zed.h"
void Plink::calcStratifiedAlleleFreqs()
{
// w/ Modification to output counts by John Novembre
// Assume SNP-major data
if (!par::SNP_major) Ind2SNP();
// This is called *after* any filters are applied
// (i.e. unlike the original --freq command)
// This means that various things will have been fixed already,
// such as het haploid calls, and which allele is the minor one
if (par::summ_nonfounders)
printLOG("Writing stratified allele frequencies (all individuals) to [ " +
par::output_file_name + ".frq.strat ] \n");
else
printLOG("Writing stratified allele frequencies (founders-only) to [ " +
par::output_file_name + ".frq.strat ] \n");
ofstream FRQ;
string f = par::output_file_name + ".frq.strat";
FRQ.open(f.c_str(), ifstream::out);
FRQ.precision(4);
FRQ << setw(4) << "CHR" << " "
<< setw(par::pp_maxsnp) << "SNP" << " "
<< setw(8) << "CLST" << " "
<< setw(4) << "A1" << " "
<< setw(4) << "A2" << " "
<< setw(8) << "MAF" << " "
<< setw(6) << "MAC" << " "
<< setw(8) << "NCHROBS" // Modified by JN 5/24/07
<< "\n";
//////////////////////////////////////////
// Calculate allele frequencies, and FST
vector<Locus*>::iterator loc = locus.begin();
vector<CSNP*>::iterator s = SNP.begin();
while ( loc != locus.end() )
{
// Track Fst
vector_t het(nk);
double tothet = 0;
// Consider each cluster
for (int k=0; k<nk; k++)
{
FRQ << setw(4) << (*loc)->chr << " "
<< setw(par::pp_maxsnp) << (*loc)->name << " ";
(*loc)->freq = 0;
// count 1 per allele, for frequency
double nmfreq = 0;
double totfreq = 0;
double count = 0;
// count 1 per genotype, for missingness
int geno_nm = 0;
bool X = false;
bool haploid = false;
// Determine type of SNP
if (par::chr_sex[(*loc)->chr]) X=true;
else if (par::chr_haploid[(*loc)->chr]) haploid=true;
///////////////////////////////
// Iterate over each individual
vector<bool>::iterator i1 = (*s)->one.begin();
vector<bool>::iterator i2 = (*s)->two.begin();
vector<Individual*>::iterator person = sample.begin();
while ( person != sample.end() )
{
bool s1 = *i1;
bool s2 = *i2;
// For allele frequencies
// only consider founders?
if ( par::summ_nonfounders || (*person)->founder )
{
if ( (*person)->sol == k )
{
if ( haploid || ( X && (*person)->sex ) )
{
//////////////////
// Haploid counts
// "1" allele count
// Possible count of 1 allele
totfreq++;
if ( (!s1) && (!s2) ) // FF = hom(11)
{
(*loc)->freq++;
nmfreq++;
}
else if ( s1 && s2 ) // TT = hom(22)
{
nmfreq++;
}
}
else
{
//////////////////
// Autosomal count
// "1" allele count
// Possible count of 2 alleles
totfreq+=2;
if (!s1)
{
if (!s2) // 00 = hom(11)
{
(*loc)->freq+=2;
nmfreq+=2;
}
else // 01 = het(12)
{
(*loc)->freq+=1;
nmfreq+=2;
}
}
else if ( s2 ) // 11 = hom(22)
{
nmfreq+=2;
}
}
}
}
// Next individual
person++;
i1++;
i2++;
}
if (nmfreq>0){
count=(*loc)->freq; // Added by JN 5/24/07
(*loc)->freq /= (double)nmfreq;
}
string a1 = (*loc)->allele1;
if (a1=="") a1="0";
FRQ << setw(8) << kname[k] << " "
<< setw(4) << a1 << " "
<< setw(4) << (*loc)->allele2 << " "
<< setw(8) << (*loc)->freq << " "
<< setw(6) << count << " "
<< setw(8) << nmfreq << " " // Modified by JN 5/24/07
<< "\n";
}
// Next SNP
loc++;
s++;
}
FRQ.close();
shutdown();
}
void Plink::findMissRuns(Individual * person, ofstream & RUN)
{
int l=0;
int nmiss = 0; // now means 'not missing'
bool run = false;
int start = 0;
int end = 0;
while ( l < nl_all )
{
// Outside of a run?
if (!run)
{
// A new run? (missing)
if (person->one[l] && (!person->two[l]))
{
start = l;
nmiss=1;
run=true;
}
}
else // if already in a run, either end or increase length?
{
// found a non-missing? 00, 11, 01
if ( person->one[l] == person->two[l] || person->two[l])
{
nmiss++;
// Average non-missing rate now too high?, given we have at least
// a certain number of SNPs in run
// (l-start) = number of SNPs in run currently
if ((double)nmiss / (double)(l-start) >= par::miss_run_level && (l-start) >= par::miss_run_length)
{
end = l-1;
run = false;
}
}
else if ( locus[l]->chr != locus[start]->chr ) // different chromosome?
{
end = l-1;
run = false;
}
else if ( l == (nl_all -1) ) // or end of all SNPs?
{
end = l;
run = false;
}
}
// Check run length?
if (!run)
{
if (par::miss_run_length_kb)
{
if ( locus[end]->bp - locus[start]->bp >= par::miss_run_length * 1000 )
RUN << setw(par::pp_maxfid) << person->fid << " "
<< setw(par::pp_maxiid) << person->iid << " "
<< setw(8) << person->phenotype << " "
<< setw(4) << locus[start]->chr << " "
<< setw(par::pp_maxsnp) << locus[start]->name << " "
<< setw(par::pp_maxsnp) << locus[end]->name << " "
<< setw(10) << (double)(locus[end]->bp - locus[start]->bp)/(double)1000 << " "
<< setw(10) << end - start +1 << " "
<< setw(10) << (double)nmiss/(double)(end - start + 1) << "\n";
}
else
{
if ( end - start +1 >= par::miss_run_length )
RUN << person->fid << "\t"
<< person->iid << "\t"
<< locus[start]->chr << "\t"
<< locus[start]->name << "\t"
<< locus[end]->name << "\t"
<< (double)(locus[end]->bp - locus[start]->bp)/(double)1000 << "\t"
<< end - start + 1 << "\t"
<< (double)nmiss/(double)(end - start + 1) << "\n";
}
//////////////////
// Clear counters
start = end = nmiss = 0;
}
///////////////
// Next locus
l++;
}
}
void Plink::sexCheck()
{
// Get range of X chromosome markers
if (par::SNP_major)
SNP2Ind();
ofstream HET;
string f = par::output_file_name + ".sexcheck";
HET.open(f.c_str(),ios::out);
HET.precision(4);
printLOG("Writing X-chromosome sex check results to [ "+f+" ] \n");
HET << setw(par::pp_maxfid) << "FID" << " "
<< setw(par::pp_maxiid) << "IID" << " "
<< setw(12) << "PEDSEX" << " "
<< setw(12) << "SNPSEX" << " "
<< setw(12) << "STATUS" << " "
<< setw(12) << "F" << "\n";
for (int i1=0; i1<n; i1++)
calcInbreeding(sample[i1],0,nl_all-1,HET);
HET.close();
return;
}
void Plink::calcFst()
{
ofstream FST;
string f = par::output_file_name + ".fst";
FST.open(f.c_str(),ios::out);
FST.precision(4);
printLOG("Writing Fst measures to [ "+f+" ] \n");
FST << setw(4) << "CHR" << " "
<< setw(par::pp_maxsnp) << "SNP" << " "
<< setw(20) << "CLST" << " "
<< setw(8) << "N" << " "
<< setw(8) << "HET" << "\n";
for (int l = 0 ; l < nl_all; l++)
{
bool skip = false;
if ( par::chr_sex[locus[l]->chr] ||
par::chr_haploid[locus[l]->chr] ) skip = true;
if ( locus[l]->nm <= 1 || locus[l]->freq < 1e-8 )
skip = true;
if ( skip )
continue;
double f = 0;
vector_t hs(nk);
double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq );
// Calculate Fst here
// double avg_hs = 0;
// for (int k = 0; k < nk ; k++ )
// avg_hs += het[k];
// avg_hs /= (double)nk;
// double f = ( hs - ht ) / ht;
for ( int k = 0 ; k < nk ; k++ )
{
// FST << setw(4) << locus[l]->chr << " "
// << setw(par::pp_maxsnp) << locus[l]->name << " "
// << setw(20) << kname[k] << " "
// << setw(8) << kind[k] << " "
// << setw(12) << het[k] << "\n";
}
FST << setw(4) << locus[l]->chr << " "
<< setw(par::pp_maxsnp) << locus[l]->name << " "
<< setw(20) << "_FST_" << " "
<< setw(8) << locus[l]->nm << " "
<< setw(12) << f << "\n";
}
FST.close();
return;
}
double Plink::calcInbreeding(Individual * p1, int m1, int m2, ofstream & HET)
{
// P(Homo) = F + (1-F)P(Homo by chance)
// P(Homo by chance) = p^2+q^2 for a biallelic locus.
// For an individual with N genotyped loci, we
// 1. count the total observed number of loci which are homozygous (O),
// 2. calculate the total expected number of loci homozygous by chance (E)
// Then, using the method of moments, we have
// O = NF + (1-F)E
// Which rearranges to give
// F = (O-E)/(N-E)
// Count of nonmissing loci
double N=0;
double O=0;
double E=0;
// Consider all loci
for (int l=m1; l<=m2;l++)
{
////////////////////////////////////////////////
// Skip X and haploid chromosome markers, or not
if ( par::check_sex ) // For sex-checks
{
// only consider the X chromosome
if ( ! par::chr_sex[locus[l]->chr] ) continue;
}
else // normal heterozygosity calculation
{
// so skip haploid markers
if ( par::chr_sex[locus[l]->chr] ||
par::chr_haploid[locus[l]->chr] ) continue;
}
// Skip monomorphic markers, uninformative markers
if ( locus[l]->nm <= 1 || locus[l]->freq < 1e-8 )
continue;
//////////////////
// Observed data
// check not missing:
if (!(p1->one[l] && (!p1->two[l])))
{
// homozygous non-missing loci
if (p1->one[l] == p1->two[l]) O++;
// non-missing loci
N++;
/////////////////////////
// Expected homozygousity
// E = 2pq . 2N/(2N-1)
// (Using Nei's unbiased estimator)
E += 1
- ( 2 * locus[l]->freq * ( 1 - locus[l]->freq )
* ( locus[l]->nm / ( locus[l]->nm - 1 ) ) );
}
}
double F = (O-E)/(N-E);
if ( par::check_sex)
{
HET << setw(par::pp_maxfid) << p1->fid << " "
<< setw(par::pp_maxiid) << p1->iid << " "
<< setw(12) << p1->sexcode << " ";
if ( F > par::sex_threshold_male )
{
HET << setw(12) << 1 << " ";
if (p1->sexcode == "1")
HET << setw(12) << "OK" << " ";
else
{
HET << setw(12) << "PROBLEM" << " ";
if (par::impute_sex)
{
p1->sexcode = "1";
p1->sex = true;
}
}
}
else if ( F < par::sex_threshold_female )
{
HET << setw(12) << 2 << " ";
if (p1->sexcode == "2")
HET << setw(12) << "OK" << " ";
else
{
HET << setw(12) << "PROBLEM" << " ";
if (par::impute_sex)
{
p1->sexcode = "2";
p1->sex = false;
}
}
}
else
{
HET << setw(12) << 0 << " "
<< setw(12) << "PROBLEM" << " ";
if (par::impute_sex)
{
p1->sexcode = "0";
p1->sex = false;
if (!par::ignore_missing_sex)
p1->missing = true;
}
}
HET << setw(12) << F << "\n";
}
else
HET << setw(par::pp_maxfid) << p1->fid << " "
<< setw(par::pp_maxiid) << p1->iid << " "
<< setw(12) << (int)O << " "
<< setw(12) << E << " "
<< setw(12) << (int)N << " "
<< setw(12) << F << "\n";
return F;
}
Z Plink::calcGenomeIBS(Individual * p1, Individual * p2)
{
// Vector of average genome-wide IBS
Z IBSg;
// Count of nonmissing loci
int cnt=0;
// Other metrics ( in Plink:: )
pvIBS0 = 0;
pvIBS2het = 0;
int last_chr = -1;
int last_bp = -1;
// Consider all autosomal loci
vector<bool>::iterator ia1 = p1->one.begin();
vector<bool>::iterator ia2 = p1->two.begin();
vector<bool>::iterator ib1 = p2->one.begin();
vector<bool>::iterator ib2 = p2->two.begin();
int l=0;
while ( ia1 != p1->one.end() )
{
// Skip X and haploid chromosome markers
if ( par::chr_sex[locus[l]->chr] ||
par::chr_haploid[locus[l]->chr] )
{
l++;
ia1++;
ia2++;
ib1++;
ib2++;
continue;
}
// Only count if both genotypes nonmissing
bool a1 = *ia1;
bool a2 = *ia2;
if (a1 && !a2)
{
l++;
ia1++;
ia2++;
ib1++;
ib2++;
continue;
}
bool b1 = *ib1;
bool b2 = *ib2;
if (b1 && !b2)
{
l++;
ia1++;
ia2++;
ib1++;
ib2++;
continue;
}
// Calculate IBS from genotypes
// 10 = missing
// 00 = 11hom
// 01 = 12het
// 11 = 22hom
if ( a1 == b1 && a2 == b2 ) IBSg.z2++; // IBS 2
else if ( a1 != b1 && a2 != b2 ) IBSg.z0++; // IBS 0
else IBSg.z1++; // IBS 1
cnt++;
// Also calculate p-value binomial test
if ( ! ( par::matrix || par::cluster || par::genome_output ) )
{
ia1++;
ia2++;
ib1++;
ib2++;
l++;
continue;
}
if ( a1 != b1 && a2 != b2 ) // IBS 0 hom/hom
{
// Can we count this?
if (locus[l]->chr != last_chr ||
locus[l]->bp > last_bp + par::ibstest_gap)
{
pvIBS0++;
last_chr = locus[l]->chr;
last_bp = locus[l]->bp;
}
}
else if ( a1 != a2 && b1 != b2 ) // IBS 2 het/het
{
// Can we count this?
if (locus[l]->chr != last_chr ||
locus[l]->bp > last_bp + par::ibstest_gap)
{
pvIBS2het++;
last_chr = locus[l]->chr;
last_bp = locus[l]->bp;
}
}
// Next SNP
ia1++;
ia2++;
ib1++;
ib2++;
l++;
}
if (cnt==0)
{
string msg = "No nonmissing markers for individuals "
+ p1->fid + " "
+ p1->iid + " - "
+ p2->fid + " "
+ p2->iid;
error(msg);
}
// Standard genetic distance (proportion IBS 0 to 1)
if ( par::cluster_euclidean )
dst = sqrt((IBSg.z1*0.5 + IBSg.z2*2)/(IBSg.z0+IBSg.z1+IBSg.z2*2));
else
dst = (IBSg.z1*0.5 + IBSg.z2)/(IBSg.z0+IBSg.z1+IBSg.z2);
// Also calculate p-value binomial test
if ( par::cluster_missing || ! ( par::matrix || par::cluster || par::genome_output ) )
return IBSg;
// Calculate p-value for IBS test
// IBS0 : IBS2(het) in 1:2 ratio
// n.b. 0.2222222 = 0.666*(1-0.666)
double z = (pvIBS2het/(pvIBS0+pvIBS2het)-0.666666)
/ (sqrt(0.2222222/(pvIBS0+pvIBS2het)));
// Store p-value in Plink::pv
pv = normdist(z);
// Return counts
return IBSg;
}
void Plink::preCalcGenomeIBD()
{
// Take pairwise IBS and information on allele frequencies
// to generate genome-wide IBD estimates
// Expected IBS given IBD
// Bias-corrected versison of estimator for expected proportion of
// IBS SNP pairs given IBD status (cf. Nei bias-corrected
// heterozygosity estimator).
// All possible permutations of taking 4 alleles from 2N = 2N(2N-1)(2N-2)(2N-3)
// x = count of allele 1
// y = count of allele 2
// p = x/2N, q=y/2N
// Of these,
// x(x-1)y(y-1) will be of order 11 22,
// y(y-1)x(x-1) will be of order 22 11
// Therefore the probability of IBS 0 given IBS 0 is
// E00 = 2 p*p*q*q * ( (x-1)/x * (y-1)/y * (2N/(2N-1)) * (2N/(2N-2)) * (2N/(2N-3)) )
// and so on for E01, etc
// E(IBD)(IBS)
// IBS >= IBD
E00=E10=E20=E01=E11=E21=E02=E12=E22=0;
int cnt = 0;
for (int l=0; l<nl_all; l++)
{
if ( par::chr_sex[locus[l]->chr] ||
par::chr_haploid[locus[l]->chr] ) continue;
double p = locus[l]->freq;
double q = 1 - p;
double Na = locus[l]->nm; // = # alleles = 2N where N is number of individuals
double x = p * Na;
double y = q * Na;
// Original, non bias-corrected versions
// E00 += 2*p*p*q*q;
// E01 += 4*p*p*p*q+4*p*q*q*q;
// E02 += q*q*q*q + p*p*p*p + 4*p*p*q*q;
// E11 += 2*p*p*q + 2*p*q*q;
// E12 += p*p*p + q*q*q + p*p*q + p*q*q;
double a00 = 2*p*p*q*q * ( (x-1)/x * (y-1)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
double a01 = 4*p*p*p*q * ( (x-1)/x * (x-2)/x * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) )
+ 4*p*q*q*q * ( (y-1)/y * (y-2)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
double a02 = q*q*q*q * ( (y-1)/y * (y-2)/y * (y-3)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) )
+ p*p*p*p * ( (x-1)/x * (x-2)/x * (x-3)/x * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) )
+ 4*p*p*q*q * ( (x-1)/x * (y-1)/y * (Na/(Na-1)) * (Na/(Na-2)) * (Na/(Na-3)) );
double a11 = 2*p*p*q * ( (x-1)/x * Na/(Na-1) * Na/(Na-2) )
+ 2*p*q*q * ( (y-1)/y * Na/(Na-1) * Na/(Na-2) );
double a12 = p*p*p * ((x-1)/x * (x-2)/x * Na/(Na-1) * Na/(Na-2))
+ q*q*q * ( (y-1)/y * (y-2)/y * Na/(Na-1) * Na/(Na-2))
+ p*p*q * ( (x-1)/x * Na/(Na-1) * Na/(Na-2) )
+ p*q*q * ((y-1)/y * Na/(Na-1) * Na/(Na-2));
if ( realnum(a00) &&
realnum(a01) &&
realnum(a02) &&
realnum(a11) &&
realnum(a12) )
{
E00 += a00;
E01 += a01;
E02 += a02;
E11 += a11;
E12 += a12;
cnt++;
}
}
E00 /= cnt; E10 = 0; E20 = 0;
E01 /= cnt; E11 /= cnt; E21 = 0;
E02 /= cnt; E12 /= cnt; E22 = 1;
if (par::verbose) {
cout << "P(IBS|IBD) -- IBS row; IBD col\n";
cout << E00 << "\t" << E10 << "\t" << E20 << "\n";
cout << E01 << "\t" << E11 << "\t" << E21 << "\n";
cout << E02 << "\t" << E12 << "\t" << E22 << "\n";
cout << "\n";
}
}
Z Plink::calcGenomeIBD(Individual * p1, Individual * p2, Z IBSg)
{
Z z;
double S = IBSg.z0 + IBSg.z1 + IBSg.z2;
// E_IBS[row=IBS][col=IBD]
// E(IBD)(IBS)
double e00 = E00*S;
double e10 = E10*S;
double e20 = E20*S;
double e01 = E01*S;
double e11 = E11*S;
double e21 = E21*S;
double e02 = E02*S;
double e12 = E12*S;
double e22 = E22*S;
z.z0 = IBSg.z0 / e00;
z.z1 = (IBSg.z1 - z.z0*e01) / e11;
z.z2 = (IBSg.z2 - z.z0*e02 - z.z1*e12) / e22;
if (par::debug)
cout << "DEBUG\t"
<< z.z0 << " "
<< z.z1 << " "
<< z.z2 << "\n";
// Bound IBD estimates to sum to 1
// and fall within 0-1 range
if (par::bound)
{
if (z.z0>1) { z.z0=1; z.z1=z.z2=0; }
if (z.z1>1) { z.z1=1; z.z0=z.z2=0; }
if (z.z2>1) { z.z2=1; z.z0=z.z1=0; }
if (z.z0<0) { double S=z.z1+z.z2; z.z1/=S; z.z2/=S; z.z0=0; }
if (z.z1<0) { double S=z.z0+z.z2; z.z0/=S; z.z2/=S; z.z1=0; }
if (z.z2<0) { double S=z.z0+z.z1; z.z0/=S; z.z1/=S; z.z2=0; }
}
// Possibly constrain IBD estimates to within possible triangle
// i.e. 0.5 0.0 0.5 is invalid
//
// For purposes of sample checks, etc, we do not automatically do this (--genome)
// For PLINK analysis we do (--plink)
//
// Constraint : z1^2 - 4 z0 z2 >= 0
// : x^2 - 2 pi x + z2 = 0
//
// where pi = (z1 + 2 z2) / 2
//
// So the constaint can also be written as
//
// pi^2 >= z2
double pihat = z.z1/2 + z.z2 ;
double impossible = false;
if ( ( pihat * pihat ) < z.z2 )
{
impossible = true;
// find new value for z1 (z1*) which satisfies the equation
//
// (z1* + 2 pi^2) / 2 = pi
//
// this gives
//
// z1* = 2pi(1-pi)
// the transformed IBD probabilities would be
// 1 - 2pi(1-pi) - pi^2, 2pi(1-pi), pi^2
if (par::nudge)
{
z.z0 = ( 1 - pihat) * ( 1 - pihat);
z.z1 = 2 * pihat * (1-pihat);
z.z2 = pihat * pihat;
}
}
if ( par::genome_output_minimal )
{
ZOUTFILE << dbl2str_fixed(dst,6) << " "
<< dbl2str(pv) << " "
<< dbl2str(z.z1/2 + z.z2) << "\n";
}
else if (par::genome_output)
{
if ( (!par::pihat_filter) ||
( pihat >= par::MIN_PIHAT && pihat <= par::MAX_PIHAT) )
{
ZOUTFILE << sw( p1->fid, par::pp_maxfid)
<< sw( p1->iid, par::pp_maxiid)
<< sw( p2->fid, par::pp_maxfid)
<< sw( p2->iid, par::pp_maxiid);
string rt = relType(p1,p2);
ZOUTFILE << sw(rt,3);
if ( rt == "UN" )
ZOUTFILE << sw("NA", 6);
else
ZOUTFILE << sw( genrel(p1,p2) , 6 );
if (par::show_impossible_IBD || !impossible)
ZOUTFILE << sw(z.z0, 4,8)
<< sw(z.z1, 4,8)
<< sw(z.z2, 4,8);
else
ZOUTFILE << sw( -z.z0, 8)
<< sw( -z.z1, 8)
<< sw( -z.z2, 8);
ZOUTFILE << sw( z.z1/2 + z.z2, 4, 8);
if (par::bt)
{
if ( (!p1->aff) && (!p2->aff) )
ZOUTFILE << sw("-1", 4);
else if ( p1->aff && p2->aff )
ZOUTFILE << sw("1",4);
else if ((!p1->aff) && p2->aff)
ZOUTFILE << sw("0",4);
else if (p1->aff && !p2->aff)
ZOUTFILE << sw("0",4);
else
ZOUTFILE << sw("NA",4);
}
else
ZOUTFILE << sw("NA",4);
ZOUTFILE << sw(dst,6,10);
ZOUTFILE << sw(pv,4,8);
double ov = (double)pvIBS2het / (double)pvIBS0;
if ( realnum(ov) )
ZOUTFILE << sw(ov,4,8);
else
ZOUTFILE << sw("NA",8);
if ( par::genome_output_full )
ZOUTFILE << sw((int)IBSg.z0, 8)
<< sw((int)IBSg.z1, 8)
<< sw((int)IBSg.z2, 8)
<< sw(pvIBS0, 4,8)
<< sw(pvIBS2het, 4, 8);
ZOUTFILE << "\n";
}
}
return z;
}
void Plink::displayGenomeWideInfo()
{