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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 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 <fstream>
#include <sstream>
#include <iomanip>
#include <cmath>
#include <algorithm>
#include <map>
#include "plink.h"
#include "stats.h"
#include "helper.h"
#include "options.h"
using namespace std;
void Plink::tagMode()
{
////////////////////////////
// Look-up table by SNP name
map<string,int> mlocus;
for (int l = 0 ; l < nl_all ; l++ )
mlocus.insert(make_pair( locus[l]->name, l ));
set<int> toTag;
bool testAll = par::gettag_file == "all";
if ( !testAll )
{
checkFileExists(par::gettag_file);
printLOG("Reading SNPs to tag from [ "
+ par::gettag_file + " ] \n");
ifstream IN2(par::gettag_file.c_str(),ios::in);
int cnt = 0;
while ( ! IN2.eof() )
{
string snp;
string code;
if ( par::gettag_mode1 )
IN2 >> snp;
else if ( par::gettag_mode2 )
{
vector<string> tokens = tokenizeLine(IN2);
if ( tokens.size() == 0 )
continue;
if ( tokens.size() != 2 )
error("Expected two columns per line\n");
snp = tokens[0];
code = tokens[1];
if ( code == "0" )
continue;
}
if ( snp == "" )
continue;
++cnt;
// Can we find this SNP?
map<string,int>::iterator i = mlocus.find( snp );
if ( i == mlocus.end() )
continue;
// Add to list
toTag.insert(i->second);
}
printLOG("Read " + int2str(cnt)
+ " SNPs to tag, of which "
+ int2str(toTag.size())
+ " are unique and present\n");
IN2.close();
}
else
{
printLOG("Setting to tag all " + int2str(nl_all) + " SNPs in dataset\n");
for (int l=0;l<nl_all;l++)
toTag.insert(l);
}
///////////////////////
// Find tags and output
// input
// rs0001
// rs0004
// output
// rs0001
// rs0002
// rs0003
// rs0004
ofstream O2;
if ( par::gettag_listall )
{
printLOG("Writing list of specific tags per SNP to [ " + par::output_file_name + ".tags.list ]\n");
O2.open( ( par::output_file_name + ".tags.list").c_str() , ios::out );
O2 << setw( par::pp_maxsnp ) << "SNP" << " "
<< setw(4) << "CHR" << " "
<< setw(10) << "BP" << " "
<< setw(4) << "NTAG" << " "
<< setw(10) << "LEFT" << " "
<< setw(10) << "RIGHT" << " "
<< setw(8) << "KBSPAN" << " "
<< "TAGS\n";
}
set<int>::iterator i = toTag.begin();
set<int> tagged;
while ( i != toTag.end() )
{
// SNP to tag
int l = *i;
tagged.insert(l);
set<int> thisTagged;
int dist_left = locus[l]->bp;
int dist_right = locus[l]->bp;
// Move forwards and backwards, within range, and
// add any with r^2 above threshold to tagged set
int j = l - 1;
int chr = locus[l]->chr;
int pos = locus[l]->bp;
while (1)
{
if ( j < 0 )
break;
if ( locus[j]->chr != chr )
break;
if ( pos - locus[j]->bp > par::gettag_kb )
break;
if ( ! par::gettag_listall )
{
if ( tagged.find(j) != tagged.end() )
{
--j;
continue;
}
}
double rsq = correlation2SNP( l,j,true,false);
if ( realnum(rsq) && rsq >= par::gettag_r2 )
{
tagged.insert(j);
if ( par::gettag_listall )
{
thisTagged.insert(j);
if ( locus[j]->bp < dist_left )
dist_left = locus[j]->bp;
}
}
--j;
}
// Now move right
j = l+1;
while (1)
{
if ( j == nl_all )
break;
if ( locus[j]->chr != chr )
break;
if ( locus[j]->bp - pos > par::gettag_kb )
break;
if ( ! par::gettag_listall )
{
if ( tagged.find(j) != tagged.end() )
{
++j;
continue;
}
}
double rsq = correlation2SNP( l,j,true,false);
if ( realnum(rsq) && rsq >= par::gettag_r2 )
{
tagged.insert(j);
if ( par::gettag_listall )
{
thisTagged.insert(j);
if ( locus[j]->bp > dist_right )
dist_right = locus[j]->bp;
}
}
++j;
}
if ( par::gettag_listall )
{
O2 << setw( par::pp_maxsnp ) << locus[l]->name << " "
<< setw(4) << locus[l]->chr << " "
<< setw(10) << locus[l]->bp << " "
<< setw(4) << thisTagged.size() << " "
<< setw(10) << dist_left << " "
<< setw(10) << dist_right << " "
<< setw(8) << (dist_right - dist_left ) / 1000.0 << " ";
set<int>::iterator s = thisTagged.begin();
bool first = true;
while ( s != thisTagged.end() )
{
if ( first )
{
first = false;
}
else
O2 << "|";
O2 << locus[*s]->name;
++s;
}
if ( first )
O2 << "NONE";
O2 << "\n";
}
// Consider next SNP to tag
++i;
}
if ( par::gettag_listall )
O2.close();
if ( ! testAll )
{
printLOG("In total, added "
+ int2str( tagged.size() - toTag.size() )
+ " tag SNPs\n");
ofstream O1;
printLOG("Writing tag list to [ " + par::output_file_name + ".tags ]\n");
O1.open( (par::output_file_name+".tags").c_str(), ios::out);
// Mode 1 : just write list
if ( par::gettag_mode1 )
{
set<int>::iterator l = tagged.begin();
while ( l != tagged.end() )
{
O1 << locus[*l]->name << "\n";
++l;
}
}
// Mode 2 : Write all SNPs, with 0/1 code
if ( par::gettag_mode2 )
{
for (int l = 0; l < nl_all ; l++ )
{
O1 << locus[l]->name << "\t";
if ( tagged.find(l) != tagged.end() )
O1 << "1\n";
else
O1 << "0\n";
}
}
O1.close();
}
}
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