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BPLINK2ACF.cpp
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BPLINK2ACF.cpp
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#include "BPLINK2ACF.h"
// #include "BAMTableObj.h"
// #include "BAMTABLEreader.h"
static unsigned int limitToReOpenFP = 200; //if the coordinate is this far away, we will re-open the file pointer
using namespace std;
uint8_t mask4=192; //11000000
uint8_t mask3= 48; //00110000
uint8_t mask2= 12; //00001100
uint8_t mask1= 3; //00000011
uint8_t masks [4] = {mask1,mask2,mask3,mask4};
void BPLINK2ACF::setVarsEPO(ReadTabix * rtEPO,string & epoChr,unsigned int & epoCoord,bool & cpgEPO,char & allel_ref,char & allel_chimp,char & allel_anc,bool & lineLeftEPO){
//lineLeftEPO=(rtEPO->readLine( lineFromEPO ));
lineLeftEPO=(rtEPO->readLineKS( ));
//cerr<<kstringPtrEPO->s<<endl;
if(!lineLeftEPO){
cerr<<"Error, missing data in the EPO file"<<endl;
exit(1);
}
char *p, *q;
int i;
for (p = kstrtok(kstringPtrEPO->s, "\t", &aux), i = 0; p; p = kstrtok(0, 0, &aux), ++i) {
q = (char*)aux.p;
*q = 0;
//cout<<i<<" >"<<p<<"< "<<endl;
if(i==0){//chr
epoChr = string(p);
continue;
}
if(i==1){//coord
epoCoord = (unsigned int)strtoul(p, NULL, 0);//strtoul(p);
continue;
}
if(i==2){//human ref
allel_ref = p[0];
continue;
}
if(i==3){//ancestor
allel_anc = p[0];
continue;
}
if(i==4){//chimp
allel_chimp = p[0];
continue;
}
if(i<9) continue;
if(i==9){
if(strcmp(p,"1")==0){
cpgEPO=true;
}else{
cpgEPO=false;
}
continue;
}
break;
}
// vector<string> fieldsEPO = allTokens(lineFromEPO,'\t');
// epoChr = fieldsEPO[0];
// epoCoord = string2uint(fieldsEPO[1]);
// if(fieldsEPO[9] == "1")
// cpgEPO=true;
// else
// cpgEPO=false;
// allel_ref = fieldsEPO[2][0];//reference allele
// allel_anc = fieldsEPO[3][0];//inferred ancestor
// allel_chimp = fieldsEPO[4][0];//chimp;
}
BPLINK2ACF::BPLINK2ACF(){
}
BPLINK2ACF::~BPLINK2ACF(){
}
string BPLINK2ACF::usage() const{
const string usage=string("")+ " bplink2acf [options] <BPLINK prefix> "+"\n"+
"\nThis program convert BPLINK files into ACF (prints to the stdout)\n"+
"\nPlease note that since only variants are normally present in PLINK files, the CpG flag will not be set\n"+
"\nThe <BPLINK prefix> must include the following files:\n"+
"\t<BPLINK prefix>.bed\n"+
"\t<BPLINK prefix>.bim\n"+
"\t<BPLINK prefix>.fam\n"+
"\n"+
"\t"+"--fai [file]" + "\t\t"+"Fasta index for genome (produced by \"samtools faidx\") (default: none)\n"+
"\t"+"-u" + "\t\t\t"+"Produce uncopressed output (default: "+booleanAsString(uncompressed)+")\n"+
"\t"+"--epo [EPO file]" +"\t" +"Use file as EPO alignment to set the (default: none)\n"+
"\t"+" " +"\t" +"ancestral/root alleles for hominin samples\n"+
"";
return usage;
}
int BPLINK2ACF::run(int argc, char *argv[]){
// cout<<INT_MAX<<endl;
// bool ancAllele = false;
int lastOpt=1;
//last arg is program name
for(int i=1;i<(argc);i++){
if((string(argv[i]) == "-") ){
lastOpt=i;
break;
}
if(string(argv[i])[0] != '-' ){
lastOpt=i;
break;
}
if(strcmp(argv[i],"--epo") == 0 ){
epoFile=string(argv[i+1]);
epoFileB=true;
i++;
continue;
}
if(string(argv[i]) == "-u"){
uncompressed=true;
continue;
}
if(string(argv[i]) == "--fai"){
fastaIndex=string(argv[i+1]);
i++;
continue;
}
// if(strcmp(argv[i],"--useanc") == 0 ){
// ancAllele =true;
// continue;
// }
cerr<<"Wrong option "<<argv[i]<<endl;
exit(1);
}
if(lastOpt != (argc-1)){
cerr<<"The last argument is <BPLINK prefix> "<<endl;
return 1;
}
if(fastaIndex.size()==0 ){
cerr<<"Must specify fai file "<<endl;
return 1;
}
if( !strEndsWith(fastaIndex,".fai") ){
cerr<<"fasta index must end with .fai file "<<endl;
return 1;
}
fastaFile = fastaIndex.substr(0,fastaIndex.size()-4);
if(!epoFileB){
if(!isFile( fastaFile ) ){
cerr<<"If you do not specify EPO file, we need the fasta index as this file format does not have the reference information"<<endl<<"fasta file "<<fastaFile<<" does not exist"<<endl;
return 1;
}
//cerr<<"Must specify EPO file as this file format does not have the reference information "<<endl;
//return 1;
}
vector<chrinfo> chrFound;
uint64_t genomeLength;
readFastaIndex(fastaIndex,chrFound,genomeLength);
//cerr<<"Filter used: "<<*filtersVCF<<endl;
//VCFreader vcfr (string(argv[argc-3]),5);
// BAMTABLEreader btr (),5);
string inputFileEIGprefix = string(argv[lastOpt]);
string bedFile = string(argv[argc-1])+".bed";
string bimFile = string(argv[argc-1])+".bim";
string famFile = string(argv[argc-1])+".fam";
// string genoFile = inputFileEIGprefix+".geno";
// string snpFile = inputFileEIGprefix+".snp";
// string indFile = inputFileEIGprefix+".ind";
if(!isFile(bedFile)){
cerr<<".bed file "<<bedFile<<" does not exist"<<endl;
exit(1);
}
if(!isFile(bimFile)){
cerr<<".bim file "<<bimFile<<" does not exist"<<endl;
exit(1);
}
if(!isFile(famFile)){
cerr<<".fam file "<<famFile<<" does not exist"<<endl;
exit(1);
}
igzstream myfileBED;
myfileBED.open(bedFile.c_str(), ios::in | ios::binary);
if (!myfileBED.good()){
cerr << "Unable to open file "<<bedFile<<endl;
return 1;
}
igzstream myfileBIM;
myfileBIM.open(bimFile.c_str(), ios::in);
if (!myfileBIM.good()){
cerr << "Unable to open file "<<bimFile<<endl;
return 1;
}
igzstream myfileFAM;
myfileFAM.open(famFile.c_str(), ios::in);
if (!myfileFAM.good()){
cerr << "Unable to open file "<<famFile<<endl;
return 1;
}
BamTools::Fasta fastaReference;
string epoFileidx = epoFile+".tbi";
string epoChr;
unsigned int epoCoord;
ReadTabix * rtEPO =NULL;
//string lineFromEPO;
bool lineLeftEPO;
bool cpgEPO=false;
bool firstLine=true;
char allel_chimp;
char allel_ref;
char allel_anc;
// 75060,
// 75070,
// 5);
//header
unsigned int totalRec=0;
unsigned int writtenRec=0;
string header="";
header+="#ACF\n";
string programLine;
for(int i=0;i<(argc);i++){
programLine+=(string(argv[i])+" ");
}
header+="#PG:"+programLine+"\n";;
header+="#GITVERSION: "+returnGitHubVersion(argv[-1],"")+"\n";;
header+="#DATE: "+getDateString()+"\n";;
header+="#BPLINK2ACF:\n";
map<string,uint16_t> chr2index;
uint16_t chrCurrentIndex=0;
for(unsigned j=0;j<(chrFound.size());j++){
header+= string("#SQ\tSN:")+chrFound[j].name+"\tLN:"+stringify(chrFound[j].length)+"\n";
chr2index[chrFound[j].name]=chrCurrentIndex++;
if(chrCurrentIndex == 0xFFFF){
cerr<<"Too many chromosomes for this build, more than 65535"<<endl;
return 1;
}
}
header+="#chr\tcoord\tREF,ALT\troot\tanc";
bool foundPop=false;
bool foundAnc=false;
int indexAnc=-1;
bool foundRoot=false;
int indexRoot=-1;
string lineFAM;
int sizePopRead=0;
//int allPopFound=0;
int indexPop=-1;
while ( getline (myfileFAM,lineFAM)){
//header<<line<<endl;
trimWhiteSpacesBothEnds(&lineFAM);
vector<string> fields = allTokensWhiteSpaces( lineFAM );
if(fields.size() != 6){
cerr<<"Line "<<lineFAM<<" should have 6 TAB/space deliminated fields, found "<<fields.size()<<" tab/space deliminated fields"<<endl;
return 1;
}
//allPopFound++;
indexPop++;
if(fields[0] == "root"){ foundRoot=true; indexRoot=indexPop; continue; }
if(fields[0] == "anc") { foundAnc=true; indexAnc =indexPop; continue; }
sizePopRead++;
header+="\t"+fields[1];
foundPop=true;
}
myfileFAM.close();
if( (foundAnc || foundRoot) && epoFileB){
cerr<<"ERROR: we found a pop called root and anc in the FAM file:"<<famFile<<" but the EPO file is used. We cannot determine from where to take the ancestral/root information from, exiting"<<endl;
return 1;
}
if(!foundPop){
cerr<<"ERROR: did not find any data in the individual file"<<endl;
return 1;
}
header+="\n";
int bytesToRead=ceil( double(sizePopRead)/4.0 );
//cerr<<header<<endl;
//return 1;
GlacWriter * gw=NULL;
//cerr<<"sizePopRead "<<sizePopRead<<endl;
gw = new GlacWriter(sizePopRead, //gp.getSizePops(),
false, //gp.isGLFormat(),
2, //gp.isACFormat()?2:1,
1, //compression threads
uncompressed);
if(!gw->writeHeader(header)){
cerr<<"GlacViewer: error writing header "<<endl;
exit(1);
}
//checking magic numbers
char c;
myfileBED.read((char*)&c,sizeof(char));
if(int(c) != 108){
cerr<<"BPLINK2ACF: error in magic numbers found "<<int(c)<<" expected 108"<<endl;
exit(1);
}
myfileBED.read((char*)&c,sizeof(char));
if(int(c) != 27){
cerr<<"BPLINK2ACF: error in magic numbers found "<<int(c)<<" expected 27"<<endl;
exit(1);
}
myfileBED.read((char*)&c,sizeof(char));
if(int(c) != 1){
cerr<<"BPLINK2ACF: error in magic numbers found "<<int(c)<<" expected 1"<<endl;
exit(1);
}
string lineBIM;
//
while ( getline (myfileBIM,lineBIM)){
//header<<line<<endl;
trimWhiteSpacesBothEnds(&lineBIM);
totalRec++;
//write code to retrieve data from bed file here
vector<string> fields = allTokensWhiteSpaces( lineBIM );
if(fields.size() != 6){
cerr<<"Line "<<lineBIM<<" should have 6 TAB/space deliminated fields, found "<<fields.size()<<" tab/space deliminated fields"<<endl;
return 1;
}
//token[0];//SNPname
string chr = fields[0];//chr
//1 - ID
//2 pos in CM
//token[2];//genetic position
unsigned int pos = destringify<unsigned int>(fields[3]);//physical position
char genotypeMin = fields[4][0];//minor first
char genotypeMaj = fields[5][0];//major second
if(firstLine){
firstLine=false;
if(epoFileB){
rtEPO = new ReadTabix( epoFile.c_str() ,
epoFileidx.c_str() ,
chr,
int(pos),INT_MAX ); //the destructor should be called automatically
kstringPtrEPO = rtEPO->getKstringPtr();
memset(&aux, 0, sizeof(ks_tokaux_t));
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}else{
if ( !fastaReference.Open(fastaFile , fastaIndex) ){
cerr << "ERROR: failed to open fasta file " <<fastaFile<<" and index " <<fastaIndex<<endl;
return 1;
}
}
}
if(epoFileB){
if(!lineLeftEPO){
cerr<<"Error, no data in the EPO file "<< chr <<":"<< int(pos) <<endl;
return 1;
}
if(epoChr != chr){
if( (pos - epoCoord ) >= limitToReOpenFP){ //seeking in the file
rtEPO->repositionIterator(chr , int(pos),INT_MAX);
}
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}
while(epoCoord != pos){
if(epoCoord > pos){
cerr<<"Error, are all the sites in EPO there? Difference between coords "<<(lineBIM)<<"\tEPO="<<kstringPtrEPO->s<<endl;
return 1;
}
if( (pos - epoCoord ) >= limitToReOpenFP){ //seeking in the file
rtEPO->repositionIterator(chr , int(pos),INT_MAX);
}
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}
if(epoCoord != pos){
cerr<<"Error, are all the sites in EPO there? Difference between coords "<<lineBIM<<"\tEPO="<<kstringPtrEPO->s<<endl;
return 1;
}
}else{ //end if epoFileB
//allel_ref =
if ( !fastaReference.GetBase(chr2index[chr], pos-1, allel_ref ) ) {
cerr << "glactools ERROR: could not read reference base from FASTA file at chr:"<<chr2index[chr]<<" position:"<<(pos) << endl;
return 1;
}
}
//to be safe
allel_ref = toupper( allel_ref );
allel_anc = toupper( allel_anc );
char alt='N';
string s="ACGT";
string chimpString;
string ancString;
SingleAllele root;
SingleAllele anc;
AlleleRecords arToWrite (false);
//bool refIsAltfromSNPfile=false;
char genotypeRef;
char genotypeAlt;
bool majorIsRef=false;
bool minorIsRef=false;
int indexOfIndividual=0;
vector<SingleAllele> allexeptRootAnc;
//need an allele that is A,C,G,T
if(!isResolvedDNA(genotypeMin)){
goto nextline;
}
if(!isResolvedDNA(genotypeMaj)){
goto nextline;
}
//cerr<<"pos:"<<pos<<" ref:"<<allel_ref<<" maj:"<<genotypeMaj<<" min:"<<genotypeMin<<endl;
if(isResolvedDNA(allel_ref)){
//need to set genotypeAlt
if(allel_ref == genotypeMaj){//if the reference is the Max
majorIsRef=true;
genotypeRef=allel_ref;
if(isResolvedDNA(genotypeMin)){//minor is resolved
if(genotypeMaj!=genotypeMin){
genotypeAlt = genotypeMin;
}else{
genotypeAlt = 'N';
}
}else{//minor is not resolved, should not happen
genotypeAlt = 'N';
}
}else{
if(allel_ref == genotypeMin){//if the reference is the Max
minorIsRef=true;
genotypeRef=allel_ref;
if(isResolvedDNA(genotypeMaj)){//major is resolved
if(genotypeMaj!=genotypeMin){//difference
genotypeAlt = genotypeMaj;
}else{
genotypeAlt = 'N';//should not happen
}
}else{//minor is not resolved, should not happen
genotypeAlt = 'N';
}
}else{
//ref not found
cerr<<"bplink2acf: WARNING: The reference allele between the EPO/FASTA ("<<allel_ref<<") was not found in the the .bim file (found: "<<genotypeMaj<<","<<genotypeMin<<") at chr:pos "<<chr<<":"<<pos<<" at line "<<lineBIM<<endl;
return 1;
goto nextline;
}
}
}else{//if not resolved for allele refs
goto nextline;
}
//cerr<<"pos:"<<pos<<" majorIsRef:"<<majorIsRef<<" minorIsRef:"<<minorIsRef<<endl;
if(!majorIsRef && !minorIsRef){
cerr<<"bplink2acf: WARNING: The reference allele between the EPO/FASTA ("<<allel_ref<<") was not found in the the .bim file (found: "<<genotypeMaj<<","<<genotypeMin<<") at chr:pos "<<chr<<":"<<pos<<endl;
goto nextline;
}
if(!epoFileB){ //no epo file
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
anc.setRefCount(0); anc.setAltCount(0); anc.setIsCpg(false);
}else{
//unresolved ancestral allele (A,C,G,T)
if(!isResolvedDNA(allel_chimp)){
//chimpString="0,0:0";
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
}
//resolved ancestral allele
else{
if(allel_chimp == allel_ref){//no diff between chimp and reference
//chimpString="1,0:"+string(cpgEPO?"1":"0");
root.setRefCount(1); root.setAltCount(0); root.setIsCpg(cpgEPO);
}else{
if(alt == 'N'){//no alt defined, the chimp becomes the alt
alt = allel_chimp;
//chimpString="0,1:"+string(cpgEPO?"1":"0");
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}else{
if(alt == allel_chimp){//alt is chimp
//chimpString="0,1:"+string(cpgEPO?"1":"0");
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}else{ //tri-allelic site, discard
//continue;
goto nextline;
}
}
}
}
if(!isResolvedDNA(allel_anc)){
//ancString="0,0:0";
anc.setRefCount(0); anc.setAltCount(0); anc.setIsCpg(false);
}
//resolved ancestral allele
else{
if(allel_anc == allel_ref){//no diff between ancestor and reference
//ancString="1,0:"+string(cpgEPO?"1":"0");
anc.setRefCount(1); anc.setAltCount(0); anc.setIsCpg(cpgEPO);
}else{
if(alt == 'N'){//no alt defined, the ancestor becomes the alt
alt = allel_anc;
//ancString="0,1:"+string(cpgEPO?"1":"0");
anc.setRefCount(0); anc.setAltCount(1); anc.setIsCpg(cpgEPO);
}else{
if(alt == allel_anc){//alt is ancestor
//ancString="0,1:"+string(cpgEPO?"1":"0");
anc.setRefCount(0); anc.setAltCount(1); anc.setIsCpg(cpgEPO);
}else{ //tri-allelic site, discard
//continue;
goto nextline;
}
}
}
}
}
if(alt!='N'){
if(genotypeAlt != alt ){ // has alternative
cerr<<"bplink2acf: WARNING The alternative allele between the EPO and the .bim file disagrees, could be triallelic at chr:pos "<<chr<<":"<<thousandSeparator(pos)<<", skipping"<<endl;
goto nextline;
}
}
arToWrite.chri = chr2index[chr];
arToWrite.coordinate = pos;
arToWrite.sizePops = uint32_t(sizePopRead);
arToWrite.ref = genotypeRef;
arToWrite.alt = genotypeAlt;
arToWrite.vectorAlleles = new vector<SingleAllele> ();
// SingleAllele root;
// SingleAllele anc;
//cerr<<"bytesToRead "<<bytesToRead<<endl;
for(int i=0;i<bytesToRead;i++){
unsigned char data;
myfileBED.read((char*)&data,sizeof(char));
//mask and shift
//cerr<<"data: "<<var2binary(data)<<" "<<indexOfIndividual<<" "<<(indexOfIndividual%4)<<" "<<sizePopRead<<endl;
for(int indBytes=0;indBytes<4;indBytes++){
if(indexOfIndividual>indexPop)
break;
unsigned char dataInd;
//cerr<<"mask: "<<var2binary(masks[ (indexOfIndividual%4) ])<<endl;
dataInd = (data & masks[ (indexOfIndividual%4) ]);
// cerr<<"dataInd1: "<<var2binary(dataInd)<<endl;
// cerr<<indexOfIndividual<<" "<<(indexOfIndividual%4)<<" "<<((indexOfIndividual%4)*2)<<endl;
dataInd = (dataInd >> ( (indexOfIndividual%4)*2 ));
//cerr<<"dataInd2: "<<var2binary(dataInd)<<endl;
int g =int(dataInd);
//cerr<<"g: "<<g<<endl;
int refCount=0;
int altCount=0;
//homo for minor
if(g == 0){
if(majorIsRef){
refCount = 0; altCount = 2;
}else{//minor is ref
refCount = 2; altCount = 0;
}
}
//missing
if(g == 1){
refCount = 0; altCount = 0;
}
//het
if(g == 2){
refCount = 1; altCount = 1;//refIsAltfromSNPfile does not matter
}
//homo minor
if(g == 3){
if(majorIsRef){
refCount = 2; altCount = 0;
}else{//minor is ref
refCount = 0; altCount = 2;
}
}
if( indexOfIndividual == indexAnc){
anc.setRefCount(refCount); anc.setAltCount(altCount); anc.setIsCpg(false);
}else{
if( indexOfIndividual == indexRoot){
root.setRefCount(refCount); root.setAltCount(altCount); root.setIsCpg(false);
}else{
SingleAllele sample (refCount, altCount, 0);//no CpG provided
allexeptRootAnc.push_back(sample);
}
}
//cerr<<"indexOfIndividual "<<indexAnc<<" "<<indexRoot<<" "<<indexOfIndividual<<" "<< indexPop <<" sizes:"<<allexeptRootAnc.size()<<endl;
indexOfIndividual++;
}
}//for each char in lineG
//cerr<<"writing sizes:"<<allexeptRootAnc.size()<<endl;
arToWrite.vectorAlleles->push_back(root);
arToWrite.vectorAlleles->push_back(anc);
for(unsigned int j=0;j<allexeptRootAnc.size();j++){
//cerr<<j<<" "<<allexeptRootAnc[j]<<endl;
arToWrite.vectorAlleles->push_back(allexeptRootAnc[j]);
}
if(!gw->writeAlleleRecord(&arToWrite)){
cerr<<"bplink2acf: error writing header "<<endl;
exit(1);
}
writtenRec++;
nextline:
continue;
}
myfileBIM.close();
myfileBED.close();
if(rtEPO != NULL)
delete(rtEPO);
delete(gw);
cerr<<"Program "<<argv[0]<<" looked at "<<totalRec<<" records, wrote "<<writtenRec<<" terminated gracefully"<<endl;
return 0;
}
/*
string lineG;//geno
string lineS;//snp
bool hasDataG= (bool)getline (myfileG,lineG);
bool hasDataS= (bool)getline (myfileS,lineS);
while (hasDataG ){
if(!hasDataS){
cerr<<"bplink2acf: data seems to be missing in the .snp file, stopped at line in .geno "<<lineG<<endl;
return 1;
}
totalRec++;
// cout<<lineS<<endl;
// cout<<lineG<<endl;
trimWhiteSpacesBothEnds(&lineS);
vector<string> token= allTokensWhiteSpaces(lineS);
if(token.size() != 6){
cerr<<"Error, SNP line should contain 6 fields"<<endl;
return 1;
}
//token[0];//SNPname
string chr = token[1];//chr
//token[2];//genetic position
unsigned int pos = destringify<unsigned int>(token[3]);//physical position
char genotypeRef = token[4][0];
char genotypeAlt = token[5][0];
if(firstLine){
firstLine=false;
if(epoFileB){
rtEPO = new ReadTabix( epoFile.c_str() ,
epoFileidx.c_str() ,
chr,
int(pos),INT_MAX ); //the destructor should be called automatically
kstringPtrEPO = rtEPO->getKstringPtr();
memset(&aux, 0, sizeof(ks_tokaux_t));
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}else{
if ( !fastaReference.Open(fastaFile , fastaIndex) ){
cerr << "ERROR: failed to open fasta file " <<fastaFile<<" and index " <<fastaIndex<<endl;
return 1;
}
}
}
if(epoFileB){
if(!lineLeftEPO){
cerr<<"Error, no data in the EPO file "<< chr <<":"<< int(pos) <<endl;
return 1;
}
if(epoChr != chr){
if( (pos - epoCoord ) >= limitToReOpenFP){ //seeking in the file
rtEPO->repositionIterator(chr , int(pos),INT_MAX);
}
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}
while(epoCoord != pos){
if(epoCoord > pos){
cerr<<"Error, are all the sites in EPO there? Difference between coords "<<(lineS)<<"\tEPO="<<kstringPtrEPO->s<<endl;
return 1;
}
if( (pos - epoCoord ) >= limitToReOpenFP){ //seeking in the file
rtEPO->repositionIterator(chr , int(pos),INT_MAX);
}
setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO);
}
if(epoCoord != pos){
cerr<<"Error, are all the sites in EPO there? Difference between coords "<<lineS<<"\tEPO="<<kstringPtrEPO->s<<endl;
return 1;
}
}else{ //end if epoFileB
//allel_ref =
if ( !fastaReference.GetBase(chr2index[chr], pos, allel_ref ) ) {
cerr << "glactools ERROR: could not read reference base from FASTA file at chr:"<<chr2index[chr]<<" position:"<<(pos) << endl;
return 1;
}
}
char alt='N';
string s="ACGT";
string chimpString;
string ancString;
SingleAllele root;
SingleAllele anc;
AlleleRecords arToWrite (false);
bool refIsAltfromSNPfile=false;
//need an allele that is A,C,G,T
if(!isResolvedDNA(genotypeRef)){
goto nextline;
}
if(!isResolvedDNA(genotypeAlt)){
goto nextline;
}
if(epoFileB){
if(isResolvedDNA(allel_ref)){
if(allel_ref != genotypeRef){
//cerr<<"eigen2acf: WARNING: The reference allele between the EPO ("<<allel_ref<<") and the ref from the .geno file ("<<genotypeRef<<") disagrees at chr:pos "<<chr<<":"<<pos<<endl;
if(allel_ref != genotypeAlt){
cerr<<"bplink2acf: WARNING: The reference allele between the EPO ("<<allel_ref<<") and the alt from the .geno file ("<<genotypeRef<<") also disagrees at chr:pos "<<chr<<":"<<pos<<", skiping"<<endl;
goto nextline;
}else{
refIsAltfromSNPfile=true;
char c_ = genotypeRef;
genotypeRef = genotypeAlt;
genotypeAlt = c_;
}
}else{
//fine
}
}else{
goto nextline;
}
}else{
if(isResolvedDNA(allel_ref)){
if(allel_ref != genotypeRef){
//cerr<<"eigen2acf: WARNING: The reference allele between the EPO ("<<allel_ref<<") and the ref from the .geno file ("<<genotypeRef<<") disagrees at chr:pos "<<chr<<":"<<pos<<endl;
if(allel_ref != genotypeAlt){
cerr<<"bplink2acf: WARNING: The reference allele between the EPO ("<<allel_ref<<") and the alt from the .geno file ("<<genotypeRef<<") also disagrees at chr:pos "<<chr<<":"<<pos<<", skiping"<<endl;
goto nextline;
}else{
refIsAltfromSNPfile=true;
char c_ = genotypeRef;
genotypeRef = genotypeAlt;
genotypeAlt = c_;
}
}else{
//fine
}
}else{
goto nextline;
}
}
//todo
// if ( !m_fastaReference->GetBase(pileupData.RefId, posAlign-1, referenceBase ) ) {
// cerr << "bamtools convert ERROR: pileup conversion - could not read reference base from FASTA file at chr "<<pileupData.RefId<<" position "<<(posAlign-1) << endl;
// exit(1);
// }
//determine alternative allele
// for(int i=0;i<4;i++){
// if(s[i] != allel_ref){
// if(genotype.find(s[i]) != string::npos){ //new non-ref allele found
// //toprint->hasAllele(i+1) ){
// alt=s[i];
// }
// }
// }
if(!epoFileB){ //no epo file
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
anc.setRefCount(0); anc.setAltCount(0); anc.setIsCpg(false);
}else{
//unresolved ancestral allele (A,C,G,T)
if(!isResolvedDNA(allel_chimp)){
//chimpString="0,0:0";
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
}
//resolved ancestral allele
else{
if(allel_chimp == allel_ref){//no diff between chimp and reference
//chimpString="1,0:"+string(cpgEPO?"1":"0");
root.setRefCount(1); root.setAltCount(0); root.setIsCpg(cpgEPO);
}else{
if(alt == 'N'){//no alt defined, the chimp becomes the alt
alt = allel_chimp;
//chimpString="0,1:"+string(cpgEPO?"1":"0");
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}else{
if(alt == allel_chimp){//alt is chimp
//chimpString="0,1:"+string(cpgEPO?"1":"0");
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}else{ //tri-allelic site, discard
//continue;
goto nextline;
}
}
}
}
if(!isResolvedDNA(allel_anc)){
//ancString="0,0:0";
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}
//resolved ancestral allele
else{
if(allel_anc == allel_ref){//no diff between ancestor and reference
//ancString="1,0:"+string(cpgEPO?"1":"0");
anc.setRefCount(1); anc.setAltCount(0); anc.setIsCpg(cpgEPO);
}else{
if(alt == 'N'){//no alt defined, the ancestor becomes the alt
alt = allel_anc;
//ancString="0,1:"+string(cpgEPO?"1":"0");
anc.setRefCount(0); anc.setAltCount(1); anc.setIsCpg(cpgEPO);
}else{
if(alt == allel_anc){//alt is ancestor
//ancString="0,1:"+string(cpgEPO?"1":"0");
anc.setRefCount(0); anc.setAltCount(1); anc.setIsCpg(cpgEPO);
}else{ //tri-allelic site, discard
//continue;
goto nextline;
}
}
}
}
}
if(alt!='N'){
if(genotypeAlt != alt ){ // has alternative
cerr<<"bplink2acf: WARNING The alternative allele between the EPO and the .geno file disagrees, could be triallelic at chr:pos "<<chr<<":"<<thousandSeparator(pos)<<", skipping"<<endl;
goto nextline;
}