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AXT2ACF.cpp
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AXT2ACF.cpp
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#include "AXT2ACF.h"
using namespace std;
AXT2ACF::AXT2ACF(){
}
AXT2ACF::~AXT2ACF(){
}
string AXT2ACF::usage() const{
const string usage=string("")+ " axt2acf [options] <chr name> <name sample> <axt file>\n"+
"\nThis program will parse an AXT alignment for a single chromosome and output an ACF file (to STDOUT)\n"+
"The first sequence has to be the genome of the reference. For instance, to import chimp for the human reference:\n"+
" glactools axt2acf 1 PanTro5 chr1.hg19.panTro5.net.axt.gz > output.acf.gz\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"+
"";
return usage;
}
int AXT2ACF::run(int argc, char *argv[]){
// cout<<INT_MAX<<endl;
// bool ancAllele = false;
int lastOpt=1;
string fastaIndex;
//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(string(argv[i]) == "-u"){
uncompressed=true;
continue;
}
if(string(argv[i]) == "--fai"){
fastaIndex=string(argv[i+1]);
i++;
continue;
}
cerr<<"Wrong option "<<argv[i]<<endl;
exit(1);
}
if(lastOpt != (argc-3)){
cerr<<"The last 3 arguments are <chr name> <name sample> <axt file> "<<lastOpt<<" "<<argc<<endl;
return 1;
}
if(fastaIndex.size()==0){
cerr<<"Must specify fai file "<<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);
uint16_t chrIdx = UINT16_MAX;
string chrname = string(argv[lastOpt+0]);
string nameSample = string(argv[lastOpt+1]);
string axtfile = string(argv[lastOpt+2]);
bool foundChr=false;
for(unsigned int i=0;i<chrFound.size();i++){
if(chrFound[i].name == chrname){
chrIdx = uint16_t(i);
foundChr = true;
break;
}
}
if(!foundChr){
cerr << "Unable to find chromosome "<<chrname<<" in fasta index"<<endl;
return 1;
}
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+="#AXT2ACF:"+chrname+" "+nameSample+" "+axtfile+"\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\t"+nameSample+"\n";
GlacWriter * gw=NULL;
gw = new GlacWriter(1, //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);
}
string line;
string lineSp1;
string lineSp2;
igzstream myAXTFile;
myAXTFile.open(axtfile.c_str(), ios::in);
SingleAllele root;
SingleAllele anc;
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
anc.setRefCount(0); anc.setAltCount(0); anc.setIsCpg(false);
if (myAXTFile.good()){
while ( getline (myAXTFile,line)){
if(strBeginsWith(line,"#"))
continue;
vector<string> allToks = allTokens(line,' ');
if(allToks[1] != chrname){
if(allToks[1] != "chr"+chrname){
cerr<<"The chromosome name "<<allToks[1]<<" does not match the one provided on the command line ("<<"chr"<<chrname<<"), full line:"<<line<<endl;
return 1;
}else{
chrname="chr"+chrname;
}
}
unsigned int startC = destringify<unsigned int>(allToks[2]);
unsigned int endC = destringify<unsigned int>(allToks[3]);
unsigned int coordC =startC;
unsigned int lastC = startC;
bool lastCharWasC=false;
if(allToks.size() == 9){
getline (myAXTFile,lineSp1);
getline (myAXTFile,lineSp2);
//string lastToPrintS="";
AlleleRecords lastToPrint (false);
bool lastToPrintSet = false;
for(unsigned i=0;i<lineSp1.size();i++){
totalRec++;
if(lineSp1[i] == '-'){
}else{
if(lineSp2[i] == '-'){
}else{
writtenRec++;
AlleleRecords arCurrent (false);
arCurrent.chri = chrIdx;
arCurrent.coordinate = coordC;
arCurrent.sizePops = 1;
arCurrent.vectorAlleles = new vector<SingleAllele> ();
//cout<<coordC<<"\t"<<lineSp1[i]<<lineSp2[i]<<endl;
//string toprintS=chrname+"\t"+stringify(coordC)+"\t";
SingleAllele sample;
char cRef= char(toupper(lineSp1[i]));
char cAlt= char(toupper(lineSp2[i]));
//string toprint;
if(cRef == cAlt){
//toprintS+=stringify(cRef)+",N\t";
//toprint = "1,0";
sample.setRefCount(1); sample.setAltCount(0);
arCurrent.ref = cRef;
arCurrent.alt = 'N';
}else{
//toprintS+=stringify(cRef)+","+stringify(cAlt)+"\t";
//toprint = "0,1";
sample.setRefCount(0); sample.setAltCount(1);
arCurrent.ref = cRef;
arCurrent.alt = cAlt;
}
bool cpgFlag=false;
if( (lastC+1) == coordC){
if(lastCharWasC && (cRef == 'G' || cAlt == 'G' )){
cpgFlag=true;
}
}
//sample.setIsCpg(cpgEPO);
arCurrent.vectorAlleles->push_back(root);
arCurrent.vectorAlleles->push_back(anc);
//arToWrite.vectorAlleles->push_back(sample);
if(cpgFlag){
if(lastToPrintSet){
lastToPrint.vectorAlleles->at(2).setIsCpg(true);//setting CpG for previous record
if(!gw->writeAlleleRecord(&lastToPrint)){
cerr<<"AXT2ACF: error writing header "<<endl;
exit(1);
}
}
sample.setIsCpg(true);
arCurrent.vectorAlleles->push_back(sample);
if(!gw->writeAlleleRecord(&arCurrent)){//printing for current record
cerr<<"AXT2ACF: error writing header "<<endl;
exit(1);
}
lastToPrintSet=false;//was flushed
// if(!lastToPrintS.empty())
// cout<<lastToPrintS<<":1"<<endl; //print last line
// toprintS+="0,0:0\t0,0:0\t"+toprint+":1"; //print current line
// cout<<toprintS<<endl; //print current line
// lastToPrintS="";
}else{
if(lastToPrintSet){
lastToPrint.vectorAlleles->at(2).setIsCpg(false);//setting CpG for previous record
if(!gw->writeAlleleRecord(&lastToPrint)){
cerr<<"AXT2ACF: error writing header "<<endl;
exit(1);
}
}
sample.setIsCpg(false);
arCurrent.vectorAlleles->push_back(sample);
lastToPrint = arCurrent;
lastToPrintSet = true;
// if(!lastToPrintS.empty())
// cout<<lastToPrintS<<":0"<<endl; //print last line
// toprintS+="0,0:0\t0,0:0\t"+toprint; //store current line
// lastToPrintS=toprintS;
}
//cout<<toPrintS<<endl;
//cpg
if(cRef == 'C' || cAlt == 'C')
lastCharWasC = true;
else
lastCharWasC = false;
lastC = coordC;
}
coordC++;
}
}//end loop
if(lastToPrintSet){
lastToPrint.vectorAlleles->at(2).setIsCpg(false);//setting CpG for previous record
if(!gw->writeAlleleRecord(&lastToPrint)){
cerr<<"AXT2ACF: error writing header "<<endl;
exit(1);
}
}
// if(!lastToPrintS.empty())
// cout<<lastToPrintS<<":0"<<endl;
if((coordC-1) != endC){
cerr<<"The block did not end with the proper coordinate got:"<<coordC<<" expected "<<endC<<endl;
return 1;
}
// cout<<startC<<"\t"<<endC<<endl;
// return 1;
getline (myAXTFile,line);
}else{
cerr<<"Wrong number of fields for line "<<line<<endl;
return 1;
}
}
myAXTFile.close();
}else{
cerr << "Unable to open file "<<axtfile<<endl;
return 1;
}
// string line;
// bool hasData= getline (myfile,line);
// while (hasData ){
// totalRec++;
// // while(btr.hasData()){
// // BAMTableObj * toprint=btr.getData();
// vector<string> token= allTokens(line,'\t');
// // cout<<"line "<<line<<endl;
// string chr = token[1];
// unsigned int pos = destringify<unsigned int>(token[2]);
// string genotype = token[3];
// // if(passedFilters(toprint,filtersVCF)){
// 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
// setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_ref,allel_chimp,allel_anc,lineLeftEPO,lineFromEPO);
// }
// }
// if(epoFileB){
// if(!lineLeftEPO){
// cerr<<"Error, no data in the EPO file "<< chr <<":"<< int(pos) <<endl;
// return 1;
// }
// if(epoChr != chr){
// cerr<<"Error, the chromosome does not match the one in the EPO file = "<<epoChr <<" and not "<<chr<<endl;
// return 1;
// }
// // cout<<"2"<<endl;
// while(epoCoord != pos){
// if(epoCoord > pos){
// cerr<<"Error, are all the sites in EPO there? Difference between coords "<<(line)<<"\t"<<lineFromEPO<<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,lineFromEPO);
// // lineLeftEPO=(rtEPO->readLine( lineFromEPO ));
// // vector<string> fieldsEPO = allTokens(lineFromEPO,'\t');
// // epoChr = fieldsEPO[0];
// // epoCoord = string2uint(fieldsEPO[1]);
// // if(fieldsEPO[9] == "1")
// // cpgEPO=true;
// // else
// // cpgEPO=false;
// // if(ancAllele){
// // allel_chimp = fieldsEPO[3][0];//inferred ancestor
// // }else{
// // allel_chimp = fieldsEPO[4][0];//chimp;
// // }
// // if(!lineLeftEPO){
// // cerr<<"Error, missing data in the EPO file"<<*toprint<<endl;
// // return 1;
// // }
// }
// if(epoCoord != pos){
// cerr<<"Error, are all the sites in EPO there? Difference between coords "<<line<<"\t"<<lineFromEPO<<endl;
// return 1;
// }
// }
// //int refIdx =base2int(allel_ref);
// // int chimpIdx=base2int(allel_chimp);
// char alt='N';
// string s="ACGT";
// string chimpString;
// string ancString;
// SingleAllele root;
// SingleAllele anc;
// //need an allele that is A,C,G,T
// //cout<<pos<<"\t"<<allel_ref<<endl;
// if(!isResolvedDNA(allel_ref)){
// goto nextline;
// }
// // cout<<"3"<<endl;
// //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];
// }
// }
// }
// // cout<<*toprint<<endl;
// // cout<<lineFromEPO<<endl;
// // SingleAllele root;
// // SingleAllele anc;
// if(!epoFileB){ //no epo file
// // chimpString="0,0:0";
// // ancString="0,0:0";
// 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;
// }
// }
// }
// }
// }
// // cout<<"4"<<endl;
// if( (alt!='N' && genotype.find(alt) != string::npos) ) // has alternative
// {//no alt in bam table
// int refCount=0;
// int altCount=0;
// string rr = stringify(allel_ref)+ stringify(allel_ref);
// string ra = stringify(allel_ref)+ stringify(alt);
// string ar = stringify(alt) + stringify(allel_ref);
// string aa = stringify(alt) + stringify(alt);
// if(genotype == rr ){
// refCount=2;
// }else{
// if(genotype == aa){
// altCount=2;
// }else{
// if( (genotype == ra) ||
// (genotype == ar) ){
// refCount=1;
// altCount=1;
// }else{
// //goto nextline;
// cerr<<"Error: Potential error in the 23 and me file where the reference allele is not there "<<line<<"\t"<<lineFromEPO<<endl; //error
// goto nextline;
// }
// }
// }
// //cout<<refIdx<<endl;
// writtenRec++;
// AlleleRecords arToWrite (false);
// arToWrite.chri = chr2index[chr];
// arToWrite.coordinate = pos;
// arToWrite.sizePops = 1;
// arToWrite.ref = allel_ref;
// arToWrite.alt = alt;
// arToWrite.vectorAlleles = new vector<SingleAllele> ();
// // SingleAllele root;
// // SingleAllele anc;
// SingleAllele sample (refCount, altCount, 0);//no CpG provided
// arToWrite.vectorAlleles->push_back(root);
// arToWrite.vectorAlleles->push_back(anc);
// arToWrite.vectorAlleles->push_back(sample);
// if(!gw->writeAlleleRecord(&arToWrite)){
// cerr<<"Vcf2ACF: error writing header "<<endl;
// exit(1);
// }
// // cout<<chr<<"\t"<< pos<<"\t"<<
// // allel_ref<<","<<
// // alt<<"\t"<<
// // chimpString<<"\t"<<
// // ancString<<"\t"<<
// // refCount<<","<<
// // altCount<<
// // ":"<<("0")<<endl;//no cpg info
// }else{
// goto nextline;
// //continue;//triallelic, skip
// }
// nextline:
// hasData = getline (myfile,line);
// }
delete(gw);
cerr<<"Program "<<argv[0]<<" looked at "<<totalRec<<" records, wrote "<<writtenRec<<" terminated gracefully"<<endl;
return 0;
}