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BAM2ACF.cpp
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/*
* BAM2ACF
* Date: Jul-30-2017
* Author : Gabriel Renaud gabriel.reno [at sign here] gmail.com
*
*/
#include "BAM2ACF.h"
//using namespace BamTools;
using namespace std;
#define MAXCOV 1000
#define MINLENGTHFRAGMENT 0
#define MAXLENGTHFRAGMENT 1000000
#define MAXBASEQUAL 64 // maximal base quality score, greater qual score do not make a lot of sense
#define MAXMAPPINGQUAL 37 // maximal mapping quality
//#define DEBUGHTS
//#define DEBUGALT
#define MIN2(a,b) (((a)<(b))?(a):(b))
//#define MIN(a,b) (((a)<(b))?(a):(b))
bool hasLineToPrint;
//string lineToPrint;
AlleleRecords * arToPrint;
char offsetQual=33;
static unsigned int limitToReOpenFP = 200; //if the coordinate is this far away, we will re-open the file pointer
string alphabetHTSLIB = "NACNGNNNTNNNNNNN";
int alphabetHTSLIB2idx [16] = {-1, 0, 1,-1, // N A C N
2,-1,-1,-1, // G N N N
3,-1,-1,-1, // T N N N
-1,-1,-1,-1}; // N N N N
bool onlyPP=false;
int minMQ=0;
void BAM2ACF::setVarsEPO(ReadTabix * rtEPO,string & epoChr,unsigned int & epoCoord,bool & cpgEPO,char & allel_chimp,char & allel_anc,bool & lineLeftEPO,string & lineFromEPO){
lineLeftEPO=(rtEPO->readLine( lineFromEPO ));
if(!lineLeftEPO){
cerr<<"Error, missing data in the EPO file"<<endl;
exit(1);
}
vector<string> fieldsEPO = allTokens(lineFromEPO,'\t');
epoChr = fieldsEPO[0];
epoCoord = string2uint(fieldsEPO[1]);
if(fieldsEPO[9] == "1")
cpgEPO=true;
else
cpgEPO=false;
allel_anc = fieldsEPO[3][0];//inferred ancestor
allel_chimp = fieldsEPO[4][0];//chimp;
}
BAM2ACF::BAM2ACF(){
}
BAM2ACF::~BAM2ACF(){
}
static int read_bamACF(void *data, bam1_t *b){ // read level filters better go here to avoid pileup
aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
int ret;
while (1){
ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->hdr, b);
if ( ret<0 ) break;
//skip fragments marked as:
//1: unmapped
//2: secondary alignment, only retain primary
//3: QC failed
//4: PCR duplicates
//this is not modifiable for now
if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
//if a reads is paired and not properly paired, skip if the user said pp
if(onlyPP)
if( bam_is_paired( b) &&
!bam_is_properpair(b) ){
continue;
}
if ( (int)b->core.qual < minMQ ) continue;
//if ( (int)b->core.qual < aux->min_mapQ ) continue;
break;
}
return ret;
}
string BAM2ACF::usage() const{
string usage=string("")+" bam2acf [options] <fasta file> <bam file> <name sample> "+
"\n\nThis program produces a ACF matrix given a BAM file\n\n"+
"\t<fasta file> is the fasta file of the reference genome used for mapping\n"+
"\t<name sample> is the name you wish the sample to have\n"+
"\tOptions\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"+"--bed [BED file]" +"\t" +"Restrict positions to those in a BED file (default: none)\n"+
"\t"+"--pp " +"\t" +"Restrict pairs to proper pairs (default: "+booleanAsString(onlyPP)+")\n"+
"\t"+" " +"\t" +"ancestral/root alleles for hominin samples\n"+
//"\t"+"--qc"+"\t\t\t"+"Use the reads that have failed quality control (Default: "+boolStringify(useQCFail)+" )\n"+
"\t"+"--qual"+"\t\t\t"+"Base quality cutoffs on a PHRED scale (Default: "+stringify(minBaseQual)+" )\n"+
"\t"+"--mq"+"\t\t\t"+"Mapping quality cutoffs on a PHRED scale (Default: "+stringify(minMQ)+" )\n"+
// "\t\t"+"--het"+"\t"+"Produce two fasta files containing the alleles for het sites (Default: "+boolStringify(printRoot)+" )\n"
"\n"+
"\tBy default, the bam2acf filters reads that are:\n"+
"\t\t1: unmapped\n"+
"\t\t2: secondary alignment, only retain primary\n"+
"\t\t3: QC failed\n"+
"\t\t4: PCR duplicates\n"+
"\n";
return usage;
}
int BAM2ACF::run(int argc, char *argv[]){
hasLineToPrint=false;
//lineToPrint ="";
arToPrint= NULL;
epoFileB=false;
int lastOpt=1;
string bedfilename;
//all but last arg
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]) == "--qc"){
// useQCFail=true;
// continue;
// }
if( string(argv[i]) == "--pp"){
onlyPP=true;
continue;
}
if( string(argv[i]) == "--bed"){
bedfilename = string(argv[i+1]);
i++;
continue;
}
if( string(argv[i]) == "--mq"){
minMQ=destringify<int>(argv[i+1]);
i++;
continue;
}
if( string(argv[i]) == "--qual"){
minBaseQual=destringify<int>(argv[i+1]);
i++;
continue;
}
cerr<<"Unknown option "<<string(argv[i])<<endl;
return 1;
}
if(argc < 4 ||
(argc == 2 && (string(argv[1]) == "-h" || string(argv[1]) == "--help") )
){
cerr << "Usage "<<usage()<<endl;
return 1;
}
if(lastOpt != (argc-3)){
cerr<<"The last 3 arguments are <fasta file> <bam file> <name sample> "<<endl;
return 1;
}
string fastaFile = string(argv[lastOpt+0]);//fasta file
string bamFileToOpen= string(argv[lastOpt+1]);
string nameSample = string(argv[lastOpt+2]);//fasta file
//string epoFile = string(argv[argc-1]);
string epoFileidx = epoFile+".tbi";
// string epoChr;
// unsigned int epoCoord;
// ReadTabix * rtEPO ;
// string lineFromEPO;
// bool lineLeftEPO;
// bool cpgEPO=false;
// bool firstLine=true;
// char allel_chimp;
// char allel_anc;
// string regionToUse = string(argv[argc-3]);//chr:st-end
// BamReader reader;
int i;
int n;
int tid;
// int reg_tid;
int beg;
int end;
int pos;
int *n_plp;
int baseQ = 0;
int mapQ = 0;
int min_len = MINLENGTHFRAGMENT;
int all = 1; //status = EXIT_SUCCESS,
int max_depth = MAXCOV;
const bam_pileup1_t **plp;
bool reg = false;//!region.empty();
void *bed = 0; // BED data structure
if(!bedfilename.empty()){
bed = bed_read(bedfilename.c_str()); // BED or position list file can be parsed now
}
bam_hdr_t * headerBAM = NULL; // BAM header of the 1st input
aux_t **data;
bam_mplp_t mplp;
int last_pos = -1, last_tid = -1, ret;
data = (aux_t **)calloc(1, sizeof(aux_t*)); // data[i] for the i-th input
//reg_tid = 0;
beg = 0;
end = INT_MAX; // set the default region
int rf;
data[0] = (aux_t *)calloc(1, sizeof(aux_t));
data[0]->fp = sam_open_format(bamFileToOpen.c_str(), "r", NULL); // open BAM
if (data[0]->fp == NULL) {
cerr<<"ERROR: Could not open BAM file "<<bamFileToOpen<<""<<endl;
exit(1);
}
rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ;
if (baseQ) rf |= SAM_QUAL;
data[0]->min_mapQ = mapQ; // set the mapQ filter
data[0]->min_len = min_len; // set the qlen filter
data[0]->hdr = sam_hdr_read(data[0]->fp); // read the BAM header
if (data[0]->hdr == NULL) {
cerr<<"ERROR: Could not read header for bamfile "<<bamFileToOpen<<""<<endl;
exit(1);
}
headerBAM = data[0]->hdr;
string fastaIndex=fastaFile+".fai";
if( !isFile(fastaFile) ){
cerr<<"The fasta file "<<fastaFile<<" does not exists"<<endl;
return 1;
}
if( !isFile(fastaIndex) ){
cerr<<"The fasta file "<<fastaFile<<" does not have an index: "<<fastaIndex<<endl;
return 1;
}
BamTools::Fasta * fastaReference=new BamTools::Fasta();
if ( !fastaReference->Open(fastaFile , fastaIndex) ){
cerr << "ERROR: failed to open fasta file " <<fastaFile<<" and fasta index " << fastaIndex<<""<<endl;
return 1;
}
vector<chrinfo> chrFound;
uint64_t genomeLength;
readFastaIndex(fastaIndex,chrFound,genomeLength);
// vector<chrinfo> chrFound;
//uint64_t genomeLength;
// for(int ns=0;ns<faidx_nseq(fai);ns++){
// chrinfo toadd;
// toadd.name = string( faidx_iseq(fai,ns ) );
// toadd.length = faidx_seq_len(fai, toadd.name.c_str() );
// }
//
// readFastaIndex(fastaIndex,chrFound,genomeLength);
GlacWriter * gw=NULL;
gw = new GlacWriter(1, //gp.getSizePops(),
false, //gp.isGLFormat(),
2,//gp.isACFormat()?2:1,
1,//compression threads
uncompressed);
string header="";
//cout<<"#ACF"<<endl;
header+="#ACF\n";
string programLine;
for(int i=0;i<(argc);i++){
programLine+=(string(argv[i])+" ");
}
//cout<<"#PG:"<<programLine<<endl;
header+="#PG:"+programLine+"\n";;
header+="#GITVERSION: "+returnGitHubVersion(argv[-1],"")+"\n";;
//cout<<"#DATE: "<<getDateString()<<endl;
header+="#DATE: "+getDateString()+"\n";;
header+="#BAM2ACF:\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";
if(!gw->writeHeader(header)){
cerr<<"GlacViewer: error writing header "<<endl;
return 1;
}
//EPO stuff
// string epoFile;
// string epoFileidx;
//bool epoFileB;
string epoChr;
unsigned int epoCoord;
ReadTabix * rtEPO = NULL;
string lineFromEPO;
bool lineLeftEPO;
bool cpgEPO;
bool firstLine=true;
char allel_chimp;
char allel_anc;
unsigned int previousPosAlign=0;
bool hasCpreviousPos=false;
#ifdef AROUNDINDELS
int prevPos=-1000;
#endif
unsigned int totalBasesL=0;//=cv->getTotalBases();
unsigned int totalSitesL=0; //=cv->getTotalSites();
n=1;//number of bam files
// the core multi-pileup loop
mplp = bam_mplp_init(n, read_bamACF, (void**)data); // initialization
if (0 < max_depth)
bam_mplp_set_maxcnt(mplp,max_depth); // set maximum coverage depth
else
if (!max_depth)
bam_mplp_set_maxcnt(mplp,INT_MAX);
n_plp = (int *)calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
plp = (const bam_pileup1_t **)calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp)
while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position
unsigned int posAlign = pos+1;
int posAlignInt = int(pos+1);
//cerr<<endl<<(posAlign)<<" "<<"TNAME "<< headerBAM->target_name[tid]<<" -----------------------"<<endl;
if (pos < beg || pos >= end) continue; // out of range; skip
if (tid >= headerBAM->n_targets) continue; // diff number of @SQ lines per file?
char refC='N';
char altBase = 'N';
if ( !fastaReference->GetBase(tid, pos, refC ) ) {
cerr << "ERROR: pileup conversion - could not read reference base from FASTA file" << endl;
exit(1);
}
refC=toupper(refC);
if(refC == 'N'){//skip unresolved
continue;
}
#ifdef DEBUGHTS
cerr<<endl<<(posAlign)<<" "<<refC<<" -----------------------"<<endl;
#endif
//EPO
if(firstLine){
firstLine=false;
if(epoFileB){
rtEPO = new ReadTabix( epoFile.c_str() ,
epoFileidx.c_str() ,
headerBAM->target_name[tid],
posAlignInt,
INT_MAX ); //the destructor should be called automatically
BAM2ACF::setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_chimp,allel_anc,lineLeftEPO,lineFromEPO);
}
}
if(epoFileB){
if(!lineLeftEPO){
cerr<<"Error, no data in the EPO file "<< headerBAM->target_name[tid] <<":"<< (posAlign) <<endl;
exit(1);
}
if(epoChr != headerBAM->target_name[tid]){
//cerr<<"Error, the chromosome does not match the one in the EPO file = "<<epoChr <<" and not "<<m_references[pileupData.RefId].RefName<<endl;
//exit(1);
//try to reposition
rtEPO->repositionIterator( headerBAM->target_name[tid] , posAlignInt,INT_MAX);
BAM2ACF::setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_chimp,allel_anc,lineLeftEPO,lineFromEPO);
if(epoChr != headerBAM->target_name[tid]){
cerr<<"Error, the repositioning did not work, the chromosome does not match the one in the EPO file = "<<epoChr <<" and not "<<headerBAM->target_name[tid]<<endl;
exit(1);
}
}
while(epoCoord != posAlign){
if(epoCoord > posAlign){
cerr<<"Error, are all the sites in EPO there? Difference between coords "<<posAlignInt<<"\t"<<lineFromEPO<<endl;
exit(1);
}
if( ((posAlign) - epoCoord ) >= limitToReOpenFP){ //seeking in the file
rtEPO->repositionIterator(headerBAM->target_name[tid] , pos+1,INT_MAX);
}
BAM2ACF::setVarsEPO(rtEPO,epoChr,epoCoord,cpgEPO,allel_chimp,allel_anc,lineLeftEPO,lineFromEPO);
}
}
// #ifdef EPO
// #endif
//
// END EPO
//
int countRef=0;
int countAlt=0;
int basesRetained=0;
bool foundSites=false;
if (all) {
while (tid > last_tid) {
if (last_tid >= 0 && !reg) {
// Deal with remainder or entirety of last tid.
while (++last_pos < int(headerBAM->target_len[last_tid])) {
//cerr<<(last_pos+1)<<endl;
//exit(1);
// // Horribly inefficient, but the bed API is an obfuscated black box.
if (bed && bed_overlap(bed, headerBAM->target_name[last_tid], last_pos, last_pos + 1) == 0)
continue;
totalSitesL++;
}
}
last_tid++;
last_pos = -1;
if (all < 2)
break;
}
// Deal with missing portion of current tid
while (++last_pos < pos) {
if (last_pos < beg) continue; // out of range; skip
if (bed && bed_overlap(bed, headerBAM->target_name[tid], last_pos, last_pos + 1) == 0)
continue;
totalSitesL++;
}
last_tid = tid;
last_pos = pos;
}
if (bed && bed_overlap(bed, headerBAM->target_name[tid], pos, pos + 1) == 0) continue;
#ifdef DEBUGHTS
cerr<<endl<<(posAlign)<<" "<<refC<<" -----------------------"<<endl;
#endif
#ifdef AROUNDINDELS
//if indels are found, remove
if( (prevPos+1) == pos){
prevIndel = currIndel;
prevIndelSet = currIndelSet;
// prevLevelsi = currLevelsi;
// for(int ci=0;ci<currLevelsi;ci++){
// prevLevels[ci] = currLevels[ci];
// }
}else{
prevIndel =false;
//prevLevelsi =0;
prevIndelSet.clear();
}
#endif
//totalSitesL++;
for (i = 0; i < n; ++i) { // base level filters have to go here
int j;
int m = 0;//amount of invalid bases at site j that need to be removed from coverage calculations
#ifdef AROUNDINDELS
currIndel =false;
// int currLevels [2*MAXCOV];
// int currLevelsi =0;
currIndelSet.clear();
#endif
for (j = 0; j < n_plp[i]; ++j) {//each base
const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
#ifdef DEBUGHTS
cerr<<"i="<<i<<" "<< bam1_qname(p->b)<<" j="<<j<<" "<<int((p->b)->core.flag)<<" "<<p->b->core.n_cigar<<" p="<<(p->cd.p)<<" i="<<int(p->cd.i)<<" f="<<float(p->cd.f)<<" isdel="<<p->is_del<<" isrefsk="<<p->is_refskip<<" indel="<<p->indel<<" "<<p->level<<" "<<p->aux<<" "<<endl;
#endif
//base level filters go here
if (p->is_del || p->is_refskip){
#ifdef AROUNDINDELS
//currLevels[currLevelsi++] = p->level;
currIndel = true;
//cerr<<"inserting "<<bam1_qname(p->b)<<endl;
currIndelSet.insert( bam1_qname(p->b) );
#endif
++m; // having dels or refskips at tid:pos
continue;
}
// This variable will not be zero if the next position is a a deletion of a base in the read or insert in the reference
// if ( p->indel != 0 ){// having dels or refskips at the next
// ++m;
// continue;
// }
#ifdef AROUNDINDELS
//cerr<<"prevIndel3: "<<prevIndel<<" "<<prevIndelSet.size()<<endl;
if(prevIndel){
//cerr<<"prevIndel, testing "<<bam1_qname(p->b)<<""<<endl;
// for(set<string>::iterator it = prevIndelSet.begin(); it != prevIndelSet.end(); it++) {
// cerr<<"record: "<<*it<<endl;
// }
if( prevIndelSet.find(bam1_qname(p->b)) != prevIndelSet.end() ){//skip reads previously flagged as indels. Since indels are few, this should be a quicker solution than to read ahead
//cerr<<"found "<<bam1_qname(p->b)<<" in a previous indel"<<endl;
continue;
}
// bool skippos=false;
// for(int pi=0;pi<prevLevelsi;pi++){
// if(p->level == prevLevels[prevLevelsi]){
// skippos=true;
// break;
// }
// }
// if(skippos){
// continue;
// }
}
#endif
if( j>=MAXCOV){
break;
}
int bIndex = alphabetHTSLIB2idx[ bam_seqi(bam_get_seq(p->b),p->qpos) ];
if(bIndex == -1){ continue; } //skip unresolved
char b = "ACGT"[bIndex];
int q = MIN2( int(bam_get_qual(p->b)[p->qpos] ), MAXBASEQUAL);//offsetqual?
//int m = MIN2( bam_mqual(p->b) , MAXMAPPINGQUAL );
#ifdef DEBUGHTS
bool isRev = bam_is_rev(p->b);
#endif
if(q<minBaseQual){
continue;
}
// piToAdd.baseC[bIndex]++;
//probMM += likeMismatchProbMap[m];
if(b != refC){
if(altBase == 'N'){
altBase = b;
countAlt++;
}else{
if(b == altBase){
countAlt++;
}else{ //tri-allelic site
goto skiptonextpos;
}
}
}else{
countRef++;
}
basesRetained++;
#ifdef DEBUGALT
cerr<<"alt1\t"<<chr2index[ headerBAM->target_name[tid] ]<<"\t"<<posAlign<<"\t"<<refC<<"\t"<<altBase<<"\t"<<countRef<<"\t"<<countAlt<<endl;
#endif
foundSites=true;
#ifdef DEBUGHTS
//cerr<<isRev<<" "<<"ACGT"[int(sr_.base)]<<" "<<int(sr_.qual)<<" "<<int(sr_.mapq)<<" "<<int(m)<<" "<<int(sr_.lengthF)<<" "<<int(sr_.pos5p)<<" "<< bam1_qname(p->b)<<" "<<int((p->b)->core.flag)<<" "<<p->b->core.n_cigar<<" p="<<(p->cd.p)<<" i="<<int(p->cd.i)<<" f="<<float(p->cd.f)<<" "<<p->indel<<" "<<p->level<<endl;
//cerr<<"ADD "<<isRev<<" "<<int(sr_.base)<<" "<<int(sr_.qual)<<" "<<int(sr_.mapq)<<" "<<int(m)<<" "<<int(sr_.lengthF)<<" "<<int(sr_.pos5p)<<" "<< bam1_qname(p->b)<<" "<<int((p->b)->core.flag)<<endl;
cerr<<"ADD "<<isRev<<" "<<bam_seqi(bam_get_seq(p->b),p->qpos)<<" "<<"ACGT"[bIndex]<<" "<<uint8_t(q)<<" "<<int( (p->b)->core.l_qseq )<<" "<< bam1_qname(p->b)<<" "<<int((p->b)->core.flag)<<endl;
//<<" "<<int(sr_.pos5p)<<" "<< bam1_qname(p->b)<<" "<<int((p->b)->core.flag)<<endl;
#endif
// if(isRev){
// sr_.pos5p = uint8_t( pileupData.PileupAlignments[i].Alignment.Length-pileupData.PileupAlignments[i].PositionInAlignment-1 );
// sr_.base = 3 - sr_.base;//complement
// }else{
// sr_.pos5p = uint8_t( pileupData.PileupAlignments[i].PositionInAlignment );
// }
// sr_.isrv=isRev;
totalBasesL++;
//piToAdd.readsVec.push_back(sr_);
//currLevelVec.push_back(p->level);
//totalBasesL ++;
#ifdef DEBUGHTS
if(0){
// printf("%d,",p->b);
// printf("%d,",bam_get_seq(p->b));
// @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
// 8 for T and 15 for N. Two bases are packed in one byte with the base
// at the higher 4 bits having smaller coordinate on the read. It is
// recommended to use bam_seqi() macro to get the base.
// */
//coord
//printf("%d,",p->qpos);
cerr<<p->qpos<<"/"<<int(uint8_t( (p->b)->core.l_qseq )) <<",";
//flag
//printf("%d,",(p->b)->core.flag);
cerr<<((p->b)->core.flag)<<",";
//base
//printf("%d,",bam_seqi(bam_get_seq(p->b),p->qpos));
//printf("%c,",alphabetHTSLIB[ bam_seqi(bam_get_seq(p->b),p->qpos) ]);
cerr<<alphabetHTSLIB[ bam_seqi(bam_get_seq(p->b),p->qpos) ]<<",";
//int c = seq_nt16_int[bam_seqi(seq, p->qpos)];
//qual
//printf("%d,",bam_get_qual(p->b)[p->qpos]);
cerr<<int(bam_get_qual(p->b)[p->qpos])<<",";
//strand
//printf("%d,",bam_is_rev(p->b));
cerr<<bam_is_rev(p->b)<<",";
//paired
//printf("%d,",bam_is_paired(p->b));
cerr<<bam_is_paired(p->b)<<",";
cerr<<"D="<<p->is_del<<",RS="<<p->is_refskip<<",";
//fail
//printf("%d-",bam_is_failed(p->b));
cerr<<bam_is_failed(p->b)<<",";
cerr<<bam_mqual(p->b)<<"-";
}
#endif
}//end for each base at pos
if(countRef != 0 || countAlt != 0 ){//we add
// char alt=altBase;//(toprint->getAlt()=="."?'N':toprint->getAlt()[0]);
SingleAllele root;
SingleAllele anc;
//unresolved ancestral allele (A,C,G,T)
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{
if(!isResolvedDNA(allel_chimp)){
//chimpString="0,0:0";
root.setRefCount(0); root.setAltCount(0); root.setIsCpg(false);
}
//resolved ancestral allele
else{
if(allel_chimp == refC){//no diff between chimp and reference
//chimpString="1,0:"+string(cpgEPO?"1":"0");
root.setRefCount(1); root.setAltCount(0); root.setIsCpg(cpgEPO);
}else{
if(altBase == 'N'){//no alt defined, the chimp becomes the alt
altBase = allel_chimp;
//chimpString="0,1:"+string(cpgEPO?"1":"0");
root.setRefCount(0); root.setAltCount(1); root.setIsCpg(cpgEPO);
}else{
if(altBase == 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 skiptonextpos;
}
}
}
}
// cerr<<posAlign<<"\talt2\t"<<altBase<<endl;
if(!isResolvedDNA(allel_anc)){
//ancString="0,0:0";
anc.setRefCount(0); anc.setAltCount(0); anc.setIsCpg(false);
}
//resolved ancestral allele
else{
if(allel_anc == refC){//no diff between ancestor and reference
//ancString="1,0:"+string(cpgEPO?"1":"0");
anc.setRefCount(1); anc.setAltCount(0); anc.setIsCpg(cpgEPO);
}else{
if(altBase == 'N'){//no alt defined, the ancestor becomes the alt
altBase = allel_anc;
//ancString="0,1:"+string(cpgEPO?"1":"0");
anc.setRefCount(0); anc.setAltCount(1); anc.setIsCpg(cpgEPO);
}else{
if(altBase == 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 skiptonextpos;
}
}
}
}
}
#ifdef DEBUGALT
cerr<<"alt2\t"<<chr2index[ headerBAM->target_name[tid] ]<<"\t"<<posAlign<<"\t"<<refC<<"\t"<<altBase<<"\t"<<countRef<<"\t"<<countAlt<<endl;
#endif
//TODO put tri-allelic to skip to label
AlleleRecords * arCurrent = new AlleleRecords (false);
arCurrent->chri = chr2index[ headerBAM->target_name[tid] ]; //m_references[pileupData.RefId].RefName];//probably redundant
arCurrent->coordinate = posAlign;
arCurrent->sizePops = 1;
arCurrent->ref = refC;
arCurrent->alt = altBase;
arCurrent->vectorAlleles = new vector<SingleAllele>();
SingleAllele sample (countRef, countAlt, false);//to set CpG flag
arCurrent->vectorAlleles->push_back(root);
arCurrent->vectorAlleles->push_back(anc);
arCurrent->vectorAlleles->push_back(sample);
if( hasLineToPrint && //case of CpG
previousPosAlign == (posAlign-1) &&
hasCpreviousPos &&
( refC == 'G' || altBase == 'G')){
arToPrint->vectorAlleles->at(2).setIsCpg(true);
if(!gw->writeAlleleRecord(arToPrint)){
cerr<<"BAM2ACF: error writing header "<<endl;
exit(1);
}
delete(arToPrint);
arCurrent->vectorAlleles->at(2).setIsCpg(true);
if(!gw->writeAlleleRecord(arCurrent)){
cerr<<"BAM2ACF: error writing header "<<endl;
exit(1);
}
delete(arCurrent);
hasLineToPrint=false;
arToPrint=NULL;
}else{//no CpG
if(hasLineToPrint){
arToPrint->vectorAlleles->at(2).setIsCpg(false);
if(!gw->writeAlleleRecord(arToPrint)){
cerr<<"BAM2ACF: error writing allele record "<<endl;
exit(1);
}
delete(arToPrint);
}
hasLineToPrint=true;
arToPrint = arCurrent;
}
}else{ //else if(countRef != 0 || countAlt != 0 ){
//no line to print
if(hasLineToPrint){
arToPrint->vectorAlleles->at(2).setIsCpg(false);
if(!gw->writeAlleleRecord(arToPrint)){
cerr<<"BAM2ACF: error writing allele record "<<endl;
exit(1);
}
delete(arToPrint);
}
hasLineToPrint=false;
}
skiptonextpos:
previousPosAlign = posAlign;
hasCpreviousPos = ( refC == 'C' || altBase == 'C');
}//closes pos
if( foundSites ){// && !triAllelic ){
totalSitesL++;
}
#ifdef AROUNDINDELS
prevPos = pos;
#endif
}//end for all pos
//flushing last one if need be
if(hasLineToPrint){
arToPrint->vectorAlleles->at(2).setIsCpg(false);
if(!gw->writeAlleleRecord(arToPrint)){
cerr<<"BAM2ACF: error writing allele record "<<endl;
exit(1);
}
delete(arToPrint);
}
//end while mpileup
if (ret < 0){ //status = EXIT_FAILURE;
cerr<<"Problem parsing region in bamfile "<<bamFileToOpen<<endl;
exit(1);
}
free(n_plp); free(plp);
bam_mplp_destroy(mplp);
// if (all) {
// // Handle terminating region
// if (last_tid < 0 && reg && all > 1) {
// last_tid = reg_tid;
// last_pos = beg-1;
// }
// while (last_tid >= 0 && last_tid < h->n_targets) {
// while (++last_pos < int(h->target_len[last_tid])) {
// if (last_pos >= end) break;
// if (bed && bed_overlap(bed, h->target_name[last_tid], last_pos, last_pos + 1) == 0)
// continue;
// totalSitesL++;
// }
// last_tid++;
// last_pos = -1;
// if (all < 2 || reg)
// break;
// }
// }
// for (i = 0; i < n && data; ++i) {
bam_hdr_destroy(data[0]->hdr);
if (data[0]->fp) sam_close(data[0]->fp);
hts_itr_destroy(data[0]->iter);
free(data);
//}
//free(reg);
if (bed) bed_destroy(bed);
cerr<<"Program bam2acf terminated gracefully, considered "<<totalBasesL<<" bases at "<<totalSitesL<<" sites"<<endl;
//clean up