void ReadContainer::GetSampleInfo() {
BamTools::SamHeader header = reader.GetHeader();
if (!header.HasReadGroups()) {
PrintMessageDieOnError("No read groups found", ERROR);
}
BamTools::SamReadGroupDictionary read_groups = header.ReadGroups;
for (BamTools::SamReadGroupIterator it = read_groups.Begin();
it != read_groups.End(); it++) {
const BamTools::SamReadGroup& rg = *it;
string rg_sample;
if (!rg.HasSample()) {
PrintMessageDieOnError("No sample in read group for " + rg.ID, WARNING);
rg_sample = rg.ID;
} else {
rg_sample = rg.Sample;
}
if (my_verbose) {
PrintMessageDieOnError("Adding sample " + rg_sample + " " + rg.ID, PROGRESS);
}
rg_id_to_sample.insert(pair<string,string>(rg.ID,rg_sample));
if (find(samples_list.begin(), samples_list.end(), rg_sample) ==
samples_list.end()) {
samples_list.push_back(rg_sample);
}
}
}
void BamHeaderHelper::GetFlowOrder(BamTools::BamReader &bamReader){
BamTools::SamHeader samHeader = bamReader.GetHeader();
if (!samHeader.HasReadGroups()) {
//bamReader.Close();
cerr << "ERROR: there is no read group in " << "this file" << endl;
//exit(1);
}
for (BamTools::SamReadGroupIterator itr = samHeader.ReadGroups.Begin(); itr != samHeader.ReadGroups.End(); ++itr) {
if (itr->HasFlowOrder()) {
flow_order_set.push_back(itr->FlowOrder);
//flowKey = itr->KeySequence;
}
}
}
int scanBam()
{
std::vector< std::map<std::string, ScanResults> > resultlist;
// std::ostream* pWriter;
// pWriter = &std::cout;
bool isExome = opt::exomebedfile.size()==0? false: true;
std::cout << opt::bamlist << "\n";
std::cout << opt::bamlist.size() << " BAMs" << std::endl;
for(std::size_t i=0; i<opt::bamlist.size(); i++) {
// storing results for each read group (RG tag). use
// read group ID as key.
std::map<std::string, ScanResults> resultmap;
// store where the overlap was last found in the case of exome seq
std::map<std::string, std::vector<range>::iterator> lastfound;
std::vector<range>::iterator searchhint;
std::cerr << "Start analysing BAM " << opt::bamlist[i] << "\n";
// Open the bam files for reading/writing
BamTools::BamReader* pBamReader = new BamTools::BamReader;
pBamReader->Open(opt::bamlist[i]);
// get bam headers
const BamTools::SamHeader header = pBamReader ->GetHeader();
// for(BamTools::SamSequenceConstIterator it = header.Sequences.Begin();
// it != header.Sequences.End();++it){
// std::cout << "Assembly ID:" << it->AssemblyID << ", Name:" << it->Name << std::endl;
// }
// exit(0);
bool rggroups=false;
if(opt::ignorerg){ // ignore read groups
std::cerr << "Treat all reads in BAM as if they were from a same sample" << std::endl;
ScanResults results;
results.sample = opt::unknown;
resultmap[opt::unknown]=results;
}else{
std::map <std::string, std::string> readgroups;
std::map <std::string, std::string> readlibs;
rggroups = header.HasReadGroups();
if(rggroups){
for(BamTools::SamReadGroupConstIterator it = header.ReadGroups.Begin();
it != header.ReadGroups.End();++it){
readgroups[it->ID]= it->Sample;
if(it->HasLibrary()){
readlibs[it->ID] = it -> Library;
}else{
readlibs[it->ID] = opt::unknown;
}
}
std::cerr<<"Specified BAM has "<< readgroups.size()<< " read groups" << std::endl;
for(std::map<std::string, std::string>::iterator it = readgroups.begin(); it != readgroups.end(); ++it){
ScanResults results;
std::string rgid = it -> first;
results.sample = it -> second;
results.lib = readlibs[rgid];
resultmap[rgid]=results; //results are identified by RG tag.
}
}else{
std::cerr << "Warning: can't find RG tag in the BAM header" << std::endl;
std::cerr << "Warning: treat all reads in BAM as if they were from a same sample" << std::endl;
ScanResults results;
results.sample = opt::unknown;
results.lib = opt::unknown;
resultmap[opt::unknown]=results;
}
}
BamTools::BamAlignment record1;
bool done = false;
int nprocessed=0; // number of reads analyzed
int ntotal=0; // number of reads scanned in bam (we skip some reads, see below)
while(!done)
{
ntotal ++;
done = !pBamReader -> GetNextAlignment(record1);
std::string tag = opt::unknown;
if(rggroups){
// skip reads that do not have read group tag
if(record1.HasTag("RG")){
record1.GetTag("RG", tag);
// std::cerr << c << " reads:{" << record1.QueryBases << "} tag:{" << tag << "}\n";
}else{
std::cerr << "can't find RG tag for read at position {" << record1.RefID << ":" << record1.Position << "}" << std::endl;
std::cerr << "skip this read" << std::endl;
continue;
}
}
// skip reads with readgroup not defined in BAM header
if(resultmap.find(tag) == resultmap.end()){
std::cerr << "RG tag {" << tag << "} for read at position ";
std::cerr << "{" << record1.RefID << ":" << record1.Position << "} doesn't exist in BAM header.";
continue;
}
// for exome, exclude reads mapped to the exome regions.
if(isExome){
range rg;
rg.first = record1.Position;
rg.second = record1.Position + record1.Length;
std::string chrm = refID2Name(record1.RefID);
if(chrm != "-1"){ // check if overlap exome when the read is mapped to chr1-22, X, Y
// std::cerr << "read: " << chrm << " " << rg << "\n" << std::endl;
std::map<std::string, std::vector<range> >::iterator chrmit = opt::exomebed.find(chrm);
if(chrmit == opt::exomebed.end())
{
// std::cerr<<"chromosome or reference sequence: " << chrm << " is not present in the specified exome bed file." <<std::endl;
// std::cerr<<"please check sequence name encoding, i.e. for chromosome one, is it chr1 or 1" << std::endl;
// unmapped reads can have chr names as a star (*). We also don't consider MT reads.
resultmap[tag].n_exreadsChrUnmatched +=1;
}else{
std::vector<range>::iterator itend = opt::exomebed[chrm].end();
std::map<std::string, std::vector<range>::iterator>::iterator lastfoundchrmit = lastfound.find(chrm);
if(lastfoundchrmit == lastfound.end()){ // first entry to this chrm
lastfound[chrm] = chrmit->second.begin();// start from begining
}
// set the hint to where the previous found is
searchhint = lastfound[chrm];
std::vector<range>::iterator itsearch = searchRange(searchhint, itend, rg);
// if found
if(itsearch != itend){// if found
searchhint = itsearch;
resultmap[tag].n_exreadsExcluded +=1;
lastfound[chrm] = searchhint; // update search hint
continue;
}
}
}
}
resultmap[tag].numTotal +=1;
if(record1.IsMapped())
{
resultmap[tag].numMapped += 1;
}
if(record1.IsDuplicate()){
resultmap[tag].numDuplicates +=1;
}
double gc = calcGC(record1.QueryBases);
int ptn_count = countMotif(record1.QueryBases, opt::PATTERN, opt::PATTERN_REV);
// when the read length exceeds 100bp, number of patterns might exceed the boundary
if (ptn_count > ScanParameters::TEL_MOTIF_N-1){
continue;
}
resultmap[tag].telcounts[ptn_count]+=1;
if(gc >= ScanParameters::GC_LOWERBOUND && gc <= ScanParameters::GC_UPPERBOUND){
// get index for GC bin.
int idx = floor((gc-ScanParameters::GC_LOWERBOUND)/ScanParameters::GC_BINSIZE);
assert(idx >=0 && idx <= ScanParameters::GC_BIN_N-1);
// std::cerr << c << " GC:{"<< gc << "} telcounts:{"<< ptn_count <<"} GC idx{" << idx << "}\n";
if(idx > ScanParameters::GC_BIN_N-1){
std::cerr << nprocessed << " GC:{"<< gc << "} telcounts:{"<< ptn_count <<"} GC bin index out of bound:" << idx << "\n";
exit(EXIT_FAILURE);
}
resultmap[tag].gccounts[idx]+=1;
}
// if(resultmap[tag].n_exreadsChrUnmatched > 1000){
// std::cerr<<"too many reads found with unmatched chromosome ID between BAM and exome BED. \n" << std::endl;
// }
nprocessed++;
if( nprocessed%10000000 == 0){
std::cerr << "[scan] processed " << nprocessed << " reads \n" ;
}
}
pBamReader->Close();
delete pBamReader;
// consider each BAM separately
resultlist.push_back(resultmap);
std::cerr << "[scan] total reads in BAM scanned " << ntotal << std::endl;
std::cerr << "Completed scanning BAM\n";
}
if(opt::onebam){
merge_results_by_readgroup(resultlist);
}
outputresults(resultlist);
if(isExome){
printlog(resultlist);
}
std::cerr << "Completed writing results\n";
return 0;
}