int readerToMeth(BamTools::BamReader & reader1,
BamTools::BamReader & reader2,
std::map<std::string, std::vector<std::string> > & lociMeth1,
std::map<std::string, std::vector<std::string> > & lociMeth2,
BamTools::RefVector::const_iterator i,
int d,
const BamTools::RefVector refs,
std::string sample)
{
const int r1=reader1.GetReferenceID(i->RefName);
const int r2=reader2.GetReferenceID(i->RefName);
const int rl=i->RefLength;
if(reader1.SetRegion(r1,0, r1, rl) & reader2.SetRegion(r2,0, r2, rl))
{
std::cerr << "Processing " << i->RefName << std::endl;
BamTools::BamAlignment al;
while (reader1.GetNextAlignment(al)){
//std::cout << al.RefID << std::endl;
byread(al, d, lociMeth1, refs, sample);
}
while (reader2.GetNextAlignment(al)){
//std::cout << al.RefID << std::endl;
byread(al, d, lociMeth2, refs, sample);
}
}
reader1.Rewind();
reader2.Rewind();
return 0;
}
position BamAlignmentReader::GetLastPositionInBam(const std::string& bamPath, Region::SharedPtr regionPtr)
{
BamTools::BamReader bamReader;
if (!bamReader.Open(bamPath))
{
throw "Unable to open bam file";
}
bamReader.LocateIndex();
int refID = bamReader.GetReferenceID(regionPtr->getReferenceID());
auto referenceData = bamReader.GetReferenceData();
bamReader.Close();
return referenceData[refID].RefLength;
}